[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"        "-oTBRCA-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/BRCA-TP/10005900/BRCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/BRCA-TP/10013754/transformed.cor.cli.txt"

nPatients in clinical file=1017, in cluster file=1044, common to both=995
[1]  80 995
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              188               807 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              188               807 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              649               346 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              649               346 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              113               882 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              113               882 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               71               924 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               71               924 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              131               864 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              131               864 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              197               798 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              197               798 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               74               921 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               74               921 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               70               925 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               70               925 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              290               705 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              290               705 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              194               801 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              194               801 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              190               805 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              190               805 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              136               859 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              136               859 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              283               712 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              283               712 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              239               756 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              239               756 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              270               725 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              270               725 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              494               501 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              494               501 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
              128               867 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
              128               867 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              108               887 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              108               887 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               200                795 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               200                795 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               117                878 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               117                878 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
               129                866 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
               129                866 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                89                906 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                89                906 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               214                781 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               214                781 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               181                814 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               181                814 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                86                909 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                86                909 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               134                861 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               134                861 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                83                912 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                83                912 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               443                552 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               443                552 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               129                866 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               129                866 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               101                894 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               101                894 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               208                787 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               208                787 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               163                832 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               163                832 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
               138                857 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
               138                857 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               170                825 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               170                825 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               201                794 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               201                794 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               383                612 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               383                612 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               417                578 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               417                578 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               187                808 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               187                808 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                94                901 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                94                901 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              130               865 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              130               865 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              226               769 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              226               769 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               50               945 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               50               945 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
              168               827 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
              168               827 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
              190               805 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
              190               805 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              170               825 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              170               825 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               93               902 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               93               902 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              324               671 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              324               671 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              288               707 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              288               707 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              130               865 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              130               865 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              212               783 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              212               783 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              170               825 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              170               825 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              250               745 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              250               745 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
              104               891 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
              104               891 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
              113               882 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
              113               882 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              362               633 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              362               633 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               81               914 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               81               914 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              296               699 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              296               699 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              268               727 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              268               727 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               159                836 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               159                836 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               213                782 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               213                782 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               253                742 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               253                742 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               338                657 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               338                657 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
               139                856 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
               139                856 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
               117                878 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
               117                878 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               408                587 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               408                587 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               240                755 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               240                755 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               296                699 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               296                699 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               154                841 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               154                841 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               546                449 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               546                449 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               532                463 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               532                463 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
               250                745 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
               250                745 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               293                702 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               293                702 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               294                701 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               294                701 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               176                819 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               176                819 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               149                846 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               149                846 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                85                910 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                85                910 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                47                948 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                47                948 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               164                831 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               164                831 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               440                555 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               440                555 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              164               831 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              164               831 
[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] "NUMBER.OF.LYMPH.NODES"                 
[18] "RACE"                                  
[19] "ETHNICITY"                             
[20] "BATCHNUMBER"                           

Input Data has 20 rows and 995 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
         259          437         1321         1463          434         1437 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
         635          416           NA          242         1196          852 
TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R 
         584          554         3188           NA         1276         2499 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
        2246          671           NA         1948         1686         1099 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
        3820         1964           NA         3409         2813         2695 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW 
        3283         2298         2289           NA         1930         1948 
TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 
        1728          643         1051         1027          875          767 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER 
        3094         2718         2442         3273         2426         2263 
TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
        1127         1066         1043          968          905          752 
TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX 
         735         3017         1662           NA           NA         1534 
TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 
        1347          533          521           NA          569          624 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE 
         531          575          631          990          769          554 
TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK 
         469          666          659          441          566          588 
TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX 
         445          965           NA          714          528         1119 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
         683          616          584          595          501         1596 
TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
        3276          496          523          552         2796          322 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV 
         635         1206           NA         2525           NA          428 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW 
        1505         1168         1064          973         1167          222 
TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 
         274          268          271          365          205          104 
TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 
        1165         1074         1043         1079          931         1139 
TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G 
        1085         1007          965          326          387          718 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I 
         899          954          738          722          724          661 
TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
         627          679          345          322          313          343 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD 
         408          447          364          454          418          441 
TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX 
         644          545          448          368          326          336 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06N TCGA-A8-A06O 
         313          285          317          266           NA          396 
TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X 
         396           31          547         1249           NA           NA 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B 
         791           31          518         1642          274         1004 
TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
         608          577          577          426          365          518 
TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W 
         304          334          273          243          303          304 
TCGA-A8-A07Z TCGA-A8-A081 TCGA-A8-A082 TCGA-A8-A083 TCGA-A8-A084 TCGA-A8-A085 
         853           NA          549           NA          458         1124 
TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G 
         396           30          702          608          549          607 
TCGA-A8-A08H TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P 
          NA          365           NA           NA          943          943 
TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A090 
          30          580         2830         1034         1217           NA 
TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A094 TCGA-A8-A095 TCGA-A8-A096 
         580          487          546           NA         1277           NA 
TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D 
         365          304          304          365           31          396 
TCGA-A8-A09E TCGA-A8-A09G TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N 
         943           NA         1006          912          457           31 
TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X 
         761          273          579          457           30           NA 
TCGA-A8-A09Z TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 
          NA          365          579          396          640           30 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G 
         396          518         1157           29           72          330 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF 
          81           45         1172         1162         1234         1686 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI 
        1125         1180           NA         1542           31           28 
TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN 
          69           30           21          451          286           34 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V 
          55           51           47           40           47            2 
TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A8OP 
          34           55           36           21           13           53 
TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A 
          10           10            7           10           19           90 
TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM 
          54           52          244          224          198            5 
TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ 
          10           10           10          196          141          242 
TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV 
         213          231          218          191          183           10 
TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN 
          11           10           10           10           10           10 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU 
         375            9           10           10           10           10 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O 
         162          170         2442         1455         2031           NA 
TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 
        2576         2091         1456           NA          886          997 
TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 
         651          537          735         1140          618          680 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE 
        1613          655         1542         1547         2190         2335 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM 
         650          798         1172         1887         1683         2184 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A 
        3120         3019         2850         2877         2923         2755 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
        2359         1948         1743         1471         1266          863 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT 
         448         2513         1882         2141           16          541 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 
         754          819         3957           NA          475          402 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
          78          665          304         2521         1500           NA 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
        1138         1730          905          739         1972           NA 
TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 
        2316         1988         2134           NA         2317         1684 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM 
        2298         1881         1605         1559         1485         1903 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS 
        1330         1325         1216         1310           NA         1242 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H 
        1409         1295         1072         1103          615         3333 
TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
        1548         2221         1991         2074         1998           26 
TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V 
        2009         1746         1888         1620         1623         1648 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 
        1550         1465         1574         1708         1374         1236 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LK 
        1212         1059           NA         3913           NA         1304 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
         224         1218          520          633          516          620 
TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 
        1665          488          622           NA           NA         4361 
TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
        4550           NA         6719           NA           NA           NA 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
          NA           NA         5383           NA         3836           NA 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH 
        3350         3374         4285         6435         2082         5749 
TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP 
        7126           NA           NA         5261         4929           NA 
TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS 
          NA           NA         2721         3991         4788           NA 
TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ 
        5739           NA          547           NA           NA         3941 
TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC 
          NA         5672           NA           NA           NA         1326 
TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 
        3088         2236         4233         5176         2596         1651 
TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW 
        1519         2521         1673          746         1180          622 
TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 
         777          867         1428         1242         1203         1191 
TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC 
        1471         1732         1733         1572         1132          974 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM 
         554          782          756          660         1340         1876 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT 
        1085         1481          827         1633         1641         1386 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 
        1519          355         1492         1270         1339         1464 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI 
        1305         1394          948          713         1156          673 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS 
         423         1467          525          476           98           78 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 
        1170         1374         1442          495          134          477 
TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB 
         435          293         1363         1405           NA          745 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
         943          743          923          328          461         1149 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB 
        1080          747          702         1247         1611          806 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU 
         620          178           76          414         1121          392 
TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 
        1561          829         1545          170          728          759 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18H 
        1288         1363          701          268           61           NA 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N 
         220           NA           NA           NA           NA           NA 
TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 
          NA           NA           NA          210           22           NA 
TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
          NA           NA           NA          324          196          612 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12K TCGA-C8-A12L TCGA-C8-A12M 
          30         3324          272           NA          363          358 
TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12T TCGA-C8-A12U 
         358          385          358            2           NA          385 
TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 
         385          385          385           NA           NA           95 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A133 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 
          54           44           NA           21           19          117 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ 
         114          375          332          345          345            5 
TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V 
         366          317           70           99           NA            9 
TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 
           7           11           13          252          294            1 
TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 
           1            1          371           30            1            7 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 
         362          635          403          626          425          431 
TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA 
         410          643          584          431          532          502 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG 
         569          480          552          575          366          366 
TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM 
         426          577          611          612          611          590 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 
         620          639          371          405          447          565 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB 
         541          509          783          727          839          552 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK 
          81          522          463          448          664          441 
TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS 
         606          538          242          499          482          496 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ 
         193          395          461          385          503          466 
TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F 
         472          116          433          430          530          488 
TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M 
         409          397          439          287          499          410 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W 
         146           23          307          398          381          373 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 
         441          563          223         1308         1047          837 
TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F 
        1417         1229         1141         1220          865          878 
TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S 
        1434         1359         1246         1163         1174         1009 
TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y 
        1013         1318         1042          974          972          870 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 
         518          773          825          707          591          640 
TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D 
         726          450          762          710          694          526 
TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J 
         630          658          554          393          530          590 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R 
         275          626          235          396          595          519 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 
         428          456         2329         1631         1613          911 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF 
         984          867          501          520         1165         1138 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
         997         1026         1025          865          689          118 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 
         675          638          337         1648          834         1205 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH 
         598          748         1231           NA          574         3247 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX 
        3121           NA         1309          515          168          478 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N3 TCGA-E9-A1N4 
         219          549          677          605           NA          584 
TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC 
        1120          410          365          399         1112         1203 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI 
         383         1088          610          656           NA          300 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 
         362          435           19           64          186           42 
TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD 
          84          645          976          633         1224           20 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 
        1054          200          647         1052         1084         1038 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D 
          24          381          405         1189          692           NA 
TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A245 
         392          715          733          519           21           26 
TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS 
         828           59           29          382           22          540 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X 
          23          793          560           19          478           NA 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE 
           7           12            8            7           NA          468 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 
         371         1208          258          554          575          403 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX 
         504          477          875          789          694          911 
TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 
         908         1229         1251         1210         1611          907 
TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB 
         703          562          915           NA          575          608 
TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH 
         187          424          320          439         1051          607 
TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 
        1673         1604          788          672          647          532 
TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
         309          322          225         3342           NA         5909 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI 
        1616         1628         1309         1299         1286         1883 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
        1896         2763         2331         2352         1623         3361 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV 
        1162          982         2108         1641         1753          412 
TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 
         551          360          352          252          203          140 
TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM 
          20           91          109          210          169          143 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y 
         111           97           99           80          118          126 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LQ-A4E4 
         137          137          170           98          189          484 
TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA 
          85           64          385         1416          229         1357 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
         841          733          797          513          429          313 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L 
         298          449          721         1658         1031          945 
TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-S3-A6ZG TCGA-W8-A86G 
         554          220          135          207          161 
Variable 1:'AGE':	nDistinctValues=65,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=111,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=655,	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=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=16,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=25,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=29,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'BATCH.NUMBER':	nDistinctValues=39,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "NEOPLASM.DISEASESTAGE"                 
 [3] "PATHOLOGY.T.STAGE"                     
 [4] "PATHOLOGY.N.STAGE"                     
 [5] "PATHOLOGY.M.STAGE"                     
 [6] "GENDER"                                
 [7] "HISTOLOGICAL.TYPE"                     
 [8] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [9] "NUMBER.OF.LYMPH.NODES"                 
[10] "RACE"                                  
[11] "ETHNICITY"                             
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 995 columns, 1 survival variables, and 11 non-survival variables.
AGE, nv=65, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=13, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
258 581 117  36 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
258 581 117  36 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
258 581 117  36 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
258 581 117  36 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
468 330 111  70 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
468 330 111  70 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2  N3 
468 330 111  70 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
468 330 111  70 
PATHOLOGY.M.STAGE, nv=4, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=7, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=29, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED   169  18
  1P GAIN WILD-TYPE 691  96
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              187               787 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               18                96 
$`1P GAIN MUTATED`
TCGA-A1-A0SF TCGA-A1-A0SM TCGA-A1-A0SP TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W 
       48.10         7.96        19.20        73.84        22.06        64.04 
TCGA-A2-A04Y TCGA-A2-A0CM TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CX TCGA-A2-A0D0 
       36.13        24.79        75.25         5.19        56.81        21.14 
TCGA-A2-A0D2 TCGA-A2-A0SW TCGA-A2-A0T2 TCGA-A2-A0T7 TCGA-A2-A0YI TCGA-A2-A0YJ 
       33.76        44.88         8.38        20.75        14.50        18.61 
TCGA-A2-A0YK TCGA-A2-A0YM TCGA-A2-A1G0 TCGA-A2-A25B TCGA-A2-A3XS TCGA-A2-A3XZ 
       19.33        31.73        20.25        16.31        33.93        31.99 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A26E 
       38.37         7.30        35.67        31.73        12.72        31.36 
TCGA-A7-A26F TCGA-A7-A26I TCGA-A7-A3IZ TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A5ZX 
       24.26        21.73        10.59        14.50        21.17        11.05 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A8-A06Z TCGA-A8-A07O TCGA-A8-A07U TCGA-A8-A08R 
       10.29         9.37         1.02         9.99         9.96         0.99 
TCGA-A8-A08X TCGA-A8-A09M TCGA-A8-A09R TCGA-AC-A2BM TCGA-AC-A2FG TCGA-AC-A2QJ 
       33.99        15.02         8.98        38.20        36.99         2.27 
TCGA-AC-A3W6 TCGA-AC-A5XS TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AN-A04C 
        1.68         1.55         1.12         1.18         0.69         1.78 
TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FL 
        1.71         8.02         7.36         0.16         0.33         7.59 
TCGA-AN-A0FT TCGA-AN-A0FY TCGA-AO-A03R TCGA-AO-A0J2 TCGA-AO-A0JB TCGA-AO-A0JD 
        6.02         0.33        68.75        32.78        50.70        72.00 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A12F 
       21.37        26.24        94.59        96.10        64.04        48.36 
TCGA-AQ-A04L TCGA-AQ-A54O TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A1AI TCGA-AR-A1AK 
      130.09        21.86        37.41        56.88        61.84        51.25 
TCGA-AR-A24K TCGA-AR-A24X TCGA-AR-A252 TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-B6-A0I2 
       50.89        48.16        40.64        16.96        20.38       143.38 
TCGA-B6-A0I5 TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0RE TCGA-B6-A0RU TCGA-B6-A0X1 
      149.59        65.72       112.37       211.56       131.21       186.48 
TCGA-B6-A1KC TCGA-B6-A408 TCGA-BH-A0AW TCGA-BH-A0B3 TCGA-BH-A0B7 TCGA-BH-A0BF 
       43.59        49.94        20.45        39.55        56.98        25.71 
TCGA-BH-A0BL TCGA-BH-A0BZ TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DK TCGA-BH-A0DL 
       44.05        49.05        48.13        42.90        13.91        48.23 
TCGA-BH-A0DS TCGA-BH-A0DV TCGA-BH-A0E6 TCGA-BH-A0EE TCGA-BH-A0H9 TCGA-BH-A0HI 
        2.56        45.17         9.63        31.00        41.00        20.38 
TCGA-BH-A0W3 TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1FN TCGA-BH-A1FU 
       23.93        25.81        31.53        97.48        72.07        72.07 
TCGA-BH-A203 TCGA-C8-A12M TCGA-C8-A12V TCGA-C8-A135 TCGA-C8-A1HM TCGA-C8-A1HN 
       38.60        11.77        12.66         0.62         2.30         3.25 
TCGA-C8-A278 TCGA-C8-A27B TCGA-D8-A13Z TCGA-D8-A143 TCGA-D8-A1J8 TCGA-D8-A1JA 
        0.03         0.99        20.88        14.17        14.17        16.50 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JL TCGA-D8-A1JT TCGA-D8-A1X5 TCGA-D8-A1XA 
       18.71        15.78        20.09        13.32        18.58        27.58 
TCGA-D8-A1XC TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A27R 
        2.66        21.83        14.50        12.66        16.54        10.09 
TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A14N TCGA-E2-A14R TCGA-E2-A14X 
       46.59        40.41        40.11        47.15        38.60        31.96 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A159 TCGA-E2-A15K 
       17.03        25.41        27.12        19.43        25.05         9.04 
TCGA-E2-A1AZ TCGA-E2-A1II TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LH TCGA-E2-A1LI 
       60.53        33.70        27.42        39.62       106.75       102.61 
TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1RB TCGA-E9-A1RH 
       13.48        12.00        35.77        20.05        20.81        34.59 
TCGA-E9-A226 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-EW-A1J3 TCGA-EW-A1OV TCGA-EW-A1OW 
       34.13         0.62        15.72        16.57        25.94        22.82 
TCGA-EW-A1P0 TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A423 TCGA-GI-A2C9 TCGA-GM-A2D9 
       41.13         7.86        19.99        10.16       109.87        59.57 
TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-LD-A74U TCGA-LL-A441 TCGA-LL-A5YO 
       43.04        42.71        42.28         6.67         2.99         3.19 
TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-OL-A5D7 TCGA-OL-A5RW TCGA-OL-A5S0 
        3.25         3.88         4.14        46.55        26.20         9.80 
TCGA-S3-A6ZG 
        6.81 

$`1P GAIN WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI 
        8.52        14.37        43.43        14.27        47.24        20.88 
TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04N 
       13.68        31.79        39.32        28.01        18.21       104.81 
TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04X TCGA-A2-A0CK 
       18.02        41.95        82.16        63.12        55.43       125.59 
TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS 
       64.57       112.08        92.48        88.60       107.93        75.55 
TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM 
       63.45        64.04        34.55        28.77        25.22       101.72 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES 
       89.36        80.28       107.61        79.76        74.40        37.05 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY 
       35.05        34.29        31.82        29.75        24.72        24.16 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 
       99.19        54.64        27.12        50.43        44.28        17.52 
TCGA-A2-A0T1 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC 
       17.13        18.71        20.52        17.46        18.90        32.55 
TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YL 
       25.28        18.21        15.42        21.90        21.67        14.63 
TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G1 
       23.77        23.47        17.36        36.79        22.45        19.20 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A25D 
       19.56        16.47        52.47       107.70        17.19        18.15 
TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XU 
       91.92        10.59        20.88        39.65        83.01        29.98 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A4RX TCGA-A2-A4RY 
       14.07        49.48        38.40        34.98         9.01         8.81 
TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE 
        8.91        12.00         6.74         3.42        38.30        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13E 
       34.29        35.47        30.61        37.45        33.11        10.72 
TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD 
       23.61        29.56        23.74        23.80        20.61        22.32 
TCGA-A7-A3IY TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 
       11.34        10.29        11.28        13.41        14.70        11.97 
TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW 
       14.93        13.74        17.92        14.73        12.10        10.72 
TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R 
       10.42         8.75        13.02        13.02         1.02        17.98 
TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A076 
       41.06        29.03        31.00        26.01        17.03        53.98 
TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I 
        9.01        33.01        19.99        18.97        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07W 
       12.00        17.03        10.98         8.98         7.99         9.99 
TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A 
       28.04        18.05        15.06        36.95        13.02         0.99 
TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J 
       23.08        19.99        18.05        19.96        12.00        37.05 
TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z 
        9.99        31.00        31.00        19.07        93.04        40.01 
TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 
       19.07        16.01        17.95        41.98        12.00         9.99 
TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I 
        9.99        12.00         1.02        13.02        31.00        33.07 
TCGA-A8-A09K TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
       29.98         1.02        25.02        19.04        15.02         0.99 
TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 
       14.01        12.00        19.04        13.02        21.04         0.99 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G 
       13.02        17.03        38.04         0.95         2.37        10.85 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FK 
        2.66         1.48        38.53        40.57        55.43        38.79 
TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3HN 
       26.04        50.70         1.02         0.92         0.99         0.69 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3YI TCGA-AC-A3YJ 
       14.83         9.40         1.12         1.81         1.55         1.32 
TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A03Y 
        0.07         1.81         0.43         1.74         0.33         0.33 
TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A0AL TCGA-AN-A0AR 
        0.23         0.33         0.62         2.96         6.51         0.33 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FN 
        0.33         6.44         4.64         7.96         7.00         7.17 
TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FZ TCGA-AN-A0XL 
        6.28         0.33         0.36         0.33         0.33         0.33 
TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT 
        0.33        12.33         0.30         0.33         0.33         0.33 
TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N 
        0.33         5.33         5.59        80.28        47.84        66.77 
TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J3 
       81.63        84.69        47.87        59.05        29.13        21.40 
TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 
       17.65        24.16        37.48        20.32        22.36        53.03 
TCGA-AO-A0JA TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL 
       21.53        50.86        76.77        38.53        62.04        55.33 
TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A12A TCGA-AO-A12B 
       71.80       102.58        99.25        93.70        90.58        77.56 
TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ 
       57.30        41.62        28.37        14.73        82.62        61.87 
TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A0Y5 
       70.39         0.53        17.79        24.79        26.93         5.65 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ 
       15.62        13.22         2.56         9.99        82.88        49.32 
TCGA-AR-A0TR TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
        5.26        29.75        24.30        64.83        55.86        76.14 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH 
       65.36        70.16        83.87        76.18        55.36        75.55 
TCGA-AR-A1AJ TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP 
       52.77        48.82        62.56        43.73        43.56        39.98 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       43.07        17.23        40.83        46.32        42.58        35.24 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       36.26        20.22       109.58        73.02        65.46        68.19 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T 
       65.69         0.85        66.05        57.40        62.07        53.26 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 
       53.36        54.18        50.96        51.75        56.15        45.17 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LK 
       39.85        34.82        93.83       128.65        20.25        42.87 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A5QM TCGA-AR-A5QN 
        7.36        40.04        17.10        20.81        54.74        16.04 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB 
       20.45        10.59        77.62        12.13       220.90       129.57 
TCGA-B6-A0IC TCGA-B6-A0IG TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
       50.70       146.50       176.98        18.77       126.12        84.59 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
      110.14       110.93       140.88        68.45       189.01       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ 
       81.17        78.02       172.96       162.05       102.77       140.48 
TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV 
      100.70        89.46       157.41        97.48       188.68        79.63 
TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 
       17.98        21.47       113.79       129.57       129.70        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU 
       68.94        58.88       101.52        73.51       139.17       170.17 
TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV 
       85.35        54.28        82.88        55.00        24.53        38.79 
TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B5 
       25.55        28.50        46.95        40.83        39.16        48.36 
TCGA-BH-A0B6 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BG 
       56.94        51.68        37.22        32.02        18.21        24.85 
TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR 
       21.70        61.68        35.67        48.69        27.19        53.69 
TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0C0 TCGA-BH-A0C1 
       53.95        45.57        49.94        11.67        41.75        44.02 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DO 
       45.83        31.17        23.44        38.01        22.13        17.26 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DT TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
       15.65         3.22        38.47        47.41        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB 
       15.68        14.30        44.81        46.19        32.65        24.49 
TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       24.43        30.35        10.78        15.16        37.78        35.51 
TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HK TCGA-BH-A0HO 
       24.56        23.08        52.96        26.50         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY 
       13.61        36.85        12.89        51.32        27.25        50.79 
TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F 
        5.59        24.95        42.35        44.81        23.05         8.81 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M 
        2.01         7.23        20.12        90.84        26.66        72.56 
TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T 
       37.74        30.28        55.63        37.55        66.05         7.36 
TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET 
       51.39        51.16        69.93        91.99       113.82        82.85 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F5 
       42.28        12.00        55.69        49.58        17.69        89.16 
TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG 
       24.66       120.62       114.15        33.17        74.73       122.89 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A201 
       36.92        63.35        55.00        45.63       144.59         6.90 
TCGA-BH-A202 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q 
        0.72        83.31        57.83       130.16        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12L TCGA-C8-A12N 
       20.12         0.99       109.28         8.94        11.93        11.77 
TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12W TCGA-C8-A12X 
       12.66        11.77         0.07        12.66        12.66        12.66 
TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A138 
        3.12         1.78         1.45         0.69         3.85         3.75 
TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK 
       12.33        10.92        11.34        11.34         0.16        12.03 
TCGA-C8-A1HL TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z 
       10.42         0.30         0.23         0.36         0.43         8.28 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A3M7 TCGA-C8-A3M8 
        9.67         0.03         0.03        12.20         0.03         0.23 
TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A145 TCGA-D8-A146 
       11.90        13.25        20.58        13.97        13.48        21.14 
TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG 
       19.20        17.49        18.15        18.90        12.03        12.03 
TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JM TCGA-D8-A1JN 
       14.01        18.97        20.09        20.12        19.40        20.38 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 
       21.01        12.20        14.70        17.79        16.73        25.74 
TCGA-D8-A1X9 TCGA-D8-A1XB TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XL 
       23.90        18.15        17.16        15.22        14.73        19.92 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT 
       17.69         7.96        16.41        15.85        16.31         6.35 
TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 
       12.99        15.16        15.32        15.52         3.81        14.24 
TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I 
       14.14        17.42        16.04        13.45        13.05        14.43 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T 
        9.44        16.41        13.48         4.80         0.76        13.08 
TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 
       12.53        12.26        14.50        18.51         7.33        43.00 
TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14O 
       34.42        27.52        37.51        28.44        28.87        44.68 
TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V 
       40.96        38.24        33.17        33.30        43.33        34.26 
TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 
       32.02        28.60        23.24        21.04        23.87        14.79 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G 
       23.34        22.82        17.29        20.71        21.63        18.21 
TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O 
       12.92        17.42        19.40        20.58         7.73        13.02 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 
       19.56        17.06        14.07        14.99        53.62        53.03 
TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE 
       29.95        32.35        28.50        16.47        17.10        38.30 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       37.41        32.78        33.73        28.44        22.65         3.88 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LA 
       22.19        20.98        11.08        54.18        19.66        24.59 
TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 
       40.47        28.90        18.87         8.75        43.04        16.93 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 
        5.52        15.72         7.20        18.05        22.26        19.89 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND 
       19.20        36.82        13.12        36.56        39.55        12.59 
TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 
       21.57         9.86        11.90        14.30         0.62         2.10 
TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RC 
        6.12         1.38         2.76        21.21        32.09        40.24 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A227 
        0.66        34.65         6.58        21.27        35.64         0.79 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G 
       12.53        13.32        39.09        22.75        12.89        23.51 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A248 
       24.10        17.06         0.69         0.85        27.22         1.94 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO 
        0.95        12.56         0.72        17.75         0.76        26.07 
TCGA-E9-A3Q9 TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE 
       18.41         0.23         0.39         0.26         0.23        15.39 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 
       12.20        39.72         8.48        18.21        18.90        13.25 
TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P1 
       15.68        28.77        29.95        29.85        40.41        39.78 
TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA 
       52.96        29.82        23.11        18.48        30.08        18.90 
TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH 
        6.15        13.94        10.52        14.43        34.55        19.96 
TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 
       55.00        52.73        25.91        22.09        21.27        17.49 
TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DI 
       10.59         7.40       194.27        53.13        53.52        61.91 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
       62.33        90.84        76.64        77.33        53.36       110.50 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV 
       38.20        32.28        69.30        53.95        57.63        13.55 
TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A7W6 TCGA-LL-A440 
       18.12        11.84        11.57         8.28         4.60         0.66 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A6FQ 
        3.58         6.90         5.56         4.70         3.65         2.63 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LQ-A4E4 
        4.50         4.50         5.59         3.22         6.21        15.91 
TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.79         2.10        12.66         7.53        44.61        27.65 
TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I 
       24.10        16.87        14.10        10.29        14.76        23.70 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P 
       54.51        33.90        31.07        18.21         7.23         4.44 
TCGA-W8-A86G 
        5.29 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.03              0.03 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           211.56            234.28 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            22.06             21.21 
[1] "0.0 - 211.6 (22.1)" "0.0 - 234.3 (21.2)"
[1] "hr=" "1.2"
D1V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1P GAIN MUTATED        13       14        1        1        72        44
  1P GAIN WILD-TYPE      67       63        8        8       263       180
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1P GAIN MUTATED           0         22          4          9        3
  1P GAIN WILD-TYPE         2        116         23         50       14
                   vv
clus                STAGE TIS STAGE X
  1P GAIN MUTATED           1       3
  1P GAIN WILD-TYPE         0      13
D1V3, multiclass
            clus
vv           1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                 13                67
  STAGE IA                14                63
  STAGE IB                 1                 8
  STAGE II                 1                 8
  STAGE IIA               72               263
  STAGE IIB               44               180
  STAGE III                0                 2
  STAGE IIIA              22               116
  STAGE IIIB               4                23
  STAGE IIIC               9                50
  STAGE IV                 3                14
  STAGE TIS                1                 0
  STAGE X                  3                13
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  1P GAIN MUTATED    36 124  19   7
  1P GAIN WILD-TYPE 222 457  98  29
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1              36               222
  T2             124               457
  T3              19                98
  T4               7                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                 N0  N1  N2  N3
  1P GAIN MUTATED   100  60  17  10
  1P GAIN WILD-TYPE 368 270  94  60
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0             100               368
  N1              60               270
  N2              17                94
  N3              10                60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  1P GAIN MUTATED          0 158   3  27
  1P GAIN WILD-TYPE        2 687  14 104
D1V6, multiclass
          clus
vv         1P GAIN MUTATED 1P GAIN WILD-TYPE
  CM0 (I+)               0                 2
  M0                   158               687
  M1                     3                14
  MX                    27               104
[1] 4 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   186   2
  1P GAIN WILD-TYPE 798   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED    186    2
  1P GAIN WILD-TYPE  798    9
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE             186               798
  MALE                 2                 9
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  1P GAIN MUTATED                            0                           153
  1P GAIN WILD-TYPE                          1                           582
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  1P GAIN MUTATED                               17                   2
  1P GAIN WILD-TYPE                            149                   3
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  1P GAIN MUTATED                                  6                  1
  1P GAIN WILD-TYPE                               23                 13
                   vv
clus                OTHER  SPECIFY
  1P GAIN MUTATED                9
  1P GAIN WILD-TYPE             35
D1V8, multiclass
                                  clus
vv                                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                153               582
  INFILTRATING LOBULAR CARCINOMA                17               149
  MEDULLARY CARCINOMA                            2                 3
  MIXED HISTOLOGY (PLEASE SPECIFY)               6                23
  MUCINOUS CARCINOMA                             1                13
  OTHER  SPECIFY                                 9                35
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V9, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    65 123
  1P GAIN WILD-TYPE 217 590
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     65  123
  1P GAIN WILD-TYPE  217  590
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO               65               217
  YES             123               590
[1] 2 2
[1] FALSE
D1V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P GAIN MUTATED                                  0     7
  1P GAIN WILD-TYPE                                1    49
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED                          34   137
  1P GAIN WILD-TYPE                       103   571
D1V11, multiclass
                                  clus
vv                                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          7                49
  BLACK OR AFRICAN AMERICAN                     34               103
  WHITE                                        137               571
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V12, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     5 156
  1P GAIN WILD-TYPE  31 640
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      5  156
  1P GAIN WILD-TYPE   31  640
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                31
  NOT HISPANIC OR LATINO             156               640
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED   571  68
  1Q GAIN WILD-TYPE 289  46
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              639               335 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               68                46 
$`1Q GAIN MUTATED`
TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SM TCGA-A1-A0SN 
       43.43        48.10        47.24        20.88         7.96        39.32 
TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04Q TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W 
       19.20        18.21        41.95        73.84        22.06        64.04 
TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CQ TCGA-A2-A0CS 
       36.13       125.59        24.79       112.08        88.60        75.55 
TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D2 
       75.25         5.19        63.45        56.81        21.14        33.76 
TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EQ 
       28.77        25.22       101.72        89.36        80.28        79.76 
TCGA-A2-A0ET TCGA-A2-A0EV TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SV TCGA-A2-A0SW 
       35.05        31.82        24.16        99.19        27.12        44.88 
TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 
       50.43        44.28        17.52        17.13         8.38        18.71 
TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD 
       20.52        17.46        18.90        20.75        32.55        25.28 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL 
       21.90        21.67        14.50        18.61        19.33        14.63 
TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A25A 
       31.73        23.77        23.47        22.45        20.25       107.70 
TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25E TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS 
       16.31        17.19        91.92        20.88        39.65        33.93 
TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4S2 
       83.01        29.98        31.99        38.37         7.30         6.74 
TCGA-A7-A0CD TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D 
       38.30        35.47        30.61        35.67        33.11        31.73 
TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H 
       10.72        12.72        31.36        24.26        23.74        23.80 
TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A425 
       21.73        20.61        10.59        10.29        11.28        14.70 
TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF 
       11.97        14.93        13.74        14.50        21.17        17.92 
TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW 
       14.73        12.10        10.72        11.05        10.29         9.37 
TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z 
       10.42        13.02         1.02        31.00        26.01         1.02 
TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G 
       17.03        53.98        33.01        19.99        18.97        18.97 
TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z 
        9.99         8.98         7.99         9.96         9.99        28.04 
TCGA-A8-A084 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G 
       15.06         0.99        23.08        19.99        18.05        19.96 
TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 
       31.00         0.99        93.04        33.99        40.01        16.01 
TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B 
       17.95        41.98        12.00         9.99         9.99        12.00 
TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09Q 
        1.02        31.00        33.07        29.98        15.02        25.02 
TCGA-A8-A09R TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 
        8.98        15.02         0.99        14.01        12.00        19.04 
TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-AC-A23C TCGA-AC-A23E 
       13.02        21.04        13.02        17.03         0.95         2.37 
TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB 
       10.85         2.66         1.48        38.53        38.20        40.57 
TCGA-AC-A2FG TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3HN 
       36.99        26.04        50.70         0.92         2.27         0.69 
TCGA-AC-A3OD TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YJ TCGA-AC-A5XS 
       14.83         1.12         1.81         1.68         1.32         1.55 
TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A8OP 
        1.12         1.81         1.18         0.69         0.43         1.74 
TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04C 
        0.33         0.33         0.23         0.33         0.62         1.78 
TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FK 
        1.71         8.02         7.36         0.16         0.33         7.00 
TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW 
        7.59         7.17         6.28         6.02         0.33         0.36 
TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO 
        0.33         0.33         0.33         0.33         0.33        12.33 
TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XW TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A0J2 
        0.30         0.33         5.59        81.63        68.75        32.78 
TCGA-AO-A0J5 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB 
       24.16        20.32        22.36        53.03        21.53        50.70 
TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM 
       72.00        21.37        26.24        62.04        55.33        71.80 
TCGA-AO-A125 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D 
       99.25        94.59        96.10        90.58        77.56        64.04 
TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H 
       48.36        41.62        61.87        70.39        17.79        24.79 
TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP 
      130.09         5.65        13.22        21.86         9.99        82.88 
TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ 
        5.26        37.41        56.88        75.55        61.84        52.77 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AP TCGA-AR-A1AS 
       51.25        48.82        62.56        43.73        39.98        40.83 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M 
       42.58        35.24        20.22        50.89        73.02        65.46 
TCGA-AR-A24N TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24W TCGA-AR-A24X 
       68.19         0.85        66.05        57.40        50.96        48.16 
TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LK 
       56.15        40.64        39.85        93.83       128.65        42.87 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
        7.36        40.04        17.10        20.81        16.96        20.38 
TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 
       54.74        16.04        20.45        77.62       143.38       149.59 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IJ 
       12.13       220.90       129.57        65.72       112.37       176.98 
TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RH 
       84.59       110.14       110.93       140.88       211.56       189.01 
TCGA-B6-A0RI TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RS TCGA-B6-A0RU 
      234.28       172.96       162.05       102.77       100.70       131.21 
TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 
      188.68        79.63        17.98        21.47       129.57       129.70 
TCGA-B6-A0X1 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A2IU 
      186.48        58.88        43.59       101.52        73.51       170.17 
TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
       85.35        54.28        49.94        82.88        55.00        24.53 
TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 
       20.45        25.55        28.50        46.95        40.83        39.55 
TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       48.36        56.98        37.22        32.02        18.21        25.71 
TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ 
       24.85        21.70        44.05        61.68        35.67        27.19 
TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 
       53.95        45.57        49.05        41.75        44.02        48.13 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL 
       42.90        45.83        23.44        22.13        13.91        48.23 
TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       17.26        15.65         2.56        38.47        45.17        47.41 
TCGA-BH-A0E1 TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE 
       15.68         9.63        46.19        32.65        24.49        31.00 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HI TCGA-BH-A0HK 
       15.16        37.78        23.08        41.00        20.38         5.85 
TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0RX 
        2.50        13.61        36.85        12.89        27.25         5.59 
TCGA-BH-A0W3 TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18P 
       23.93         8.81         2.01        90.84        26.66        30.28 
TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V 
       55.63        37.55        66.05         7.36        51.39        51.16 
TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX 
       69.93        91.99        42.28        12.00        55.69        49.58 
TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM 
       25.81        31.53        97.48        63.35        55.00        45.63 
TCGA-BH-A1FN TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A209 
       72.07        72.07         6.90         0.72        38.60       130.16 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12O TCGA-C8-A12P 
        6.44        20.12        11.93        11.77        12.66        11.77 
TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A135 TCGA-C8-A1HE 
       12.66        12.66         3.12         1.78         0.62        12.33 
TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26X 
       11.34        12.03        10.42         2.30         3.25         0.36 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B 
        8.28         9.67         0.03         0.03         0.03         0.99 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 
        0.03         0.23        20.88        13.25        20.58        13.97 
TCGA-D8-A143 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
       14.17        21.14        14.17        17.49        16.50        18.71 
TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JI TCGA-D8-A1JJ 
       15.78        18.15        18.90        12.03        18.97        20.09 
TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1JT 
       20.12        20.09        19.40        20.38        12.20        13.32 
TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1XA TCGA-D8-A1XB 
       14.70        18.58        16.73        25.74        27.58        18.15 
TCGA-D8-A1XC TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XM TCGA-D8-A1XO 
        2.66        15.22        14.73        21.83        17.69         7.96 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY 
       15.85        16.31         6.35        15.16        12.66        16.54 
TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27G TCGA-D8-A27I TCGA-D8-A27K 
       15.52         3.81        14.14        13.45        14.43         9.44 
TCGA-D8-A27N TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 
        4.80        10.09        13.08        12.53        12.26        14.50 
TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E 
       34.42        46.59        40.41        37.51        40.11        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14T 
       28.87        47.15        44.68        38.24        38.60        33.30 
TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 
       34.26        31.96        28.60        17.03        25.41        27.12 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15D TCGA-E2-A15E 
       23.24        19.43        25.05        23.34        17.29        20.71 
TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M 
       18.21        12.92        19.40         9.04        20.58         7.73 
TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B5 TCGA-E2-A1BD TCGA-E2-A1IF 
       14.99        60.53        53.62        32.35        17.10        37.41 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IL TCGA-E2-A1IN 
       32.78        33.73        33.70        28.44         3.88        22.19 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LG TCGA-E2-A1LH 
       54.18        27.42        39.62        19.66        18.87       106.75 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z 
      102.61         8.75        16.93         5.52        15.72         7.20 
TCGA-E2-A574 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NE 
       19.89        13.48        12.00        13.12        36.56        35.77 
TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R5 
       20.05         9.86        11.90         0.62         2.10         1.38 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RF TCGA-E9-A1RG 
       21.21        32.09        20.81         0.66         6.58        21.27 
TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A22A TCGA-E9-A22E TCGA-E9-A22G 
       34.59        34.13         0.79        39.09        12.89        23.51 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A249 
       24.10        17.06         0.69         0.85        27.22         0.95 
TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A3HO TCGA-E9-A3QA TCGA-E9-A3X8 
       12.56         0.72        17.75        26.07         0.62        15.72 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1J2 TCGA-EW-A1J3 
        0.23         0.39        15.39        12.20        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1P0 
       15.68        25.94        22.82        29.95        29.85        41.13 
TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PE 
       52.96        23.11         7.86        19.99         6.15        10.52 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A423 TCGA-EW-A424 
       19.96        55.00        52.73        25.91        10.16        10.59 
TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF 
        7.40       109.87        59.57        53.52        43.04        42.71 
TCGA-GM-A2DH TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A4E0 TCGA-GM-A5PV 
       42.28        77.33       110.50        38.20        57.63        13.55 
TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 
       18.12        11.84        11.57         8.28         6.67         4.60 
TCGA-LL-A441 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO 
        2.99         6.90         5.56         4.70         3.65         3.19 
TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A7SZ 
        3.25         2.63         3.88         4.14         4.50         5.59 
TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D7 TCGA-OL-A5DA TCGA-OL-A5RU 
       15.91         2.79         2.10        46.55        44.61        27.65 
TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5S0 TCGA-OL-A66K TCGA-OL-A66N 
       24.10        26.20        16.87         9.80        33.90        18.21 
TCGA-OL-A66O TCGA-S3-A6ZG TCGA-W8-A86G 
        7.23         6.81         5.29 

$`1Q GAIN WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SG TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SO 
        8.52        14.37        14.27        13.68        31.79        28.01 
TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04X TCGA-A2-A0CL 
      104.81        18.02        82.16        63.12        55.43        64.57 
TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CW TCGA-A2-A0D1 TCGA-A2-A0EP TCGA-A2-A0ER 
       92.48       107.93        64.04        34.55       107.61        74.40 
TCGA-A2-A0ES TCGA-A2-A0EU TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0SU TCGA-A2-A0YE 
       37.05        34.29        29.75        24.72        54.64        18.21 
TCGA-A2-A0YF TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 
       15.42        17.36        36.79        19.20        19.56        16.47 
TCGA-A2-A259 TCGA-A2-A25D TCGA-A2-A25F TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX 
       52.47        18.15        10.59        14.07        49.48        38.40 
TCGA-A2-A3XY TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S3 
       34.98         9.01         8.81         8.91        12.00         3.42 
TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0D9 TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A2KD 
       35.31        34.29        37.45        23.61        29.56        22.32 
TCGA-A7-A3IY TCGA-A7-A3RF TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06R TCGA-A8-A06T 
       11.34        13.41         8.75        13.02        17.98        41.06 
TCGA-A8-A06U TCGA-A8-A079 TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07P 
       29.03         9.01        14.01        12.00        17.03        10.98 
TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L 
       18.05        36.95        13.02        12.00        37.05         9.99 
TCGA-A8-A08O TCGA-A8-A08S TCGA-A8-A091 TCGA-A8-A09D TCGA-A8-A09N TCGA-A8-A09T 
       31.00        19.07        19.07        13.02         1.02        19.04 
TCGA-A8-A0A7 TCGA-A8-A0AD TCGA-AC-A2FF TCGA-AC-A2FK TCGA-AC-A2QH TCGA-AC-A3BB 
        0.99        38.04        55.43        38.79         1.02         0.99 
TCGA-AC-A3QP TCGA-AC-A3YI TCGA-AC-A62V TCGA-AN-A04A TCGA-AN-A0AL TCGA-AN-A0AR 
        9.40         1.55         0.07         2.96         6.51         0.33 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0XS TCGA-AN-A0XT 
        0.33         6.44         4.64         7.96         0.33         0.33 
TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03P 
        0.33         5.33        80.28        47.84        66.77        84.69 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J6 
       47.87        59.05        29.13        21.40        17.65        37.48 
TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JI TCGA-AO-A124 TCGA-AO-A126 TCGA-AO-A12E 
       50.86        76.77        38.53       102.58        93.70        57.30 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KS TCGA-AQ-A04J TCGA-AQ-A1H2 
       28.37        14.73        82.62         0.53        26.93        15.62 
TCGA-AQ-A54N TCGA-AR-A0TQ TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
        2.56        49.32        29.75        24.30        64.83        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 
       76.14        65.36        70.16        83.87        76.18        55.36 
TCGA-AR-A1AO TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AU TCGA-AR-A1AX TCGA-AR-A24H 
       43.56        43.07        17.23        46.32        36.26       109.58 
TCGA-AR-A24O TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24Z 
       65.69        62.07        53.26        53.36        54.18        51.75 
TCGA-AR-A251 TCGA-AR-A255 TCGA-AR-A2LH TCGA-AR-A5QQ TCGA-B6-A0IC TCGA-B6-A0IG 
       45.17        34.82        20.25        10.59        50.70       146.50 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0RG TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RQ 
       18.77       126.12        68.45        81.17        78.02       140.48 
TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WY TCGA-B6-A0X4 TCGA-B6-A0X5 
       89.46       157.41        97.48       113.79        28.27        68.94 
TCGA-B6-A1KN TCGA-BH-A0AV TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0B9 TCGA-BH-A0BP 
      139.17        38.79        39.16        56.94        51.68        48.69 
TCGA-BH-A0BR TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0DE TCGA-BH-A0DH TCGA-BH-A0DQ 
       53.69        49.94        11.67        31.17        38.01         3.22 
TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0EI TCGA-BH-A0GY 
       16.27         4.41        14.30        44.81        24.43        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HW 
       10.78        35.51        24.56        52.96        26.50        51.32 
TCGA-BH-A0HY TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18I 
       50.79        24.95        42.35        44.81        23.05         7.23 
TCGA-BH-A18J TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EY 
       20.12        72.56        37.74       113.82        82.85        17.69 
TCGA-BH-A1F5 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE 
       89.16        24.66       120.62       114.15        33.17        74.73 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FR TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A28O 
      122.89        36.92       144.59        83.31        57.83        10.65 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12N TCGA-C8-A12Q TCGA-C8-A12U 
        0.99       109.28         8.94        11.77         0.07        12.66 
TCGA-C8-A12X TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HF 
       12.66         1.45         0.69         3.85         3.75        10.92 
TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Y TCGA-C8-A27A 
       11.34         0.16         0.30         0.23         0.43        12.20 
TCGA-D8-A13Y TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JP 
       11.90        13.48        19.20        12.03        14.01        21.01 
TCGA-D8-A1X6 TCGA-D8-A1X9 TCGA-D8-A1XD TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XQ 
       17.79        23.90        17.16        14.50        19.92        16.41 
TCGA-D8-A1XU TCGA-D8-A1XZ TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27H 
       12.99        15.32        14.24        17.42        16.04        13.05 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27P TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 
       16.41        13.48         0.76        18.51         7.33        43.00 
TCGA-E2-A108 TCGA-E2-A14P TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A155 
       27.52        40.96        33.17        43.33        32.02        21.04 
TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15C TCGA-E2-A15F TCGA-E2-A15I TCGA-E2-A15O 
       23.87        14.79        22.82        21.63        17.42        13.02 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B6 
       19.56        17.06        14.07        53.03        29.95        28.50 
TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IK TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1LA 
       16.47        38.30        22.65        20.98        11.08        24.59 
TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LL TCGA-E2-A570 TCGA-E2-A573 TCGA-E9-A1N4 
       40.47        28.90        43.04        18.05        22.26        19.20 
TCGA-E9-A1N5 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NG TCGA-E9-A1R0 TCGA-E9-A1R4 
       36.82        39.55        12.59        21.57        14.30         6.12 
TCGA-E9-A1R6 TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RI TCGA-E9-A228 TCGA-E9-A229 
        2.76        40.24        34.65        35.64        12.53        13.32 
TCGA-E9-A22B TCGA-E9-A248 TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A5FL TCGA-E9-A5UO 
       22.75         1.94         0.76        18.41         0.26         0.23 
TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J6 TCGA-EW-A1OZ 
       39.72         8.48        18.21        18.90        28.77        40.41 
TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PD 
       39.78        29.82        18.48        30.08        18.90        13.94 
TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-GM-A2DA 
       14.43        34.55        22.09        21.27        17.49       194.27 
TCGA-GM-A2DB TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DO 
       53.13        61.91        62.33        90.84        76.64        53.36 
TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A740 
       32.28        69.30        53.95         0.66         3.58         4.50 
TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5RY TCGA-OL-A5RZ 
        3.22         6.21        12.66         7.53        14.10        10.29 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66P 
       14.76        23.70        54.51        31.07         4.44 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.03              0.07 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           234.28            194.27 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            20.81             23.70 
[1] "0.0 - 234.3 (20.8)" "0.1 - 194.3 (23.7)"
[1] "hr=" "1.2"
D2V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1Q GAIN MUTATED        45       41        4        9       230       148
  1Q GAIN WILD-TYPE      35       36        5        0       105        76
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1Q GAIN MUTATED           1         84         21         42       11
  1Q GAIN WILD-TYPE         1         54          6         17        6
                   vv
clus                STAGE TIS STAGE X
  1Q GAIN MUTATED           1      11
  1Q GAIN WILD-TYPE         0       5
D2V3, multiclass
            clus
vv           1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                 45                35
  STAGE IA                41                36
  STAGE IB                 4                 5
  STAGE II                 9                 0
  STAGE IIA              230               105
  STAGE IIB              148                76
  STAGE III                1                 1
  STAGE IIIA              84                54
  STAGE IIIB              21                 6
  STAGE IIIC              42                17
  STAGE IV                11                 6
  STAGE TIS                1                 0
  STAGE X                 11                 5
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  1Q GAIN MUTATED   146 400  74  27
  1Q GAIN WILD-TYPE 112 181  43   9
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1             146               112
  T2             400               181
  T3              74                43
  T4              27                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  1Q GAIN MUTATED   306 217  67  49
  1Q GAIN WILD-TYPE 162 113  44  21
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0             306               162
  N1             217               113
  N2              67                44
  N3              49                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                CM0 (I+)  M0  M1  MX
  1Q GAIN MUTATED          1 546  11  91
  1Q GAIN WILD-TYPE        1 299   6  40
D2V6, multiclass
          clus
vv         1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CM0 (I+)               1                 1
  M0                   546               299
  M1                    11                 6
  MX                    91                40
[1] 4 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   643   6
  1Q GAIN WILD-TYPE 341   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    643    6
  1Q GAIN WILD-TYPE  341    5
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE             643               341
  MALE                 6                 5
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  1Q GAIN MUTATED                            1                           465
  1Q GAIN WILD-TYPE                          0                           270
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  1Q GAIN MUTATED                              130                   3
  1Q GAIN WILD-TYPE                             36                   2
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  1Q GAIN MUTATED                                 17                  7
  1Q GAIN WILD-TYPE                               12                  7
                   vv
clus                OTHER  SPECIFY
  1Q GAIN MUTATED               26
  1Q GAIN WILD-TYPE             18
D2V8, multiclass
                                  clus
vv                                 1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                465               270
  INFILTRATING LOBULAR CARCINOMA               130                36
  MEDULLARY CARCINOMA                            3                 2
  MIXED HISTOLOGY (PLEASE SPECIFY)              17                12
  MUCINOUS CARCINOMA                             7                 7
  OTHER  SPECIFY                                26                18
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V9, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED   184 465
  1Q GAIN WILD-TYPE  98 248
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    184  465
  1Q GAIN WILD-TYPE   98  248
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO              184                98
  YES             465               248
[1] 2 2
[1] FALSE
D2V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q GAIN MUTATED                                  1    30
  1Q GAIN WILD-TYPE                                0    26
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED                          83   474
  1Q GAIN WILD-TYPE                        54   234
D2V11, multiclass
                                  clus
vv                                 1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         30                26
  BLACK OR AFRICAN AMERICAN                     83                54
  WHITE                                        474               234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V12, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    18 519
  1Q GAIN WILD-TYPE  18 277
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     18  519
  1Q GAIN WILD-TYPE   18  277
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                  18                18
  NOT HISPANIC OR LATINO             519               277
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    93  18
  2P GAIN WILD-TYPE 767  96
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              111               863 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               18                96 
$`2P GAIN MUTATED`
TCGA-A1-A0SO TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0SX TCGA-A2-A0T1 TCGA-A2-A0T2 
       28.01        56.81        21.14        50.43        17.13         8.38 
TCGA-A2-A0YE TCGA-A2-A0YJ TCGA-A2-A1G1 TCGA-A2-A3XS TCGA-A2-A3XZ TCGA-A2-A4S1 
       18.21        18.61        19.20        33.93        31.99        12.00 
TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A26I TCGA-A7-A4SE 
       30.61        35.67        31.73        10.72        21.73        21.17 
TCGA-A7-A5ZV TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A07U 
       12.10         1.02        17.98        31.00        17.03         9.96 
TCGA-A8-A08R TCGA-A8-A097 TCGA-AC-A23H TCGA-AC-A62Y TCGA-AC-A6IW TCGA-AN-A04C 
        0.99        12.00         2.66         1.81         0.69         1.78 
TCGA-AN-A0AM TCGA-AN-A0FX TCGA-AO-A0J2 TCGA-AO-A0JD TCGA-AO-A124 TCGA-AO-A12D 
        0.16         0.33        32.78        72.00       102.58        64.04 
TCGA-AO-A12F TCGA-AO-A1KR TCGA-AR-A0TS TCGA-AR-A0TX TCGA-AR-A0U0 TCGA-AR-A0U2 
       48.36        70.39        37.41        64.83        65.36        83.87 
TCGA-AR-A24Q TCGA-B6-A0I2 TCGA-B6-A0RE TCGA-B6-A0RU TCGA-B6-A0WZ TCGA-B6-A0X1 
       66.05       143.38       211.56       131.21       129.57       186.48 
TCGA-B6-A402 TCGA-BH-A0AW TCGA-BH-A0BG TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0DL 
       54.28        20.45        24.85        41.75        44.02        48.23 
TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EV 
        9.63        46.19         7.36        51.16        69.93        12.00 
TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1FC TCGA-BH-A1FM TCGA-BH-A203 TCGA-C8-A12P 
       31.53        97.48       114.15        45.63        38.60        11.77 
TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A131 TCGA-C8-A1HK TCGA-C8-A26Y TCGA-C8-A274 
       12.66        12.66         1.78        12.03         0.43         0.03 
TCGA-C8-A278 TCGA-D8-A13Z TCGA-D8-A143 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1JK 
        0.03        20.88        14.17        19.20        14.17        20.12 
TCGA-D8-A1XF TCGA-D8-A1XL TCGA-D8-A1XU TCGA-D8-A27M TCGA-D8-A27R TCGA-E2-A109 
       15.22        19.92        12.99        13.48        10.09        46.59 
TCGA-E2-A10C TCGA-E2-A14P TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A1II 
       40.11        40.96        14.79        25.05        23.34        33.70 
TCGA-E2-A1LE TCGA-E2-A1LK TCGA-E2-A574 TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A2JS 
       28.90         8.75        19.89         6.58        34.59        17.75 
TCGA-E9-A5FL TCGA-EW-A1IY TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A2FR TCGA-GI-A2C9 
        0.26         8.48        19.99         6.15        55.00       109.87 
TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DF TCGA-LL-A5YN TCGA-LL-A5YP TCGA-LL-A7SZ 
       53.13        43.04        42.71         3.65         3.25         5.59 
TCGA-OL-A5RW TCGA-OL-A66I TCGA-OL-A66P 
       26.20        23.70         4.44 

$`2P GAIN WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP 
       20.88        13.68        31.79         7.96        39.32        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T 
       18.21       104.81        18.02        41.95        82.16        73.84 
TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK 
       22.06        63.12        64.04        55.43        36.13       125.59 
TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
       64.57        24.79       112.08        92.48        88.60       107.93 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D1 
       75.55        75.25         5.19        63.45        64.04        34.55 
TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO 
       33.76        28.77        25.22       101.72        89.36        80.28 
TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU 
      107.61        79.76        74.40        37.05        35.05        34.29 
TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU 
       31.82        29.75        24.72        24.16        99.19        54.64 
TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T3 TCGA-A2-A0T4 
       27.12        44.88        44.28        17.52        18.71        20.52 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF 
       17.46        18.90        20.75        32.55        25.28        15.42 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       21.90        21.67        14.50        19.33        14.63        31.73 
TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 
       23.77        23.47        17.36        36.79        22.45        20.25 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C 
       19.56        16.47        52.47       107.70        16.31        17.19 
TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XT 
       18.15        91.92        10.59        20.88        39.65        83.01 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 
       29.98        14.07        49.48        38.40        34.98        38.37 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 
        7.30         9.01         8.81         8.91         6.74         3.42 
TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB 
       38.30        35.31        34.29        35.47        37.45        33.11 
TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G 
       12.72        23.61        29.56        31.36        24.26        23.74 
TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 
       23.80        20.61        22.32        11.34        10.59        10.29 
TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB 
       11.28        13.41        14.70        11.97        14.93        13.74 
TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV 
       14.50        17.92        14.73        10.72        11.05        10.29 
TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06T 
        9.37        10.42         8.75        13.02        13.02        41.06 
TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B 
       29.03        26.01         1.02        53.98         9.01        33.01 
TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
       19.99        18.97        18.97        14.01        12.00        17.03 
TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07W TCGA-A8-A07Z 
        9.99        10.98         8.98         7.99         9.99        28.04 
TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B 
       18.05        15.06        36.95        13.02         0.99        23.08 
TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L 
       19.99        18.05        19.96        12.00        37.05         9.99 
TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z 
       31.00        31.00        19.07        93.04        33.99        40.01 
TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A 
       19.07        16.01        17.95        41.98         9.99         9.99 
TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K 
       12.00         1.02        13.02        31.00        33.07        29.98 
TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       15.02         1.02        25.02         8.98        19.04        15.02 
TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 
        0.99        14.01        12.00        19.04        13.02        21.04 
TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E 
        0.99        13.02        17.03        38.04         0.95         2.37 
TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF 
       10.85         1.48        38.53        38.20        40.57        55.43 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI 
       36.99        38.79        26.04        50.70         1.02         0.92 
TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN 
        2.27         0.99         0.69        14.83         9.40         1.12 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V 
        1.81         1.68         1.55         1.32         1.55         0.07 
TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A03Y 
        1.12         1.18         0.43         1.74         0.33         0.33 
TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ 
        0.23         0.33         0.62         2.96         1.71         8.02 
TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD 
        7.36         6.51         0.33         0.33         0.33         6.44 
TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        4.64         7.96         7.00         7.59         7.17         6.28 
TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL 
        6.02         0.33         0.36         0.33         0.33         0.33 
TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT 
        0.33        12.33         0.30         0.33         0.33         0.33 
TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N 
        0.33         5.33         5.59        80.28        47.84        66.77 
TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V 
       81.63        84.69        68.75        47.87        59.05        29.13 
TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 
       21.40        17.65        24.16        37.48        20.32        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF 
       53.03        21.53        50.70        50.86        76.77        21.37 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A125 
       26.24        38.53        62.04        55.33        71.80        99.25 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E 
       93.70        94.59        96.10        90.58        77.56        57.30 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS 
       41.62        28.37        14.73        82.62        61.87         0.53 
TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 
       17.79        24.79        26.93       130.09         5.65        15.62 
TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ 
       13.22         2.56        21.86         9.99        82.88        49.32 
TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0TZ 
        5.26        56.88        29.75        24.30        55.86        76.14 
TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ 
       70.16        76.18        55.36        75.55        61.84        52.77 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP 
       51.25        48.82        62.56        43.73        43.56        39.98 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       43.07        17.23        40.83        46.32        42.58        35.24 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M 
       36.26        20.22       109.58        50.89        73.02        65.46 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T 
       68.19        65.69         0.85        57.40        62.07        53.26 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 
       53.36        54.18        50.96        48.16        51.75        56.15 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE 
       45.17        40.64        39.85        34.82        93.83       128.65 
TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       20.25        42.87         7.36        40.04        17.10        20.81 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       16.96        20.38        54.74        16.04        20.45        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC 
       77.62       149.59        12.13       220.90       129.57        50.70 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM 
       65.72       146.50       112.37       176.98        18.77       126.12 
TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RH 
       84.59       110.14       110.93       140.88        68.45       189.01 
TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP 
      234.28        81.17        78.02       172.96       162.05       102.77 
TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT 
      140.48       100.70        89.46       157.41        97.48       188.68 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0X0 TCGA-B6-A0X4 
       79.63        17.98        21.47       113.79       129.70        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN 
       68.94        58.88        43.59       101.52        73.51       139.17 
TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
      170.17        85.35        49.94        82.88        55.00        24.53 
TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 
       38.79        25.55        28.50        46.95        40.83        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA 
       39.16        48.36        56.94        56.98        51.68        37.22 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM 
       32.02        18.21        25.71        21.70        44.05        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT 
       35.67        48.69        27.19        53.69        53.95        45.57 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD 
       49.94        11.67        49.05        48.13        42.90        45.83 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO 
       31.17        23.44        38.01        22.13        13.91        17.26 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       15.65         3.22         2.56        38.47        45.17        47.41 
TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0EA 
       16.27         4.41        15.68        14.30        44.81        32.65 
TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 
       24.49        31.00        24.43        30.35        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA 
       37.78        35.51        24.56        23.08        41.00        52.96 
TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ 
       26.50        20.38         5.85         2.50        13.61        36.85 
TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 
       12.89        51.32        27.25        50.79         5.59        23.93 
TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G 
       24.95        42.35        44.81        23.05         8.81         2.01 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N 
        7.23        20.12        90.84        26.66        72.56        37.74 
TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A1EO 
       30.28        55.63        37.55        66.05        51.39        91.99 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY 
      113.82        82.85        42.28        55.69        49.58        17.69 
TCGA-BH-A1F0 TCGA-BH-A1F5 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE 
       25.81        89.16        24.66       120.62        33.17        74.73 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR 
      122.89        36.92        63.35        55.00        72.07       144.59 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 
       72.07         6.90         0.72        83.31        57.83       130.16 
TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V 
       10.65         6.44        20.12         0.99       109.28         8.94 
TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12Q TCGA-C8-A12W 
       11.93        11.77        11.77        12.66         0.07        12.66 
TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 
       12.66         3.12         1.45         0.69         0.62         3.85 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ 
        3.75        12.33        10.92        11.34        11.34         0.16 
TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X 
       10.42         2.30         3.25         0.30         0.23         0.36 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 
        8.28         9.67         0.03        12.20         0.99         0.03 
TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A145 
        0.23        11.90        13.25        20.58        13.97        13.48 
TCGA-D8-A146 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD 
       21.14        17.49        16.50        18.71        15.78        18.15 
TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ 
       18.90        12.03        12.03        14.01        18.97        20.09 
TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT 
       20.09        19.40        20.38        21.01        12.20        13.32 
TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 
       14.70        18.58        17.79        16.73        25.74        23.90 
TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ 
       27.58        18.15         2.66        17.16        14.73        21.83 
TCGA-D8-A1XK TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS 
       14.50        17.69         7.96        16.41        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 
        6.35        15.16        12.66        16.54        15.32        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G 
        3.81        14.24        14.14        17.42        16.04        13.45 
TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P 
       13.05        14.43         9.44        16.41         4.80         0.76 
TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 
       13.08        12.53        12.26        14.50        18.51         7.33 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E 
       43.00        34.42        27.52        40.41        37.51        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S 
       28.87        47.15        44.68        38.24        38.60        33.17 
TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y 
       33.30        43.33        34.26        32.02        31.96        28.60 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 
       17.03        25.41        27.12        23.24        19.43        21.04 
TCGA-E2-A156 TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G 
       23.87        22.82        17.29        20.71        21.63        18.21 
TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M 
       12.92        17.42        19.40         9.04        20.58         7.73 
TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ 
       13.02        19.56        17.06        14.07        14.99        60.53 
TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC 
       53.62        53.03        29.95        32.35        28.50        16.47 
TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ 
       17.10        38.30        37.41        32.78        33.73        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       22.65         3.88        22.19        20.98        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LG 
       27.42        39.62        19.66        24.59        40.47        18.87 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX 
      106.75       102.61        43.04        16.93         5.52        15.72 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 
        7.20        18.05        22.26        19.20        36.82        13.48 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE 
       12.00        13.12        36.56        39.55        12.59        35.77 
TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       20.05        21.57         9.86        11.90        14.30         0.62 
TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA 
        2.10         6.12         1.38         2.76        21.21        32.09 
TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A1RI 
       20.81        40.24         0.66        34.65        21.27        35.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       34.13         0.79        12.53        13.32        39.09        22.75 
TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A245 
       12.89        23.51        24.10        17.06         0.69         0.85 
TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JT 
       27.22         1.94         0.95        12.56         0.72         0.76 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FK 
       26.07        18.41         0.62        15.72         0.23         0.39 
TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J1 
        0.23        15.39        12.20        39.72        18.21        18.90 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW 
       13.25        16.57        15.68        28.77        25.94        22.82 
TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 
       29.95        29.85        40.41        41.13        39.78        52.96 
TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA 
       29.82        23.11        18.48        30.08         7.86        18.90 
TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FS 
       13.94        10.52        14.43        34.55        19.96        52.73 
TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 
       25.91        22.09        21.27        17.49        10.16        10.59 
TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DC TCGA-GM-A2DH TCGA-GM-A2DI 
        7.40        59.57       194.27        53.52        42.28        61.91 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
       62.33        90.84        76.64        77.33        53.36       110.50 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV 
       38.20        32.28        69.30        53.95        57.63        13.55 
TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 
       18.12        11.84        11.57         8.28         6.67         4.60 
TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM 
        0.66         2.99         3.58         6.90         5.56         4.70 
TCGA-LL-A5YO TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 
        3.19         2.63         3.88         4.14         4.50         4.50 
TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
        3.22         6.21        15.91         2.79         2.10        12.66 
TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX 
       46.55         7.53        44.61        27.65        24.10        16.87 
TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K 
       14.10        10.29         9.80        14.76        54.51        33.90 
TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-S3-A6ZG TCGA-W8-A86G 
       31.07        18.21         7.23         6.81         5.29 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.03              0.03 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           211.56            234.28 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            21.14             21.53 
[1] "0.0 - 211.6 (21.1)" "0.0 - 234.3 (21.5)"
[1] "hr=" "1.3"
D3V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2P GAIN MUTATED         5        8        0        0        43        30
  2P GAIN WILD-TYPE      75       69        9        9       292       194
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2P GAIN MUTATED           0         13          1          7        2
  2P GAIN WILD-TYPE         2        125         26         52       15
                   vv
clus                STAGE TIS STAGE X
  2P GAIN MUTATED           0       3
  2P GAIN WILD-TYPE         1      13
D3V3, multiclass
            clus
vv           2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                  5                75
  STAGE IA                 8                69
  STAGE IB                 0                 9
  STAGE II                 0                 9
  STAGE IIA               43               292
  STAGE IIB               30               194
  STAGE III                0                 2
  STAGE IIIA              13               125
  STAGE IIIB               1                26
  STAGE IIIC               7                52
  STAGE IV                 2                15
  STAGE TIS                0                 1
  STAGE X                  3                13
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2P GAIN MUTATED    24  72  13   3
  2P GAIN WILD-TYPE 234 509 104  33
D3V4, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1              24               234
  T2              72               509
  T3              13               104
  T4               3                33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  2P GAIN MUTATED    52  38  13   8
  2P GAIN WILD-TYPE 416 292  98  62
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0              52               416
  N1              38               292
  N2              13                98
  N3               8                62
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  2P GAIN MUTATED          0  97   2  14
  2P GAIN WILD-TYPE        2 748  15 117
D3V6, multiclass
          clus
vv         2P GAIN MUTATED 2P GAIN WILD-TYPE
  CM0 (I+)               0                 2
  M0                    97               748
  M1                     2                15
  MX                    14               117
[1] 4 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   113   0
  2P GAIN WILD-TYPE 871  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED    113    0
  2P GAIN WILD-TYPE  871   11
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE             113               871
  MALE                 0                11
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  2P GAIN MUTATED                            1                           102
  2P GAIN WILD-TYPE                          0                           633
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  2P GAIN MUTATED                                4                   1
  2P GAIN WILD-TYPE                            162                   4
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  2P GAIN MUTATED                                  0                  0
  2P GAIN WILD-TYPE                               29                 14
                   vv
clus                OTHER  SPECIFY
  2P GAIN MUTATED                5
  2P GAIN WILD-TYPE             39
D3V8, multiclass
                                  clus
vv                                 2P GAIN MUTATED 2P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                102               633
  INFILTRATING LOBULAR CARCINOMA                 4               162
  MEDULLARY CARCINOMA                            1                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               0                29
  MUCINOUS CARCINOMA                             0                14
  OTHER  SPECIFY                                 5                39
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V9, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    36  77
  2P GAIN WILD-TYPE 246 636
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     36   77
  2P GAIN WILD-TYPE  246  636
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO               36               246
  YES              77               636
[1] 2 2
[1] FALSE
D3V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P GAIN MUTATED                                  1     9
  2P GAIN WILD-TYPE                                0    47
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED                          24    69
  2P GAIN WILD-TYPE                       113   639
D3V11, multiclass
                                  clus
vv                                 2P GAIN MUTATED 2P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          9                47
  BLACK OR AFRICAN AMERICAN                     24               113
  WHITE                                         69               639
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V12, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     0  96
  2P GAIN WILD-TYPE  36 700
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      0   96
  2P GAIN WILD-TYPE   36  700
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                36
  NOT HISPANIC OR LATINO              96               700
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    61   8
  2Q GAIN WILD-TYPE 799 106
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               69               905 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                8               106 
$`2Q GAIN MUTATED`
TCGA-A1-A0SO TCGA-A2-A04W TCGA-A2-A0CX TCGA-A2-A0SX TCGA-A2-A0YE TCGA-A2-A0YJ 
       28.01        64.04        56.81        50.43        18.21        18.61 
TCGA-A2-A1G1 TCGA-A2-A3XZ TCGA-A2-A4S1 TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A13D 
       19.20        31.99        12.00        30.61        35.67        31.73 
TCGA-A7-A26I TCGA-A7-A4SE TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A07U 
       21.73        21.17         1.02        17.98        31.00         9.96 
TCGA-A8-A097 TCGA-AC-A23H TCGA-AC-A62Y TCGA-AN-A04C TCGA-AO-A124 TCGA-AO-A12D 
       12.00         2.66         1.81         1.78       102.58        64.04 
TCGA-AO-A12F TCGA-AR-A24Q TCGA-B6-A0WZ TCGA-B6-A0X1 TCGA-B6-A402 TCGA-BH-A0AW 
       48.36        66.05       129.57       186.48        54.28        20.45 
TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0C1 TCGA-BH-A0DL TCGA-BH-A0E9 TCGA-BH-A18T 
       24.85        44.05        44.02        48.23        46.19         7.36 
TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1F2 TCGA-BH-A203 TCGA-C8-A12P TCGA-C8-A12U 
       51.16        69.93        31.53        38.60        11.77        12.66 
TCGA-C8-A12V TCGA-C8-A131 TCGA-C8-A26Y TCGA-C8-A274 TCGA-D8-A147 TCGA-D8-A1J8 
       12.66         1.78         0.43         0.03        19.20        14.17 
TCGA-D8-A1XU TCGA-D8-A27M TCGA-E2-A109 TCGA-E2-A10C TCGA-E2-A14P TCGA-E2-A159 
       12.99        13.48        46.59        40.11        40.96        25.05 
TCGA-E2-A15A TCGA-E2-A1LE TCGA-E2-A574 TCGA-E9-A5FL TCGA-EW-A1IY TCGA-EW-A1PB 
       23.34        28.90        19.89         0.26         8.48        19.99 
TCGA-EW-A1PC TCGA-EW-A2FR TCGA-GI-A2C9 TCGA-GM-A2DB TCGA-LL-A5YN TCGA-LL-A5YP 
        6.15        55.00       109.87        53.13         3.65         3.25 
TCGA-LL-A73Y TCGA-OL-A5RW TCGA-OL-A66I 
        4.14        26.20        23.70 

$`2Q GAIN WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP 
       20.88        13.68        31.79         7.96        39.32        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T 
       18.21       104.81        18.02        41.95        82.16        73.84 
TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL 
       22.06        63.12        55.43        36.13       125.59        64.57 
TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS 
       24.79       112.08        92.48        88.60       107.93        75.55 
TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 
       75.25         5.19        63.45        64.04        21.14        34.55 
TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO 
       33.76        28.77        25.22       101.72        89.36        80.28 
TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU 
      107.61        79.76        74.40        37.05        35.05        34.29 
TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU 
       31.82        29.75        24.72        24.16        99.19        54.64 
TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 
       27.12        44.88        44.28        17.52        17.13         8.38 
TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC 
       18.71        20.52        17.46        18.90        20.75        32.55 
TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK 
       25.28        15.42        21.90        21.67        14.50        19.33 
TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX 
       14.63        31.73        23.77        23.47        17.36        36.79 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A 
       22.45        20.25        19.56        16.47        52.47       107.70 
TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
       16.31        17.19        18.15        91.92        10.59        20.88 
TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW 
       39.65        33.93        83.01        29.98        14.07        49.48 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY 
       38.40        34.98        38.37         7.30         9.01         8.81 
TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG 
        8.91         6.74         3.42        38.30        35.31        34.29 
TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G 
       35.47        37.45        33.11        10.72        12.72        23.61 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26J 
       29.56        31.36        24.26        23.74        23.80        20.61 
TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF 
       22.32        11.34        10.59        10.29        11.28        13.41 
TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SF 
       14.70        11.97        14.93        13.74        14.50        17.92 
TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW 
       14.73        12.10        10.72        11.05        10.29         9.37 
TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06T TCGA-A8-A06U 
       10.42         8.75        13.02        13.02        41.06        29.03 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B 
       26.01         1.02        17.03        53.98         9.01        33.01 
TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
       19.99        18.97        18.97        14.01        12.00        17.03 
TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07W TCGA-A8-A07Z 
        9.99        10.98         8.98         7.99         9.99        28.04 
TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B 
       18.05        15.06        36.95        13.02         0.99        23.08 
TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L 
       19.99        18.05        19.96        12.00        37.05         9.99 
TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X 
       31.00        31.00         0.99        19.07        93.04        33.99 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 
       40.01        19.07        16.01        17.95        41.98         9.99 
TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I 
        9.99        12.00         1.02        13.02        31.00        33.07 
TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T 
       29.98        15.02         1.02        25.02         8.98        19.04 
TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 
       15.02         0.99        14.01        12.00        19.04        13.02 
TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C 
       21.04         0.99        13.02        17.03        38.04         0.95 
TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB 
        2.37        10.85         1.48        38.53        38.20        40.57 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH 
       55.43        36.99        38.79        26.04        50.70         1.02 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
        0.92         2.27         0.99         0.69        14.83         9.40 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS 
        1.12         1.81         1.68         1.55         1.32         1.55 
TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A8OP 
        0.07         1.12         1.18         0.69         0.43         1.74 
TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A 
        0.33         0.33         0.23         0.33         0.62         2.96 
TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR 
        1.71         8.02         7.36         6.51         0.16         0.33 
TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK 
        0.33         0.33         6.44         4.64         7.96         7.00 
TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW 
        7.59         7.17         6.28         6.02         0.33         0.36 
TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO 
        0.33         0.33         0.33         0.33         0.33        12.33 
TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV 
        0.30         0.33         0.33         0.33         0.33         5.33 
TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P 
        5.59        80.28        47.84        66.77        81.63        84.69 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 
       68.75        47.87        59.05        29.13        32.78        21.40 
TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 
       17.65        24.16        37.48        20.32        22.36        53.03 
TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF 
       21.53        50.70        50.86        72.00        76.77        21.37 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A125 
       26.24        38.53        62.04        55.33        71.80        99.25 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E 
       93.70        94.59        96.10        90.58        77.56        57.30 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR 
       41.62        28.37        14.73        82.62        61.87        70.39 
TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 
        0.53        17.79        24.79        26.93       130.09         5.65 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP 
       15.62        13.22         2.56        21.86         9.99        82.88 
TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW 
       49.32         5.26        37.41        56.88        29.75        24.30 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 
       64.83        55.86        76.14        65.36        70.16        83.87 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK 
       76.18        55.36        75.55        61.84        52.77        51.25 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ 
       48.82        62.56        43.73        43.56        39.98        43.07 
TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX 
       17.23        40.83        46.32        42.58        35.24        36.26 
TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       20.22       109.58        50.89        73.02        65.46        68.19 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U 
       65.69         0.85        57.40        62.07        53.26        53.36 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 
       54.18        50.96        48.16        51.75        56.15        45.17 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH 
       40.64        39.85        34.82        93.83       128.65        20.25 
TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       42.87         7.36        40.04        17.10        20.81        16.96 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       20.38        54.74        16.04        20.45        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC 
      143.38       149.59        12.13       220.90       129.57        50.70 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM 
       65.72       146.50       112.37       176.98        18.77       126.12 
TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG 
       84.59       110.14       110.93       140.88       211.56        68.45 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
      189.01       234.28        81.17        78.02       172.96       162.05 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV 
      102.77       140.48       100.70        89.46       131.21       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY 
       97.48       188.68        79.63        17.98        21.47       113.79 
TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF 
      129.70        28.27        68.94        58.88        43.59       101.52 
TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40B 
       73.51       139.17       170.17        85.35        49.94        82.88 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 
       55.00        24.53        38.79        25.55        28.50        46.95 
TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 
       40.83        39.55        39.16        48.36        56.94        56.98 
TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ 
       51.68        37.22        32.02        18.21        25.71        21.70 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       61.68        35.67        48.69        27.19        53.69        53.95 
TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C3 
       45.57        49.94        11.67        49.05        41.75        48.13 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI 
       42.90        45.83        31.17        23.44        38.01        22.13 
TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT 
       13.91        17.26        15.65         3.22         2.56        38.47 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 
       45.17        47.41        16.27         4.41        15.68        14.30 
TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI 
        9.63        44.81        32.65        24.49        31.00        24.43 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       30.35        10.78        15.16        37.78        35.51        24.56 
TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK 
       23.08        41.00        52.96        26.50        20.38         5.85 
TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX 
        2.50        13.61        36.85        12.89        51.32        27.25 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       50.79         5.59        23.93        24.95        42.35        44.81 
TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K 
       23.05         8.81         2.01         7.23        20.12        90.84 
TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R 
       26.66        72.56        37.74        30.28        55.63        37.55 
TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU 
       66.05        51.39        91.99       113.82        82.85        42.28 
TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F5 
       12.00        55.69        49.58        17.69        25.81        89.16 
TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE 
       97.48        24.66       120.62       114.15        33.17        74.73 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN 
      122.89        36.92        63.35        55.00        45.63        72.07 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A204 TCGA-BH-A208 
      144.59        72.07         6.90         0.72        83.31        57.83 
TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
      130.16        10.65         6.44        20.12         0.99       109.28 
TCGA-BH-A42V TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12Q 
        8.94        11.93        11.77        11.77        12.66         0.07 
TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 
       12.66        12.66         3.12         1.45         0.69         0.62 
TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI 
        3.85         3.75        12.33        10.92        11.34        11.34 
TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V 
        0.16        12.03        10.42         2.30         3.25         0.30 
TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A278 
        0.23         0.36         8.28         9.67         0.03         0.03 
TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A13Z 
       12.20         0.99         0.03         0.23        11.90        20.88 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 
       13.25        20.58        13.97        14.17        13.48        21.14 
TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE 
       17.49        16.50        18.71        15.78        18.15        18.90 
TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK 
       12.03        12.03        14.01        18.97        20.09        20.12 
TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT 
       20.09        19.40        20.38        21.01        12.20        13.32 
TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 
       14.70        18.58        17.79        16.73        25.74        23.90 
TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG 
       27.58        18.15         2.66        17.16        15.22        14.73 
TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ 
       21.83        14.50        19.92        17.69         7.96        16.41 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY 
       15.85        16.31         6.35        15.16        12.66        16.54 
TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E 
       15.32        15.52         3.81        14.24        14.14        17.42 
TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       16.04        13.45        13.05        14.43         9.44        16.41 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W 
        4.80         0.76        10.09        13.08        12.53        12.26 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 
       14.50        18.51         7.33        43.00        34.42        27.52 
TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O 
       40.41        37.51        28.44        28.87        47.15        44.68 
TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V 
       38.24        38.60        33.17        33.30        43.33        34.26 
TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 
       32.02        31.96        28.60        17.03        25.41        27.12 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15C 
       23.24        19.43        21.04        23.87        14.79        22.82 
TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I 
       17.29        20.71        21.63        18.21        12.92        17.42 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P 
       19.40         9.04        20.58         7.73        13.02        19.56 
TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 
       17.06        14.07        14.99        60.53        53.62        53.03 
TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE 
       29.95        32.35        28.50        16.47        17.10        38.30 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK 
       37.41        32.78        33.73        33.70        28.44        22.65 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 
        3.88        22.19        20.98        11.08        54.18        27.42 
TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LG TCGA-E2-A1LH 
       39.62        19.66        24.59        40.47        18.87       106.75 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX 
      102.61         8.75        43.04        16.93         5.52        15.72 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 
        7.20        18.05        22.26        19.20        36.82        13.48 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE 
       12.00        13.12        36.56        39.55        12.59        35.77 
TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       20.05        21.57         9.86        11.90        14.30         0.62 
TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA 
        2.10         6.12         1.38         2.76        21.21        32.09 
TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG 
       20.81        40.24         0.66        34.65         6.58        21.27 
TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
       34.59        35.64        34.13         0.79        12.53        13.32 
TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 
       39.09        22.75        12.89        23.51        24.10        17.06 
TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A 
        0.69         0.85        27.22         1.94         0.95        12.56 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA 
        0.72        17.75         0.76        26.07        18.41         0.62 
TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW 
       15.72         0.23         0.39         0.23        15.39        12.20 
TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
       39.72        18.21        18.90        13.25        16.57        15.68 
TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ 
       28.77        25.94        22.82        29.95        29.85        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 
       41.13        39.78        52.96        29.82        23.11        18.48 
TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
       30.08         7.86        18.90        13.94        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 
       34.55        19.96        52.73        25.91        22.09        21.27 
TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA 
       17.49        10.16        10.59         7.40        59.57       194.27 
TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK 
       53.52        43.04        42.71        42.28        61.91        62.33 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY 
       90.84        76.64        77.33        53.36       110.50        38.20 
TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX 
       32.28        69.30        53.95        57.63        13.55        18.12 
TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 
       11.84        11.57         8.28         6.67         4.60         0.66 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YO 
        2.99         3.58         6.90         5.56         4.70         3.19 
TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 
        2.63         3.88         4.50         4.50         5.59         3.22 
TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 
        6.21        15.91         2.79         2.10        12.66        46.55 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY 
        7.53        44.61        27.65        24.10        16.87        14.10 
TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L 
       10.29         9.80        14.76        54.51        33.90        31.07 
TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-S3-A6ZG TCGA-W8-A86G 
       18.21         7.23         4.44         6.81         5.29 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.03              0.03 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           186.48            234.28 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            23.70             21.27 
[1] "0.0 - 186.5 (23.7)" "0.0 - 234.3 (21.3)"
[1] "hr=" "1.1"
D4V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2Q GAIN MUTATED         4        5        0        0        27        22
  2Q GAIN WILD-TYPE      76       72        9        9       308       202
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2Q GAIN MUTATED           0          6          1          4        1
  2Q GAIN WILD-TYPE         2        132         26         55       16
                   vv
clus                STAGE TIS STAGE X
  2Q GAIN MUTATED           0       1
  2Q GAIN WILD-TYPE         1      15
D4V3, multiclass
            clus
vv           2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                  4                76
  STAGE IA                 5                72
  STAGE IB                 0                 9
  STAGE II                 0                 9
  STAGE IIA               27               308
  STAGE IIB               22               202
  STAGE III                0                 2
  STAGE IIIA               6               132
  STAGE IIIB               1                26
  STAGE IIIC               4                55
  STAGE IV                 1                16
  STAGE TIS                0                 1
  STAGE X                  1                15
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2Q GAIN MUTATED    14  47   9   1
  2Q GAIN WILD-TYPE 244 534 108  35
D4V4, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1              14               244
  T2              47               534
  T3               9               108
  T4               1                35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  2Q GAIN MUTATED    36  23   6   4
  2Q GAIN WILD-TYPE 432 307 105  66
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0              36               432
  N1              23               307
  N2               6               105
  N3               4                66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  2Q GAIN MUTATED          0  61   1   9
  2Q GAIN WILD-TYPE        2 784  16 122
D4V6, multiclass
          clus
vv         2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CM0 (I+)               0                 2
  M0                    61               784
  M1                     1                16
  MX                     9               122
[1] 4 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    71   0
  2Q GAIN WILD-TYPE 913  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     71    0
  2Q GAIN WILD-TYPE  913   11
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              71               913
  MALE                 0                11
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  2Q GAIN MUTATED                            0                            63
  2Q GAIN WILD-TYPE                          1                           672
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  2Q GAIN MUTATED                                3                   0
  2Q GAIN WILD-TYPE                            163                   5
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  2Q GAIN MUTATED                                  0                  0
  2Q GAIN WILD-TYPE                               29                 14
                   vv
clus                OTHER  SPECIFY
  2Q GAIN MUTATED                5
  2Q GAIN WILD-TYPE             39
D4V8, multiclass
                                  clus
vv                                 2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                 63               672
  INFILTRATING LOBULAR CARCINOMA                 3               163
  MEDULLARY CARCINOMA                            0                 5
  MIXED HISTOLOGY (PLEASE SPECIFY)               0                29
  MUCINOUS CARCINOMA                             0                14
  OTHER  SPECIFY                                 5                39
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V9, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    21  50
  2Q GAIN WILD-TYPE 261 663
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     21   50
  2Q GAIN WILD-TYPE  261  663
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO               21               261
  YES              50               663
[1] 2 2
[1] FALSE
D4V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q GAIN MUTATED                                  0     7
  2Q GAIN WILD-TYPE                                1    49
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED                          15    42
  2Q GAIN WILD-TYPE                       122   666
D4V11, multiclass
                                  clus
vv                                 2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          7                49
  BLACK OR AFRICAN AMERICAN                     15               122
  WHITE                                         42               666
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V12, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     0  60
  2Q GAIN WILD-TYPE  36 736
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      0   60
  2Q GAIN WILD-TYPE   36  736
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                36
  NOT HISPANIC OR LATINO              60               736
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED   109  19
  3P GAIN WILD-TYPE 751  95
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              128               846 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               19                95 
$`3P GAIN MUTATED`
TCGA-A2-A0CM TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0SV TCGA-A2-A0SX TCGA-A2-A0T2 
       24.79        75.55        63.45        27.12        50.43         8.38 
TCGA-A2-A0T7 TCGA-A2-A0YM TCGA-A2-A1FW TCGA-A2-A3XS TCGA-A2-A4RX TCGA-A7-A0CD 
       20.75        31.73        17.36        33.93         9.01        38.30 
TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13F TCGA-A7-A425 TCGA-A7-A4SD TCGA-A7-A4SE 
       35.67        33.11        12.72        14.70        14.50        21.17 
TCGA-A7-A6VV TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A079 TCGA-A8-A08B TCGA-A8-A08C 
       10.29        13.02         1.02         9.01        23.08        19.99 
TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A091 TCGA-A8-A093 
       18.05        12.00        37.05        31.00        19.07        17.95 
TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09Q 
       12.00         9.99        12.00        31.00        29.98        25.02 
TCGA-A8-A09R TCGA-AC-A23H TCGA-AC-A2FM TCGA-AC-A2QJ TCGA-AN-A03Y TCGA-AN-A0AS 
        8.98         2.66        26.04         2.27         0.33         0.33 
TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FZ TCGA-AN-A0XO TCGA-AO-A03O TCGA-AO-A0J4 
        0.36         0.33         0.33        12.33        81.63        17.65 
TCGA-AO-A0J7 TCGA-AO-A128 TCGA-AO-A12D TCGA-AQ-A04H TCGA-AQ-A54N TCGA-AQ-A54O 
       20.32        94.59        64.04        24.79         2.56        21.86 
TCGA-AR-A0TS TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AS TCGA-AR-A24K TCGA-AR-A24V 
       37.41        61.84        52.77        40.83        50.89        54.18 
TCGA-AR-A2LL TCGA-B6-A0IA TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RP TCGA-B6-A0RS 
        7.36       220.90       140.88       211.56       102.77       100.70 
TCGA-B6-A0RU TCGA-B6-A0WV TCGA-B6-A1KC TCGA-B6-A401 TCGA-B6-A408 TCGA-BH-A0AU 
      131.21        79.63        43.59        85.35        49.94        24.53 
TCGA-BH-A0B6 TCGA-BH-A0BL TCGA-BH-A0BR TCGA-BH-A0BT TCGA-BH-A0C0 TCGA-BH-A0DS 
       56.94        44.05        53.69        45.57        41.75         2.56 
TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0HI TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A18N 
       46.19        24.49        20.38        27.25        50.79        37.74 
TCGA-BH-A18U TCGA-BH-A1FC TCGA-BH-A202 TCGA-BH-A203 TCGA-C8-A12M TCGA-C8-A12O 
       51.39       114.15         0.72        38.60        11.77        12.66 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A1HI TCGA-C8-A27B TCGA-D8-A13Z TCGA-D8-A143 
        0.07        12.66        11.34         0.99        20.88        14.17 
TCGA-D8-A147 TCGA-D8-A1XA TCGA-D8-A1XQ TCGA-D8-A1XV TCGA-D8-A1Y2 TCGA-D8-A27R 
       19.20        27.58        16.41        15.16        14.24        10.09 
TCGA-E2-A109 TCGA-E2-A10B TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14T TCGA-E2-A14Z 
       46.59        37.51        47.15        44.68        33.30        17.03 
TCGA-E2-A154 TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A1AZ TCGA-E2-A1IH TCGA-E2-A1LG 
       19.43        20.71        18.21        60.53        33.73        18.87 
TCGA-E2-A1LI TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RF TCGA-E9-A54Y TCGA-EW-A1J6 
      102.61        20.81        40.24         6.58         0.23        28.77 
TCGA-EW-A1P8 TCGA-EW-A1PH TCGA-GM-A2DF TCGA-GM-A3XL TCGA-LL-A5YM TCGA-LL-A5YP 
        7.86        19.96        42.71        69.30         4.70         3.25 
TCGA-LL-A6FR TCGA-OL-A5RW 
        3.88        26.20 

$`3P GAIN WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
       20.88        13.68        31.79         7.96        39.32        28.01 
TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R 
       19.20        18.21       104.81        18.02        41.95        82.16 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
       73.84        22.06        63.12        64.04        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
      125.59        64.57       112.08        92.48        88.60       107.93 
TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 
       75.25         5.19        64.04        56.81        21.14        34.55 
TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO 
       33.76        28.77        25.22       101.72        89.36        80.28 
TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU 
      107.61        79.76        74.40        37.05        35.05        34.29 
TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU 
       31.82        29.75        24.72        24.16        99.19        54.64 
TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T3 TCGA-A2-A0T4 
       44.88        44.28        17.52        17.13        18.71        20.52 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF 
       17.46        18.90        32.55        25.28        18.21        15.42 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL 
       21.90        21.67        14.50        18.61        19.33        14.63 
TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 
       23.77        23.47        36.79        22.45        20.25        19.20 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C 
       19.56        16.47        52.47       107.70        16.31        17.19 
TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XT 
       18.15        91.92        10.59        20.88        39.65        83.01 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ 
       29.98        14.07        49.48        38.40        34.98        31.99 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 
       38.37         7.30         8.81         8.91        12.00         6.74 
TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 
        3.42        35.31        34.29        35.47        30.61        37.45 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F 
       31.73        10.72        23.61        29.56        31.36        24.26 
TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY 
       23.74        23.80        21.73        20.61        22.32        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A426 TCGA-A7-A4SA 
       10.59        10.29        11.28        13.41        11.97        14.93 
TCGA-A7-A4SB TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX 
       13.74        17.92        14.73        12.10        10.72        11.05 
TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06R TCGA-A8-A06T 
        9.37        10.42         8.75        13.02        17.98        41.06 
TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 
       29.03        31.00        26.01         1.02        17.03        53.98 
TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J 
       33.01        19.99        18.97        18.97        14.01        12.00 
TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U 
       17.03         9.99        10.98         8.98         7.99         9.96 
TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 
        9.99        28.04        18.05        15.06        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08G TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08S 
        0.99        19.96         9.99        31.00         0.99        19.07 
TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A099 
       93.04        33.99        40.01        16.01        41.98         9.99 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09T 
        1.02        13.02        33.07        15.02         1.02        19.04 
TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 
       15.02         0.99        14.01        12.00        19.04        13.02 
TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C 
       21.04         0.99        13.02        17.03        38.04         0.95 
TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB 
        2.37        10.85         1.48        38.53        38.20        40.57 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI 
       55.43        36.99        38.79        50.70         1.02         0.92 
TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 
        0.99         0.69        14.83         9.40         1.12         1.81 
TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X 
        1.68         1.55         1.32         1.55         0.07         1.12 
TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AN-A03X 
        1.81         1.18         0.69         0.43         1.74         0.33 
TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D 
        0.23         0.33         0.62         2.96         1.78         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AT 
        8.02         7.36         6.51         0.16         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN 
        6.44         4.64         7.96         7.00         7.59         7.17 
TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN 
        6.28         6.02         0.33         0.33         0.33         0.33 
TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV 
        0.30         0.33         0.33         0.33         0.33         5.33 
TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A03R 
        5.59        80.28        47.84        66.77        84.69        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J5 
       47.87        59.05        29.13        32.78        21.40        24.16 
TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC 
       37.48        22.36        53.03        21.53        50.70        50.86 
TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ 
       72.00        76.77        21.37        26.24        38.53        62.04 
TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 
       55.33        71.80       102.58        99.25        93.70        96.10 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
       90.58        77.56        57.30        48.36        41.62        28.37 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT 
       14.73        82.62        61.87        70.39         0.53        17.79 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A7U7 
       26.93       130.09         5.65        15.62        13.22         9.99 
TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW 
       82.88        49.32         5.26        56.88        29.75        24.30 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 
       64.83        55.86        76.14        65.36        70.16        83.87 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM 
       76.18        55.36        75.55        51.25        48.82        62.56 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AU 
       43.73        43.56        39.98        43.07        17.23        46.32 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L 
       42.58        35.24        36.26        20.22       109.58        73.02 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R 
       65.46        68.19        65.69         0.85        66.05        57.40 
TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
       62.07        53.26        53.36        50.96        48.16        51.75 
TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
       56.15        45.17        40.64        39.85        34.82        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
      128.65        20.25        42.87        40.04        17.10        20.81 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       16.96        20.38        54.74        16.04        20.45        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IB TCGA-B6-A0IC 
       77.62       143.38       149.59        12.13       129.57        50.70 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM 
       65.72       146.50       112.37       176.98        18.77       126.12 
TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
       84.59       110.14       110.93        68.45       189.01       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RT 
       81.17        78.02       172.96       162.05       140.48        89.46 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY 
      157.41        97.48       188.68        17.98        21.47       113.79 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      129.57       129.70       186.48        28.27        68.94        58.88 
TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A402 TCGA-B6-A40B 
      101.52        73.51       139.17       170.17        54.28        82.88 
TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 
       55.00        38.79        20.45        25.55        28.50        46.95 
TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 
       40.83        39.55        39.16        48.36        56.98        51.68 
TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ 
       37.22        32.02        18.21        25.71        24.85        21.70 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BV 
       61.68        35.67        48.69        27.19        53.95        49.94 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD 
       11.67        49.05        44.02        48.13        42.90        45.83 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL 
       31.17        23.44        38.01        22.13        13.91        48.23 
TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       17.26        15.65         3.22        38.47        45.17        47.41 
TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 
       16.27         4.41        15.68        14.30         9.63        44.81 
TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 
       32.65        31.00        24.43        30.35        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA 
       37.78        35.51        24.56        23.08        41.00        52.96 
TCGA-BH-A0HB TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU 
       26.50         5.85         2.50        13.61        36.85        12.89 
TCGA-BH-A0HW TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       51.32         5.59        23.93        24.95        42.35        44.81 
TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K 
       23.05         8.81         2.01         7.23        20.12        90.84 
TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S 
       26.66        72.56        30.28        55.63        37.55        66.05 
TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET 
        7.36        51.16        69.93        91.99       113.82        82.85 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 
       42.28        12.00        55.69        49.58        17.69        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD 
       31.53        89.16        97.48        24.66       120.62        33.17 
TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM 
       74.73       122.89        36.92        63.35        55.00        45.63 
TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A204 TCGA-BH-A208 
       72.07       144.59        72.07         6.90        83.31        57.83 
TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
      130.16        10.65         6.44        20.12         0.99       109.28 
TCGA-BH-A42V TCGA-C8-A12L TCGA-C8-A12N TCGA-C8-A12P TCGA-C8-A12V TCGA-C8-A12W 
        8.94        11.93        11.77        11.77        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 
       12.66         3.12         1.78         1.45         0.69         0.62 
TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ 
        3.85         3.75        12.33        10.92        11.34         0.16 
TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W 
       12.03        10.42         2.30         3.25         0.30         0.23 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
        0.36         0.43         8.28         9.67         0.03         0.03 
TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A140 
        0.03        12.20         0.03         0.23        11.90        13.25 
TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 
       20.58        13.97        13.48        21.14        14.17        17.49 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF 
       16.50        18.71        15.78        18.15        18.90        12.03 
TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL 
       12.03        14.01        18.97        20.09        20.12        20.09 
TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU 
       19.40        20.38        21.01        12.20        13.32        14.70 
TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XB 
       18.58        17.79        16.73        25.74        23.90        18.15 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK 
        2.66        17.16        15.22        14.73        21.83        14.50 
TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT 
       19.92        17.69         7.96        15.85        16.31         6.35 
TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       12.99        12.66        16.54        15.32        15.52         3.81 
TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I 
       14.14        17.42        16.04        13.45        13.05        14.43 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T 
        9.44        16.41        13.48         4.80         0.76        13.08 
TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 
       12.53        12.26        14.50        18.51         7.33        43.00 
TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F 
       34.42        27.52        40.41        40.11        28.44        28.87 
TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14V 
       40.96        38.24        38.60        33.17        43.33        34.26 
TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 
       32.02        31.96        28.60        25.41        27.12        23.24 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C 
       21.04        23.87        14.79        25.05        23.34        22.82 
TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       17.29        21.63        12.92        17.42        19.40         9.04 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
       20.58         7.73        13.02        19.56        17.06        14.07 
TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       14.99        53.62        53.03        29.95        32.35        28.50 
TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1II 
       16.47        17.10        38.30        37.41        32.78        33.70 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       28.44        22.65         3.88        22.19        20.98        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB 
       54.18        27.42        39.62        19.66        24.59        40.47 
TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 
       28.90       106.75         8.75        43.04        16.93         5.52 
TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N4 
       15.72         7.20        18.05        22.26        19.89        19.20 
TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC 
       36.82        13.48        12.00        13.12        36.56        39.55 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ 
       12.59        35.77        20.05        21.57         9.86        11.90 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 
       14.30         0.62         2.10         6.12         1.38         2.76 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A1RH 
       21.21        32.09         0.66        34.65        21.27        34.59 
TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       35.64        34.13         0.79        12.53        13.32        39.09 
TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 
       22.75        12.89        23.51        24.10        17.06         0.69 
TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
        0.85        27.22         1.94         0.95        12.56         0.72 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
       17.75         0.76        26.07        18.41         0.62        15.72 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
        0.39         0.26         0.23        15.39        12.20        39.72 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
        8.48        18.21        18.90        13.25        16.57        15.68 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 
       25.94        22.82        29.95        29.85        40.41        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 
       39.78        52.96        29.82        23.11        18.48        30.08 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
       18.90        19.99         6.15        13.94        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 
       34.55        55.00        52.73        25.91        22.09        21.27 
TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 
       17.49        10.16        10.59         7.40       109.87        59.57 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DH TCGA-GM-A2DI 
      194.27        53.13        53.52        43.04        42.28        61.91 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
       62.33        90.84        76.64        77.33        53.36       110.50 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX 
       38.20        32.28        53.95        57.63        13.55        18.12 
TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 
       11.84        11.57         8.28         6.67         4.60         0.66 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO 
        2.99         3.58         6.90         5.56         3.65         3.19 
TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 
        2.63         4.14         4.50         4.50         5.59         3.22 
TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 
        6.21        15.91         2.79         2.10        12.66        46.55 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY 
        7.53        44.61        27.65        24.10        16.87        14.10 
TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K 
       10.29         9.80        14.76        23.70        54.51        33.90 
TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-S3-A6ZG TCGA-W8-A86G 
       31.07        18.21         7.23         4.44         6.81         5.29 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.07              0.03 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           220.90            234.28 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           23.785            21.320 
[1] "0.1 - 220.9 (23.8)" "0.0 - 234.3 (21.3)"
[1] "hr=" "1.3"
D5V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3P GAIN MUTATED        11        7        0        2        53        19
  3P GAIN WILD-TYPE      69       70        9        7       282       205
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3P GAIN MUTATED           0         18          7          6        4
  3P GAIN WILD-TYPE         2        120         20         53       13
                   vv
clus                STAGE TIS STAGE X
  3P GAIN MUTATED           0       4
  3P GAIN WILD-TYPE         1      12
D5V3, multiclass
            clus
vv           3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                 11                69
  STAGE IA                 7                70
  STAGE IB                 0                 9
  STAGE II                 2                 7
  STAGE IIA               53               282
  STAGE IIB               19               205
  STAGE III                0                 2
  STAGE IIIA              18               120
  STAGE IIIB               7                20
  STAGE IIIC               6                53
  STAGE IV                 4                13
  STAGE TIS                0                 1
  STAGE X                  4                12
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  3P GAIN MUTATED    30  82   9   9
  3P GAIN WILD-TYPE 228 499 108  27
D5V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1              30               228
  T2              82               499
  T3               9               108
  T4               9                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                 N0  N1  N2  N3
  3P GAIN MUTATED    64  36  18  10
  3P GAIN WILD-TYPE 404 294  93  60
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0              64               404
  N1              36               294
  N2              18                93
  N3              10                60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  3P GAIN MUTATED          0 122   4   5
  3P GAIN WILD-TYPE        2 723  13 126
D5V6, multiclass
          clus
vv         3P GAIN MUTATED 3P GAIN WILD-TYPE
  CM0 (I+)               0                 2
  M0                   122               723
  M1                     4                13
  MX                     5               126
[1] 4 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   130   1
  3P GAIN WILD-TYPE 854  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED    130    1
  3P GAIN WILD-TYPE  854   10
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE             130               854
  MALE                 1                10
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  3P GAIN MUTATED                            0                           111
  3P GAIN WILD-TYPE                          1                           624
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  3P GAIN MUTATED                                7                   2
  3P GAIN WILD-TYPE                            159                   3
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  3P GAIN MUTATED                                  4                  1
  3P GAIN WILD-TYPE                               25                 13
                   vv
clus                OTHER  SPECIFY
  3P GAIN MUTATED                6
  3P GAIN WILD-TYPE             38
D5V8, multiclass
                                  clus
vv                                 3P GAIN MUTATED 3P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                111               624
  INFILTRATING LOBULAR CARCINOMA                 7               159
  MEDULLARY CARCINOMA                            2                 3
  MIXED HISTOLOGY (PLEASE SPECIFY)               4                25
  MUCINOUS CARCINOMA                             1                13
  OTHER  SPECIFY                                 6                38
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V9, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    40  91
  3P GAIN WILD-TYPE 242 622
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     40   91
  3P GAIN WILD-TYPE  242  622
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO               40               242
  YES              91               622
[1] 2 2
[1] FALSE
D5V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P GAIN MUTATED                                  0     8
  3P GAIN WILD-TYPE                                1    48
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED                          21    82
  3P GAIN WILD-TYPE                       116   626
D5V11, multiclass
                                  clus
vv                                 3P GAIN MUTATED 3P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          8                48
  BLACK OR AFRICAN AMERICAN                     21               116
  WHITE                                         82               626
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V12, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     5  98
  3P GAIN WILD-TYPE  31 698
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      5   98
  3P GAIN WILD-TYPE   31  698
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                31
  NOT HISPANIC OR LATINO              98               698
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED   169  24
  3Q GAIN WILD-TYPE 691  90
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              193               781 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               24                90 
$`3Q GAIN MUTATED`
TCGA-A1-A0SI TCGA-A2-A04U TCGA-A2-A0CM TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0D0 
       20.88        22.06        24.79        75.55        63.45        21.14 
TCGA-A2-A0EY TCGA-A2-A0SV TCGA-A2-A0SX TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 
       24.16        27.12        50.43        17.13         8.38        18.71 
TCGA-A2-A0T7 TCGA-A2-A0YG TCGA-A2-A0YM TCGA-A2-A1FW TCGA-A2-A1FZ TCGA-A2-A1G1 
       20.75        21.90        31.73        17.36        22.45        19.20 
TCGA-A2-A3XS TCGA-A2-A4RX TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A0DB 
       33.93         9.01        38.30        30.61        35.67        33.11 
TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A26H TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A56D 
       31.73        12.72        23.80        14.50        21.17        14.73 
TCGA-A7-A6VV TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A079 TCGA-A8-A07J 
       10.29        10.42        13.02         1.02         9.01        12.00 
TCGA-A8-A07L TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F 
       17.03         9.96         9.99        23.08        19.99        18.05 
TCGA-A8-A08I TCGA-A8-A08P TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09A TCGA-A8-A09B 
       12.00        31.00        19.07        17.95         9.99        12.00 
TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R TCGA-AC-A23H 
       31.00        29.98        15.02        25.02         8.98         2.66 
TCGA-AC-A2FM TCGA-AC-A2QJ TCGA-AC-A62X TCGA-AC-A6IW TCGA-AN-A03Y TCGA-AN-A041 
       26.04         2.27         1.12         0.69         0.33         0.23 
TCGA-AN-A049 TCGA-AN-A0AJ TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FL TCGA-AN-A0FW 
        0.62         8.02         0.16         0.33         7.59         0.36 
TCGA-AN-A0FX TCGA-AN-A0FZ TCGA-AN-A0XO TCGA-AO-A03L TCGA-AO-A03O TCGA-AO-A0J4 
        0.33         0.33        12.33        80.28        81.63        17.65 
TCGA-AO-A0J7 TCGA-AO-A128 TCGA-AO-A12D TCGA-AO-A1KR TCGA-AQ-A54N TCGA-AQ-A54O 
       20.32        94.59        64.04        70.39         2.56        21.86 
TCGA-AR-A0TS TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AS TCGA-AR-A24K TCGA-AR-A24M 
       37.41        61.84        52.77        40.83        50.89        65.46 
TCGA-AR-A24V TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LL TCGA-AR-A5QP TCGA-B6-A0I2 
       54.18        34.82        93.83         7.36        20.45       143.38 
TCGA-B6-A0IA TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IQ TCGA-B6-A0RP TCGA-B6-A0RS 
      220.90       176.98        18.77       140.88       102.77       100.70 
TCGA-B6-A0RU TCGA-B6-A0WV TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A401 TCGA-B6-A408 
      131.21        79.63        43.59       101.52        85.35        49.94 
TCGA-BH-A0AU TCGA-BH-A0B6 TCGA-BH-A0BL TCGA-BH-A0BR TCGA-BH-A0BT TCGA-BH-A0C0 
       24.53        56.94        44.05        53.69        45.57        41.75 
TCGA-BH-A0DL TCGA-BH-A0DS TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0H7 TCGA-BH-A0HI 
       48.23         2.56        46.19        24.49        23.08        20.38 
TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A18N TCGA-BH-A18Q TCGA-BH-A18U 
       12.89        27.25        50.79        37.74        55.63        51.39 
TCGA-BH-A18V TCGA-BH-A1EV TCGA-BH-A1FC TCGA-BH-A1FN TCGA-BH-A202 TCGA-BH-A203 
       51.16        12.00       114.15        72.07         0.72        38.60 
TCGA-C8-A12M TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A1HI TCGA-C8-A26W 
       11.77         0.07        12.66        12.66        11.34         0.23 
TCGA-C8-A27B TCGA-C8-A3M8 TCGA-D8-A13Z TCGA-D8-A143 TCGA-D8-A147 TCGA-D8-A1X5 
        0.99         0.23        20.88        14.17        19.20        18.58 
TCGA-D8-A1XA TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XQ TCGA-D8-A1XU 
       27.58        21.83        14.50        19.92        16.41        12.99 
TCGA-D8-A1XV TCGA-D8-A1Y2 TCGA-D8-A27R TCGA-E2-A109 TCGA-E2-A10B TCGA-E2-A14N 
       15.16        14.24        10.09        46.59        37.51        47.15 
TCGA-E2-A14O TCGA-E2-A14Z TCGA-E2-A154 TCGA-E2-A159 TCGA-E2-A15E TCGA-E2-A15G 
       44.68        17.03        19.43        25.05        20.71        18.21 
TCGA-E2-A1AZ TCGA-E2-A1IE TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1LG TCGA-E2-A1LH 
       60.53        38.30        33.73        33.70        18.87       106.75 
TCGA-E2-A1LI TCGA-E2-A1LL TCGA-E2-A573 TCGA-E9-A1N8 TCGA-E9-A1NF TCGA-E9-A1RB 
      102.61        43.04        22.26        12.00        20.05        20.81 
TCGA-E9-A1RC TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A54Y TCGA-E9-A5FL TCGA-EW-A1J6 
       40.24         6.58        34.59         0.23         0.26        28.77 
TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PH 
       22.82        29.82         7.86        19.99         6.15        19.96 
TCGA-EW-A2FS TCGA-GI-A2C8 TCGA-GM-A2DB TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A3XL 
       52.73         7.40        53.13        42.71        42.28        69.30 
TCGA-LL-A5YM TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A8F5 TCGA-OL-A5RW 
        4.70         3.25         3.88         4.14         6.21        26.20 
TCGA-OL-A5S0 
        9.80 

$`3Q GAIN WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP 
       13.68        31.79         7.96        39.32        28.01        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T 
       18.21       104.81        18.02        41.95        82.16        73.84 
TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL 
       63.12        64.04        55.43        36.13       125.59        64.57 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CT TCGA-A2-A0CU 
      112.08        92.48        88.60       107.93        75.25         5.19 
TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 
       64.04        56.81        34.55        33.76        28.77        25.22 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER 
      101.72        89.36        80.28       107.61        79.76        74.40 
TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
       37.05        35.05        34.29        31.82        29.75        24.72 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T4 
       99.19        54.64        44.88        44.28        17.52        20.52 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF 
       17.46        18.90        32.55        25.28        18.21        15.42 
TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT 
       21.67        14.50        18.61        19.33        14.63        23.77 
TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       23.47        36.79        20.25        19.56        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
      107.70        16.31        17.19        18.15        91.92        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW 
       20.88        39.65        83.01        29.98        14.07        49.48 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RY 
       38.40        34.98        31.99        38.37         7.30         8.81 
TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG 
        8.91        12.00         6.74         3.42        35.31        34.29 
TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       35.47        37.45        10.72        23.61        29.56        31.36 
TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY 
       24.26        23.74        21.73        20.61        22.32        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 
       10.59        10.29        11.28        13.41        14.70        11.97 
TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX 
       14.93        13.74        17.92        12.10        10.72        11.05 
TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U 
        9.37         8.75        13.02        17.98        41.06        29.03 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07B 
       31.00        26.01         1.02        17.03        53.98        33.01 
TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07O TCGA-A8-A07P 
       19.99        18.97        18.97        14.01         9.99        10.98 
TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 
        8.98         7.99        28.04        18.05        15.06        36.95 
TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O 
       13.02         0.99        19.96        37.05         9.99        31.00 
TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 
        0.99        19.07        93.04        33.99        40.01        16.01 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09I 
       41.98        12.00         9.99         1.02        13.02        33.07 
TCGA-A8-A09N TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 
        1.02        19.04        15.02         0.99        14.01        12.00 
TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB 
       19.04        13.02        21.04         0.99        13.02        17.03 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BK 
       38.04         0.95         2.37        10.85         1.48        38.53 
TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO 
       38.20        40.57        55.43        36.99        38.79        50.70 
TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
        1.02         0.92         0.99         0.69        14.83         9.40 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS 
        1.12         1.81         1.68         1.55         1.32         1.55 
TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AN-A03X 
        0.07         1.81         1.18         0.43         1.74         0.33 
TCGA-AN-A046 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL 
        0.33         2.96         1.78         1.71         7.36         6.51 
TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK 
        0.33         0.33         6.44         4.64         7.96         7.00 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FY TCGA-AN-A0XL 
        7.17         6.28         6.02         0.33         0.33         0.33 
TCGA-AN-A0XN TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU 
        0.33         0.30         0.33         0.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A03R 
        5.33         5.59        47.84        66.77        84.69        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J5 
       47.87        59.05        29.13        32.78        21.40        24.16 
TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC 
       37.48        22.36        53.03        21.53        50.70        50.86 
TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ 
       72.00        76.77        21.37        26.24        38.53        62.04 
TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 
       55.33        71.80       102.58        99.25        93.70        96.10 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
       90.58        77.56        57.30        48.36        41.62        28.37 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H 
       14.73        82.62        61.87         0.53        17.79        24.79 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A7U7 
       26.93       130.09         5.65        15.62        13.22         9.99 
TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW 
       82.88        49.32         5.26        56.88        29.75        24.30 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 
       64.83        55.86        76.14        65.36        70.16        83.87 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM 
       76.18        55.36        75.55        51.25        48.82        62.56 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AU 
       43.73        43.56        39.98        43.07        17.23        46.32 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L 
       42.58        35.24        36.26        20.22       109.58        73.02 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S 
       68.19        65.69         0.85        66.05        57.40        62.07 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 
       53.26        53.36        50.96        48.16        51.75        56.15 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LK 
       45.17        40.64        39.85       128.65        20.25        42.87 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM 
       40.04        17.10        20.81        16.96        20.38        54.74 
TCGA-AR-A5QN TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IB 
       16.04        10.59        77.62       149.59        12.13       129.57 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IM TCGA-B6-A0IN 
       50.70        65.72       146.50       112.37       126.12        84.59 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
      110.14       110.93       211.56        68.45       189.01       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RT 
       81.17        78.02       172.96       162.05       140.48        89.46 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY 
      157.41        97.48       188.68        17.98        21.47       113.79 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      129.57       129.70       186.48        28.27        68.94        58.88 
TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A402 TCGA-B6-A40B TCGA-B6-A40C 
       73.51       139.17       170.17        54.28        82.88        55.00 
TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 
       38.79        20.45        25.55        28.50        46.95        40.83 
TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA 
       39.55        39.16        48.36        56.98        51.68        37.22 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BM 
       32.02        18.21        25.71        24.85        21.70        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW 
       35.67        48.69        27.19        53.95        49.94        11.67 
TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE 
       49.05        44.02        48.13        42.90        45.83        31.17 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DP 
       23.44        38.01        22.13        13.91        17.26        15.65 
TCGA-BH-A0DQ TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
        3.22        38.47        45.17        47.41        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EE 
       15.68        14.30         9.63        44.81        32.65        31.00 
TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       24.43        30.35        10.78        15.16        37.78        35.51 
TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HK TCGA-BH-A0HO 
       24.56        41.00        52.96        26.50         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HW TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 
       13.61        36.85        51.32         5.59        23.93        24.95 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I 
       42.35        44.81        23.05         8.81         2.01         7.23 
TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18R 
       20.12        90.84        26.66        72.56        30.28        37.55 
TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET 
       66.05         7.36        69.93        91.99       113.82        82.85 
TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 
       42.28        55.69        49.58        17.69        25.81        31.53 
TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE 
       89.16        97.48        24.66       120.62        33.17        74.73 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR 
      122.89        36.92        63.35        55.00        45.63       144.59 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O 
       72.07         6.90        83.31        57.83       130.16        10.65 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12L 
        6.44        20.12         0.99       109.28         8.94        11.93 
TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 
       11.77        12.66        11.77        12.66        12.66         3.12 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 
        1.78         1.45         0.69         0.62         3.85         3.75 
TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL 
       12.33        10.92        11.34         0.16        12.03        10.42 
TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z 
        2.30         3.25         0.30         0.36         0.43         8.28 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A3M7 
        9.67         0.03         0.03         0.03        12.20         0.03 
TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A145 TCGA-D8-A146 
       11.90        13.25        20.58        13.97        13.48        21.14 
TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD 
       14.17        17.49        16.50        18.71        15.78        18.15 
TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ 
       18.90        12.03        12.03        14.01        18.97        20.09 
TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS 
       20.12        20.09        19.40        20.38        21.01        12.20 
TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 
       13.32        14.70        17.79        16.73        25.74        23.90 
TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XM 
       18.15         2.66        17.16        15.22        14.73        17.69 
TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XW TCGA-D8-A1XY 
        7.96        15.85        16.31         6.35        12.66        16.54 
TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F 
       15.32        15.52         3.81        14.14        17.42        16.04 
TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M 
       13.45        13.05        14.43         9.44        16.41        13.48 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 
        4.80         0.76        13.08        12.53        12.26        14.50 
TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10A 
       18.51         7.33        43.00        34.42        27.52        40.41 
TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R 
       40.11        28.44        28.87        40.96        38.24        38.60 
TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X 
       33.17        33.30        43.33        34.26        32.02        31.96 
TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 
       28.60        25.41        27.12        23.24        21.04        23.87 
TCGA-E2-A158 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15H 
       14.79        23.34        22.82        17.29        21.63        12.92 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O 
       17.42        19.40         9.04        20.58         7.73        13.02 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 
       19.56        17.06        14.07        14.99        53.62        53.03 
TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IF 
       29.95        32.35        28.50        16.47        17.10        37.41 
TCGA-E2-A1IG TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO 
       32.78        28.44        22.65         3.88        22.19        20.98 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA 
       11.08        54.18        27.42        39.62        19.66        24.59 
TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX 
       40.47        28.90         8.75        16.93         5.52        15.72 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A574 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 
        7.20        18.05        19.89        19.20        36.82        13.48 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG 
       13.12        36.56        39.55        12.59        35.77        21.57 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 
        9.86        11.90        14.30         0.62         2.10         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RD TCGA-E9-A1RE 
        1.38         2.76        21.21        32.09         0.66        34.65 
TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
       21.27        35.64        34.13         0.79        12.53        13.32 
TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 
       39.09        22.75        12.89        23.51        24.10        17.06 
TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A 
        0.69         0.85        27.22         1.94         0.95        12.56 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA 
        0.72        17.75         0.76        26.07        18.41         0.62 
TCGA-E9-A3X8 TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
       15.72         0.39         0.23        15.39        12.20        39.72 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
        8.48        18.21        18.90        13.25        16.57        15.68 
TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 
       25.94        29.95        29.85        40.41        41.13        39.78 
TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PD 
       52.96        23.11        18.48        30.08        18.90        13.94 
TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A2FW 
       10.52        14.43        34.55        55.00        25.91        22.09 
TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C9 TCGA-GM-A2D9 
       21.27        17.49        10.16        10.59       109.87        59.57 
TCGA-GM-A2DA TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
      194.27        53.52        43.04        61.91        62.33        90.84 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
       76.64        77.33        53.36       110.50        38.20        32.28 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX 
       53.95        57.63        13.55        18.12        11.84        11.57 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
        8.28         6.67         4.60         0.66         2.99         3.58 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FQ TCGA-LL-A73Z 
        6.90         5.56         3.65         3.19         2.63         4.50 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 
        4.50         5.59         3.22        15.91         2.79         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
       12.66        46.55         7.53        44.61        27.65        24.10 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J 
       16.87        14.10        10.29        14.76        23.70        54.51 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-S3-A6ZG 
       33.90        31.07        18.21         7.23         4.44         6.81 
TCGA-W8-A86G 
        5.29 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.07              0.03 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           220.90            234.28 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            21.14             21.53 
[1] "0.1 - 220.9 (21.1)" "0.0 - 234.3 (21.5)"
[1] "hr=" "1.1"
D6V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3Q GAIN MUTATED        15       13        1        2        77        38
  3Q GAIN WILD-TYPE      65       64        8        7       258       186
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3Q GAIN MUTATED           0         26          9          9        4
  3Q GAIN WILD-TYPE         2        112         18         50       13
                   vv
clus                STAGE TIS STAGE X
  3Q GAIN MUTATED           0       3
  3Q GAIN WILD-TYPE         1      13
D6V3, multiclass
            clus
vv           3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                 15                65
  STAGE IA                13                64
  STAGE IB                 1                 8
  STAGE II                 2                 7
  STAGE IIA               77               258
  STAGE IIB               38               186
  STAGE III                0                 2
  STAGE IIIA              26               112
  STAGE IIIB               9                18
  STAGE IIIC               9                50
  STAGE IV                 4                13
  STAGE TIS                0                 1
  STAGE X                  3                13
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  3Q GAIN MUTATED    43 125  19  10
  3Q GAIN WILD-TYPE 215 456  98  26
D6V4, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1              43               215
  T2             125               456
  T3              19                98
  T4              10                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                 N0  N1  N2  N3
  3Q GAIN MUTATED   101  58  22  12
  3Q GAIN WILD-TYPE 367 272  89  58
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0             101               367
  N1              58               272
  N2              22                89
  N3              12                58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  3Q GAIN MUTATED          0 175   4  18
  3Q GAIN WILD-TYPE        2 670  13 113
D6V6, multiclass
          clus
vv         3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CM0 (I+)               0                 2
  M0                   175               670
  M1                     4                13
  MX                    18               113
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED   196   1
  3Q GAIN WILD-TYPE 788  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED    196    1
  3Q GAIN WILD-TYPE  788   10
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE             196               788
  MALE                 1                10
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  3Q GAIN MUTATED                            0                           170
  3Q GAIN WILD-TYPE                          1                           565
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  3Q GAIN MUTATED                                8                   3
  3Q GAIN WILD-TYPE                            158                   2
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  3Q GAIN MUTATED                                  6                  1
  3Q GAIN WILD-TYPE                               23                 13
                   vv
clus                OTHER  SPECIFY
  3Q GAIN MUTATED                9
  3Q GAIN WILD-TYPE             35
D6V8, multiclass
                                  clus
vv                                 3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                170               565
  INFILTRATING LOBULAR CARCINOMA                 8               158
  MEDULLARY CARCINOMA                            3                 2
  MIXED HISTOLOGY (PLEASE SPECIFY)               6                23
  MUCINOUS CARCINOMA                             1                13
  OTHER  SPECIFY                                 9                35
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V9, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    63 134
  3Q GAIN WILD-TYPE 219 579
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     63  134
  3Q GAIN WILD-TYPE  219  579
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               63               219
  YES             134               579
[1] 2 2
[1] FALSE
D6V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q GAIN MUTATED                                  1    12
  3Q GAIN WILD-TYPE                                0    44
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED                          36   125
  3Q GAIN WILD-TYPE                       101   583
D6V11, multiclass
                                  clus
vv                                 3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         12                44
  BLACK OR AFRICAN AMERICAN                     36               101
  WHITE                                        125               583
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V12, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     6 156
  3Q GAIN WILD-TYPE  30 640
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      6  156
  3Q GAIN WILD-TYPE   30  640
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   6                30
  NOT HISPANIC OR LATINO             156               640
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    62   8
  4P GAIN WILD-TYPE 798 106
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               70               904 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                8               106 
$`4P GAIN MUTATED`
TCGA-A1-A0SJ TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0ET TCGA-A2-A0YM TCGA-A2-A0YT 
       13.68        75.25         5.19        35.05        31.73        23.77 
TCGA-A2-A1G0 TCGA-A2-A4S1 TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A8-A06O TCGA-A8-A075 
       20.25        12.00        13.74        21.17        13.02        17.03 
TCGA-A8-A079 TCGA-A8-A07G TCGA-A8-A07W TCGA-A8-A08G TCGA-A8-A08S TCGA-A8-A08T 
        9.01        18.97         9.99        19.96        19.07        93.04 
TCGA-A8-A091 TCGA-A8-A09K TCGA-A8-A0A9 TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A3W5 
       19.07        29.98        13.02         1.02         2.27         1.81 
TCGA-AN-A04C TCGA-AN-A0FY TCGA-AO-A0JD TCGA-AQ-A54O TCGA-AR-A0TS TCGA-AR-A0TW 
        1.78         0.33        72.00        21.86        37.41        24.30 
TCGA-AR-A2LL TCGA-B6-A0RG TCGA-BH-A0AU TCGA-BH-A0AY TCGA-BH-A0DI TCGA-BH-A0DL 
        7.36        68.45        24.53        25.55        22.13        48.23 
TCGA-BH-A0HX TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A1EN TCGA-BH-A1EW TCGA-BH-A1EX 
       27.25        26.66        37.74        69.93        55.69        49.58 
TCGA-BH-A1FM TCGA-BH-A202 TCGA-C8-A1HN TCGA-D8-A1J8 TCGA-D8-A1JD TCGA-D8-A1JG 
       45.63         0.72         3.25        14.17        18.15        12.03 
TCGA-D8-A1JH TCGA-D8-A1JT TCGA-D8-A1XZ TCGA-D8-A27M TCGA-D8-A27R TCGA-D8-A27W 
       14.01        13.32        15.32        13.48        10.09        12.26 
TCGA-E2-A109 TCGA-E2-A14S TCGA-E2-A152 TCGA-E2-A15E TCGA-E2-A1LA TCGA-E2-A56Z 
       46.59        33.17        27.12        20.71        24.59         7.20 
TCGA-E9-A1N9 TCGA-E9-A1R6 TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A247 TCGA-EW-A1P4 
       13.12         2.76        40.24        34.65        27.22        29.82 
TCGA-EW-A2FS TCGA-EW-A2FV TCGA-LL-A5YN TCGA-S3-A6ZG 
       52.73        25.91         3.65         6.81 

$`4P GAIN WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP 
       20.88        31.79         7.96        39.32        28.01        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T 
       18.21       104.81        18.02        41.95        82.16        73.84 
TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK 
       22.06        63.12        64.04        55.43        36.13       125.59 
TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
       64.57        24.79       112.08        92.48        88.60       107.93 
TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 
       75.55        63.45        64.04        56.81        21.14        34.55 
TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO 
       33.76        28.77        25.22       101.72        89.36        80.28 
TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EU TCGA-A2-A0EV 
      107.61        79.76        74.40        37.05        34.29        31.82 
TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV 
       29.75        24.72        24.16        99.19        54.64        27.12 
TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 
       44.88        50.43        44.28        17.52        17.13         8.38 
TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC 
       18.71        20.52        17.46        18.90        20.75        32.55 
TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI 
       25.28        18.21        15.42        21.90        21.67        14.50 
TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX 
       18.61        19.33        14.63        23.47        17.36        36.79 
TCGA-A2-A1FZ TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A 
       22.45        19.20        19.56        16.47        52.47       107.70 
TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
       16.31        17.19        18.15        91.92        10.59        20.88 
TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW 
       39.65        33.93        83.01        29.98        14.07        49.48 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX 
       38.40        34.98        31.99        38.37         7.30         9.01 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE 
        8.81         8.91         6.74         3.42        38.30        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB 
       34.29        35.47        30.61        37.45        35.67        33.11 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       31.73        10.72        12.72        23.61        29.56        31.36 
TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD 
       24.26        23.74        23.80        21.73        20.61        22.32 
TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 
       11.34        10.59        10.29        11.28        13.41        14.70 
TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV 
       11.97        14.93        14.50        17.92        14.73        12.10 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY 
       10.72        11.05        10.29         9.37        10.42         8.75 
TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X 
       13.02         1.02        17.98        41.06        29.03        31.00 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F 
       26.01         1.02        53.98        33.01        19.99        18.97 
TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R 
       14.01        12.00        17.03         9.99        10.98         8.98 
TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 
        7.99         9.96        28.04        18.05        15.06        36.95 
TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08I 
       13.02         0.99        23.08        19.99        18.05        12.00 
TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08X 
       37.05         9.99        31.00        31.00         0.99        33.99 
TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 
       40.01        16.01        17.95        41.98        12.00         9.99 
TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I 
        9.99        12.00         1.02        13.02        31.00        33.07 
TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       15.02         1.02        25.02         8.98        19.04        15.02 
TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 
        0.99        14.01        12.00        19.04        13.02        21.04 
TCGA-A8-A0A7 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G 
        0.99        17.03        38.04         0.95         2.37        10.85 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF 
        2.66         1.48        38.53        38.20        40.57        55.43 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3BB 
       36.99        38.79        26.04        50.70         0.92         0.99 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3YI 
        0.69        14.83         9.40         1.12         1.68         1.55 
TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV 
        1.32         1.55         0.07         1.12         1.81         1.18 
TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 
        0.69         0.43         1.74         0.33         0.33         0.23 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK 
        0.33         0.62         2.96         1.71         8.02         7.36 
TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD 
        6.51         0.16         0.33         0.33         0.33         6.44 
TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        4.64         7.96         7.00         7.59         7.17         6.28 
TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FZ TCGA-AN-A0XL 
        6.02         0.33         0.36         0.33         0.33         0.33 
TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT 
        0.33        12.33         0.30         0.33         0.33         0.33 
TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N 
        0.33         5.33         5.59        80.28        47.84        66.77 
TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V 
       81.63        84.69        68.75        47.87        59.05        29.13 
TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 
       32.78        21.40        17.65        24.16        37.48        20.32 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE 
       22.36        53.03        21.53        50.70        50.86        76.77 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM 
       21.37        26.24        38.53        62.04        55.33        71.80 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A 
      102.58        99.25        93.70        94.59        96.10        90.58 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
       77.56        64.04        57.30        48.36        41.62        28.37 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT 
       14.73        82.62        61.87        70.39         0.53        17.79 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       24.79        26.93       130.09         5.65        15.62        13.22 
TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TT 
        2.56         9.99        82.88        49.32         5.26        56.88 
TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 
       29.75        64.83        55.86        76.14        65.36        70.16 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ 
       83.87        76.18        55.36        75.55        61.84        52.77 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP 
       51.25        48.82        62.56        43.73        43.56        39.98 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       43.07        17.23        40.83        46.32        42.58        35.24 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M 
       36.26        20.22       109.58        50.89        73.02        65.46 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S 
       68.19        65.69         0.85        66.05        57.40        62.07 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
       53.26        53.36        54.18        50.96        48.16        51.75 
TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
       56.15        45.17        40.64        39.85        34.82        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
      128.65        20.25        42.87        40.04        17.10        20.81 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       16.96        20.38        54.74        16.04        20.45        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB 
       77.62       143.38       149.59        12.13       220.90       129.57 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK 
       50.70        65.72       146.50       112.37       176.98        18.77 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE 
      126.12        84.59       110.14       110.93       140.88       211.56 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
      189.01       234.28        81.17        78.02       172.96       162.05 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV 
      102.77       140.48       100.70        89.46       131.21       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY 
       97.48       188.68        79.63        17.98        21.47       113.79 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      129.57       129.70       186.48        28.27        68.94        58.88 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 
       43.59       101.52        73.51       139.17       170.17        85.35 
TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AW 
       54.28        49.94        82.88        55.00        38.79        20.45 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 
       28.50        46.95        40.83        39.55        39.16        48.36 
TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
       56.94        56.98        51.68        37.22        32.02        18.21 
TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO 
       25.71        24.85        21.70        44.05        61.68        35.67 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV 
       48.69        27.19        53.69        53.95        45.57        49.94 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 
       11.67        49.05        41.75        44.02        48.13        42.90 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DK TCGA-BH-A0DO 
       45.83        31.17        23.44        38.01        13.91        17.26 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       15.65         3.22         2.56        38.47        45.17        47.41 
TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 
       16.27         4.41        15.68        14.30         9.63        44.81 
TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY 
       46.19        32.65        24.49        31.00        24.43        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 
       10.78        15.16        37.78        35.51        24.56        23.08 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       41.00        52.96        26.50        20.38         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HY TCGA-BH-A0RX 
       13.61        36.85        12.89        51.32        50.79         5.59 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F 
       23.93        24.95        42.35        44.81        23.05         8.81 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18P 
        2.01         7.23        20.12        90.84        72.56        30.28 
TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V 
       55.63        37.55        66.05         7.36        51.39        51.16 
TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EY 
       91.99       113.82        82.85        42.28        12.00        17.69 
TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB 
       25.81        31.53        89.16        97.48        24.66       120.62 
TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
      114.15        33.17        74.73       122.89        36.92        63.35 
TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A203 
       55.00        72.07       144.59        72.07         6.90        38.60 
TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
       83.31        57.83       130.16        10.65         6.44        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N 
        0.99       109.28         8.94        11.93        11.77        11.77 
TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W 
       12.66        11.77         0.07        12.66        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 
       12.66         3.12         1.78         1.45         0.69         0.62 
TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI 
        3.85         3.75        12.33        10.92        11.34        11.34 
TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A26V TCGA-C8-A26W 
        0.16        12.03        10.42         2.30         0.30         0.23 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
        0.36         0.43         8.28         9.67         0.03         0.03 
TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y 
        0.03        12.20         0.99         0.03         0.23        11.90 
TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 
       20.88        13.25        20.58        13.97        14.17        13.48 
TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC 
       21.14        19.20        17.49        16.50        18.71        15.78 
TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL 
       18.90        12.03        18.97        20.09        20.12        20.09 
TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X5 
       19.40        20.38        21.01        12.20        14.70        18.58 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB 
       17.79        16.73        25.74        23.90        27.58        18.15 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK 
        2.66        17.16        15.22        14.73        21.83        14.50 
TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS 
       19.92        17.69         7.96        16.41        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1Y0 
        6.35        12.99        15.16        12.66        16.54        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G 
        3.81        14.24        14.14        17.42        16.04        13.45 
TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P 
       13.05        14.43         9.44        16.41         4.80         0.76 
TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 
       13.08        12.53        14.50        18.51         7.33        43.00 
TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E 
       34.42        27.52        40.41        37.51        40.11        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R 
       28.87        47.15        44.68        40.96        38.24        38.60 
TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y 
       33.30        43.33        34.26        32.02        31.96        28.60 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 
       17.03        25.41        23.24        19.43        21.04        23.87 
TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F 
       14.79        25.05        23.34        22.82        17.29        21.63 
TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       18.21        12.92        17.42        19.40         9.04        20.58 
TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
        7.73        13.02        19.56        17.06        14.07        14.99 
TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       60.53        53.62        53.03        29.95        32.35        28.50 
TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       16.47        17.10        38.30        37.41        32.78        33.73 
TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO 
       33.70        28.44        22.65         3.88        22.19        20.98 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LB 
       11.08        54.18        27.42        39.62        19.66        40.47 
TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL 
       28.90        18.87       106.75       102.61         8.75        43.04 
TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 
       16.93         5.52        15.72        18.05        22.26        19.89 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1NA TCGA-E9-A1NC 
       19.20        36.82        13.48        12.00        36.56        39.55 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ 
       12.59        35.77        20.05        21.57         9.86        11.90 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 
       14.30         0.62         2.10         6.12         1.38        21.21 
TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH 
       32.09        20.81         0.66         6.58        21.27        34.59 
TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       35.64        34.13         0.79        12.53        13.32        39.09 
TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 
       22.75        12.89        23.51        24.10        17.06         0.69 
TCGA-E9-A245 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS 
        0.85         1.94         0.95        12.56         0.72        17.75 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54Y 
        0.76        26.07        18.41         0.62        15.72         0.23 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
        0.39         0.26         0.23        15.39        12.20        39.72 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
        8.48        18.21        18.90        13.25        16.57        15.68 
TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ 
       28.77        25.94        22.82        29.95        29.85        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 
       41.13        39.78        52.96        23.11        18.48        30.08 
TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE 
        7.86        18.90        19.99         6.15        13.94        10.52 
TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FW TCGA-EW-A3E8 
       14.43        34.55        19.96        55.00        22.09        21.27 
TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 
       17.49        10.16        10.59         7.40       109.87        59.57 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH 
      194.27        53.13        53.52        43.04        42.71        42.28 
TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO 
       61.91        62.33        90.84        76.64        77.33        53.36 
TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 
      110.50        38.20        32.28        69.30        53.95        57.63 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U 
       13.55        18.12        11.84        11.57         8.28         6.67 
TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL 
        4.60         0.66         2.99         3.58         6.90         5.56 
TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y 
        4.70         3.19         3.25         2.63         3.88         4.14 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LQ-A4E4 
        4.50         4.50         5.59         3.22         6.21        15.91 
TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA 
        2.79         2.10        12.66        46.55         7.53        44.61 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       27.65        24.10        26.20        16.87        14.10        10.29 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L 
        9.80        14.76        23.70        54.51        33.90        31.07 
TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-W8-A86G 
       18.21         7.23         4.44         5.29 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.33              0.03 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            93.04            234.28 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           20.105            21.600 
[1] "0.3 - 93.0 (20.1)"  "0.0 - 234.3 (21.6)"
[1] "hr=" "1.8"
D7V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4P GAIN MUTATED         3        3        1        2        31        14
  4P GAIN WILD-TYPE      77       74        8        7       304       210
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4P GAIN MUTATED           0          9          5          4        2
  4P GAIN WILD-TYPE         2        129         22         55       15
                   vv
clus                STAGE TIS STAGE X
  4P GAIN MUTATED           0       0
  4P GAIN WILD-TYPE         1      16
D7V3, multiclass
            clus
vv           4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                  3                77
  STAGE IA                 3                74
  STAGE IB                 1                 8
  STAGE II                 2                 7
  STAGE IIA               31               304
  STAGE IIB               14               210
  STAGE III                0                 2
  STAGE IIIA               9               129
  STAGE IIIB               5                22
  STAGE IIIC               4                55
  STAGE IV                 2                15
  STAGE TIS                0                 1
  STAGE X                  0                16
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  4P GAIN MUTATED    13  45  10   6
  4P GAIN WILD-TYPE 245 536 107  30
D7V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1              13               245
  T2              45               536
  T3              10               107
  T4               6                30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  4P GAIN MUTATED    37  25   5   5
  4P GAIN WILD-TYPE 431 305 106  65
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0              37               431
  N1              25               305
  N2               5               106
  N3               5                65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  4P GAIN MUTATED          0  67   2   5
  4P GAIN WILD-TYPE        2 778  15 126
D7V6, multiclass
          clus
vv         4P GAIN MUTATED 4P GAIN WILD-TYPE
  CM0 (I+)               0                 2
  M0                    67               778
  M1                     2                15
  MX                     5               126
[1] 4 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    73   1
  4P GAIN WILD-TYPE 911  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     73    1
  4P GAIN WILD-TYPE  911   10
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE              73               911
  MALE                 1                10
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  4P GAIN MUTATED                            0                            60
  4P GAIN WILD-TYPE                          1                           675
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  4P GAIN MUTATED                                3                   1
  4P GAIN WILD-TYPE                            163                   4
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  4P GAIN MUTATED                                  2                  1
  4P GAIN WILD-TYPE                               27                 13
                   vv
clus                OTHER  SPECIFY
  4P GAIN MUTATED                7
  4P GAIN WILD-TYPE             37
D7V8, multiclass
                                  clus
vv                                 4P GAIN MUTATED 4P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                 60               675
  INFILTRATING LOBULAR CARCINOMA                 3               163
  MEDULLARY CARCINOMA                            1                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               2                27
  MUCINOUS CARCINOMA                             1                13
  OTHER  SPECIFY                                 7                37
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V9, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    19  55
  4P GAIN WILD-TYPE 263 658
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     19   55
  4P GAIN WILD-TYPE  263  658
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO               19               263
  YES              55               658
[1] 2 2
[1] FALSE
D7V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P GAIN MUTATED                                  0     2
  4P GAIN WILD-TYPE                                1    54
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED                           8    50
  4P GAIN WILD-TYPE                       129   658
D7V11, multiclass
                                  clus
vv                                 4P GAIN MUTATED 4P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                54
  BLACK OR AFRICAN AMERICAN                      8               129
  WHITE                                         50               658
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V12, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     3  57
  4P GAIN WILD-TYPE  33 739
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      3   57
  4P GAIN WILD-TYPE   33  739
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                33
  NOT HISPANIC OR LATINO              57               739
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    58   9
  4Q GAIN WILD-TYPE 802 105
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               67               907 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                9               105 
$`4Q GAIN MUTATED`
TCGA-A1-A0SJ TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0T3 TCGA-A2-A0YM TCGA-A2-A0YT 
       13.68        75.25         5.19        18.71        31.73        23.77 
TCGA-A2-A1G0 TCGA-A2-A4S1 TCGA-A7-A4SB TCGA-A8-A06O TCGA-A8-A06U TCGA-A8-A079 
       20.25        12.00        13.74        13.02        29.03         9.01 
TCGA-A8-A07G TCGA-A8-A07W TCGA-A8-A08G TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A091 
       18.97         9.99        19.96        19.07        93.04        19.07 
TCGA-A8-A0A9 TCGA-AC-A2QJ TCGA-AC-A3W5 TCGA-AN-A04C TCGA-AN-A0FY TCGA-AO-A0J3 
       13.02         2.27         1.81         1.78         0.33        21.40 
TCGA-AQ-A54O TCGA-AR-A0TS TCGA-AR-A0TW TCGA-AR-A250 TCGA-AR-A2LL TCGA-B6-A0RG 
       21.86        37.41        24.30        56.15         7.36        68.45 
TCGA-BH-A0AU TCGA-BH-A0AY TCGA-BH-A0DI TCGA-BH-A0HX TCGA-BH-A18L TCGA-BH-A18N 
       24.53        25.55        22.13        27.25        26.66        37.74 
TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1FC TCGA-BH-A1FM TCGA-D8-A1J8 TCGA-D8-A1JD 
       55.69        49.58       114.15        45.63        14.17        18.15 
TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JT TCGA-D8-A1XA TCGA-D8-A1XF TCGA-D8-A1XZ 
       12.03        14.01        13.32        27.58        15.22        15.32 
TCGA-D8-A27M TCGA-D8-A27R TCGA-D8-A27W TCGA-E2-A109 TCGA-E2-A14S TCGA-E2-A152 
       13.48        10.09        12.26        46.59        33.17        27.12 
TCGA-E2-A15E TCGA-E2-A15O TCGA-E2-A1LA TCGA-E9-A1R6 TCGA-E9-A1RC TCGA-E9-A1RE 
       20.71        13.02        24.59         2.76        40.24        34.65 
TCGA-E9-A247 TCGA-EW-A1P4 TCGA-EW-A2FS TCGA-EW-A2FV TCGA-LL-A5YN TCGA-OL-A66I 
       27.22        29.82        52.73        25.91         3.65        23.70 
TCGA-S3-A6ZG 
        6.81 

$`4Q GAIN WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP 
       20.88        31.79         7.96        39.32        28.01        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T 
       18.21       104.81        18.02        41.95        82.16        73.84 
TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK 
       22.06        63.12        64.04        55.43        36.13       125.59 
TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
       64.57        24.79       112.08        92.48        88.60       107.93 
TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 
       75.55        63.45        64.04        56.81        21.14        34.55 
TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO 
       33.76        28.77        25.22       101.72        89.36        80.28 
TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU 
      107.61        79.76        74.40        37.05        35.05        34.29 
TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU 
       31.82        29.75        24.72        24.16        99.19        54.64 
TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 
       27.12        44.88        50.43        44.28        17.52        17.13 
TCGA-A2-A0T2 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC 
        8.38        20.52        17.46        18.90        20.75        32.55 
TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI 
       25.28        18.21        15.42        21.90        21.67        14.50 
TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX 
       18.61        19.33        14.63        23.47        17.36        36.79 
TCGA-A2-A1FZ TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A 
       22.45        19.20        19.56        16.47        52.47       107.70 
TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
       16.31        17.19        18.15        91.92        10.59        20.88 
TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW 
       39.65        33.93        83.01        29.98        14.07        49.48 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX 
       38.40        34.98        31.99        38.37         7.30         9.01 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE 
        8.81         8.91         6.74         3.42        38.30        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB 
       34.29        35.47        30.61        37.45        35.67        33.11 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       31.73        10.72        12.72        23.61        29.56        31.36 
TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD 
       24.26        23.74        23.80        21.73        20.61        22.32 
TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 
       11.34        10.59        10.29        11.28        13.41        14.70 
TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D 
       11.97        14.93        14.50        21.17        17.92        14.73 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX 
       12.10        10.72        11.05        10.29         9.37        10.42 
TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06X 
        8.75        13.02         1.02        17.98        41.06        31.00 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07E 
       26.01         1.02        17.03        53.98        33.01        19.99 
TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P 
       18.97        14.01        12.00        17.03         9.99        10.98 
TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 
        8.98         7.99         9.96        28.04        18.05        15.06 
TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F 
       36.95        13.02         0.99        23.08        19.99        18.05 
TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R 
       12.00        37.05         9.99        31.00        31.00         0.99 
TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 
       33.99        40.01        16.01        17.95        41.98        12.00 
TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E 
        9.99         9.99        12.00         1.02        13.02        31.00 
TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R 
       33.07        29.98        15.02         1.02        25.02         8.98 
TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 
       19.04        15.02         0.99        14.01        12.00        19.04 
TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C 
       13.02        21.04         0.99        17.03        38.04         0.95 
TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM 
        2.37        10.85         2.66         1.48        38.53        38.20 
TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO 
       40.57        55.43        36.99        38.79        26.04        50.70 
TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
        1.02         0.92         0.99         0.69        14.83         9.40 
TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V 
        1.12         1.68         1.55         1.32         1.55         0.07 
TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A8OP 
        1.12         1.81         1.18         0.69         0.43         1.74 
TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A 
        0.33         0.33         0.23         0.33         0.62         2.96 
TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR 
        1.71         8.02         7.36         6.51         0.16         0.33 
TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK 
        0.33         0.33         6.44         4.64         7.96         7.00 
TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW 
        7.59         7.17         6.28         6.02         0.33         0.36 
TCGA-AN-A0FX TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP 
        0.33         0.33         0.33         0.33        12.33         0.30 
TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW 
        0.33         0.33         0.33         0.33         5.33         5.59 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R 
       80.28        47.84        66.77        81.63        84.69        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J5 
       47.87        59.05        29.13        32.78        17.65        24.16 
TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB 
       37.48        20.32        22.36        53.03        21.53        50.70 
TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI 
       50.86        72.00        76.77        21.37        26.24        38.53 
TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 
       62.04        55.33        71.80       102.58        99.25        93.70 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
       94.59        96.10        90.58        77.56        64.04        57.30 
TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ 
       48.36        41.62        28.37        14.73        82.62        61.87 
TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       70.39         0.53        17.79        24.79        26.93       130.09 
TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A0TP 
        5.65        15.62        13.22         2.56         9.99        82.88 
TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY 
       49.32         5.26        56.88        29.75        64.83        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 
       76.14        65.36        70.16        83.87        76.18        55.36 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM 
       75.55        61.84        52.77        51.25        48.82        62.56 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS 
       43.73        43.56        39.98        43.07        17.23        40.83 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H 
       46.32        42.58        35.24        36.26        20.22       109.58 
TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
       50.89        73.02        65.46        68.19        65.69         0.85 
TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V 
       66.05        57.40        62.07        53.26        53.36        54.18 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 
       50.96        48.16        51.75        45.17        40.64        39.85 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LM 
       34.82        93.83       128.65        20.25        42.87        40.04 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN 
       17.10        20.81        16.96        20.38        54.74        16.04 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 
       20.45        10.59        77.62       143.38       149.59        12.13 
TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH 
      220.90       129.57        50.70        65.72       146.50       112.37 
TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP 
      176.98        18.77       126.12        84.59       110.14       110.93 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM 
      140.88       211.56       189.01       234.28        81.17        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT 
      172.96       162.05       102.77       140.48       100.70        89.46 
TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW 
      131.21       157.41        97.48       188.68        79.63        17.98 
TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
       21.47       113.79       129.57       129.70       186.48        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN 
       68.94        58.88        43.59       101.52        73.51       139.17 
TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C 
      170.17        85.35        54.28        49.94        82.88        55.00 
TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 
       38.79        20.45        28.50        46.95        40.83        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA 
       39.16        48.36        56.94        56.98        51.68        37.22 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL 
       32.02        18.21        25.71        24.85        21.70        44.05 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       61.68        35.67        48.69        27.19        53.69        53.95 
TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 
       45.57        49.94        11.67        49.05        41.75        44.02 
TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH 
       48.13        42.90        45.83        31.17        23.44        38.01 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS 
       13.91        48.23        17.26        15.65         3.22         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 
       38.47        45.17        47.41        16.27         4.41        15.68 
TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB 
       14.30         9.63        44.81        46.19        32.65        24.49 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       31.00        24.43        30.35        10.78        15.16        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB 
       35.51        24.56        23.08        41.00        52.96        26.50 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU 
       20.38         5.85         2.50        13.61        36.85        12.89 
TCGA-BH-A0HW TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 
       51.32        50.79         5.59        23.93        24.95        42.35 
TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J 
       44.81        23.05         8.81         2.01         7.23        20.12 
TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S 
       90.84        72.56        30.28        55.63        37.55        66.05 
TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES 
        7.36        51.39        51.16        69.93        91.99       113.82 
TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 
       82.85        42.28        12.00        17.69        25.81        31.53 
TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE 
       89.16        97.48        24.66       120.62        33.17        74.73 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR 
      122.89        36.92        63.35        55.00        72.07       144.59 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 
       72.07         6.90         0.72        38.60        83.31        57.83 
TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
      130.16        10.65         6.44        20.12         0.99       109.28 
TCGA-BH-A42V TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P 
        8.94        11.93        11.77        11.77        12.66        11.77 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 
        0.07        12.66        12.66        12.66        12.66         3.12 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 
        1.78         1.45         0.69         0.62         3.85         3.75 
TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK 
       12.33        10.92        11.34        11.34         0.16        12.03 
TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X 
       10.42         2.30         3.25         0.30         0.23         0.36 
TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 
        0.43         8.28         9.67         0.03         0.03         0.03 
TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A13Z 
       12.20         0.99         0.03         0.23        11.90        20.88 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 
       13.25        20.58        13.97        14.17        13.48        21.14 
TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JE 
       19.20        17.49        16.50        18.71        15.78        18.90 
TCGA-D8-A1JF TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM 
       12.03        18.97        20.09        20.12        20.09        19.40 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 
       20.38        21.01        12.20        14.70        18.58        17.79 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD 
       16.73        25.74        23.90        18.15         2.66        17.16 
TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO 
       14.73        21.83        14.50        19.92        17.69         7.96 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV 
       16.41        15.85        16.31         6.35        12.99        15.16 
TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 
       12.66        16.54        15.52         3.81        14.24        14.14 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K 
       17.42        16.04        13.45        13.05        14.43         9.44 
TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 
       16.41         4.80         0.76        13.08        12.53        14.50 
TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10A 
       18.51         7.33        43.00        34.42        27.52        40.41 
TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O 
       37.51        40.11        28.44        28.87        47.15        44.68 
TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V 
       40.96        38.24        38.60        33.30        43.33        34.26 
TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 
       32.02        31.96        28.60        17.03        25.41        23.24 
TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A 
       19.43        21.04        23.87        14.79        25.05        23.34 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I 
       22.82        17.29        21.63        18.21        12.92        17.42 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R 
       19.40         9.04        20.58         7.73        19.56        17.06 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 
       14.07        14.99        60.53        53.62        53.03        29.95 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF 
       32.35        28.50        16.47        17.10        38.30        37.41 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       32.78        33.73        33.70        28.44        22.65         3.88 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 
       22.19        20.98        11.08        54.18        27.42        39.62 
TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI 
       19.66        40.47        28.90        18.87       106.75       102.61 
TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z 
        8.75        43.04        16.93         5.52        15.72         7.20 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 
       18.05        22.26        19.89        19.20        36.82        13.48 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE 
       12.00        13.12        36.56        39.55        12.59        35.77 
TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       20.05        21.57         9.86        11.90        14.30         0.62 
TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB 
        2.10         6.12         1.38        21.21        32.09        20.81 
TCGA-E9-A1RD TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 
        0.66         6.58        21.27        34.59        35.64        34.13 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E 
        0.79        12.53        13.32        39.09        22.75        12.89 
TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A248 
       23.51        24.10        17.06         0.69         0.85         1.94 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO 
        0.95        12.56         0.72        17.75         0.76        26.07 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL 
       18.41         0.62        15.72         0.23         0.39         0.26 
TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
        0.23        15.39        12.20        39.72         8.48        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV 
       18.90        13.25        16.57        15.68        28.77        25.94 
TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 
       22.82        29.95        29.85        40.41        41.13        39.78 
TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA 
       52.96        23.11        18.48        30.08         7.86        18.90 
TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
       19.99         6.15        13.94        10.52        14.43        34.55 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 
       19.96        55.00        22.09        21.27        17.49        10.16 
TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       10.59         7.40       109.87        59.57       194.27        53.13 
TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK 
       53.52        43.04        42.71        42.28        61.91        62.33 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY 
       90.84        76.64        77.33        53.36       110.50        38.20 
TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX 
       32.28        69.30        53.95        57.63        13.55        18.12 
TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 
       11.84        11.57         8.28         6.67         4.60         0.66 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YO 
        2.99         3.58         6.90         5.56         4.70         3.19 
TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 
        3.25         2.63         3.88         4.14         4.50         4.50 
TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 
        5.59         3.22         6.21        15.91         2.79         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
       12.66        46.55         7.53        44.61        27.65        24.10 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H 
       26.20        16.87        14.10        10.29         9.80        14.76 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P 
       54.51        33.90        31.07        18.21         7.23         4.44 
TCGA-W8-A86G 
        5.29 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             0.33              0.03 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           114.15            234.28 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            20.71             21.53 
[1] "0.3 - 114.2 (20.7)" "0.0 - 234.3 (21.5)"
[1] "hr=" "1.9"
D8V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4Q GAIN MUTATED         4        4        2        1        28        13
  4Q GAIN WILD-TYPE      76       73        7        8       307       211
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4Q GAIN MUTATED           0          7          5          4        2
  4Q GAIN WILD-TYPE         2        131         22         55       15
                   vv
clus                STAGE TIS STAGE X
  4Q GAIN MUTATED           0       0
  4Q GAIN WILD-TYPE         1      16
D8V3, multiclass
            clus
vv           4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                  4                76
  STAGE IA                 4                73
  STAGE IB                 2                 7
  STAGE II                 1                 8
  STAGE IIA               28               307
  STAGE IIB               13               211
  STAGE III                0                 2
  STAGE IIIA               7               131
  STAGE IIIB               5                22
  STAGE IIIC               4                55
  STAGE IV                 2                15
  STAGE TIS                0                 1
  STAGE X                  0                16
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  4Q GAIN MUTATED    17  39   8   6
  4Q GAIN WILD-TYPE 241 542 109  30
D8V4, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1              17               241
  T2              39               542
  T3               8               109
  T4               6                30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  4Q GAIN MUTATED    33  26   4   5
  4Q GAIN WILD-TYPE 435 304 107  65
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0              33               435
  N1              26               304
  N2               4               107
  N3               5                65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  4Q GAIN MUTATED          0  63   2   5
  4Q GAIN WILD-TYPE        2 782  15 126
D8V6, multiclass
          clus
vv         4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CM0 (I+)               0                 2
  M0                    63               782
  M1                     2                15
  MX                     5               126
[1] 4 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    69   1
  4Q GAIN WILD-TYPE 915  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     69    1
  4Q GAIN WILD-TYPE  915   10
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE              69               915
  MALE                 1                10
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  4Q GAIN MUTATED                            0                            57
  4Q GAIN WILD-TYPE                          1                           678
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  4Q GAIN MUTATED                                3                   2
  4Q GAIN WILD-TYPE                            163                   3
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  4Q GAIN MUTATED                                  1                  1
  4Q GAIN WILD-TYPE                               28                 13
                   vv
clus                OTHER  SPECIFY
  4Q GAIN MUTATED                6
  4Q GAIN WILD-TYPE             38
D8V8, multiclass
                                  clus
vv                                 4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                 57               678
  INFILTRATING LOBULAR CARCINOMA                 3               163
  MEDULLARY CARCINOMA                            2                 3
  MIXED HISTOLOGY (PLEASE SPECIFY)               1                28
  MUCINOUS CARCINOMA                             1                13
  OTHER  SPECIFY                                 6                38
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V9, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    20  50
  4Q GAIN WILD-TYPE 262 663
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     20   50
  4Q GAIN WILD-TYPE  262  663
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO               20               262
  YES              50               663
[1] 2 2
[1] FALSE
D8V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q GAIN MUTATED                                  0     1
  4Q GAIN WILD-TYPE                                1    55
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED                           9    47
  4Q GAIN WILD-TYPE                       128   661
D8V11, multiclass
                                  clus
vv                                 4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                55
  BLACK OR AFRICAN AMERICAN                      9               128
  WHITE                                         47               661
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V12, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     3  54
  4Q GAIN WILD-TYPE  33 742
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      3   54
  4Q GAIN WILD-TYPE   33  742
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                33
  NOT HISPANIC OR LATINO              54               742
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED   251  32
  5P GAIN WILD-TYPE 609  82
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              283               691 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               32                82 
$`5P GAIN MUTATED`
TCGA-A1-A0SJ TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A2-A04W TCGA-A2-A0CX TCGA-A2-A0EN 
       13.68        39.32        19.20        64.04        56.81        89.36 
TCGA-A2-A0EO TCGA-A2-A0EQ TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EX 
       80.28        79.76        35.05        34.29        31.82        24.72 
TCGA-A2-A0SW TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YT 
       44.88        18.90        20.75        18.21        21.90        23.77 
TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1G0 TCGA-A2-A25B TCGA-A2-A3XU TCGA-A2-A3XZ 
       17.36        36.79        20.25        16.31        29.98        31.99 
TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A0DB 
        9.01        12.00         6.74        38.30        30.61        33.11 
TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A425 TCGA-A7-A4SA 
       31.73        12.72        20.61        22.32        14.70        14.93 
TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A6VV 
       13.74        14.50        17.92        14.73        12.10        10.29 
TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06U 
        9.37        10.42        13.02         1.02        17.98        29.03 
TCGA-A8-A06Z TCGA-A8-A07G TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A086 
        1.02        18.97         9.96         9.99        28.04        13.02 
TCGA-A8-A08B TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08P TCGA-A8-A08R 
       23.08        18.05        19.96        12.00        31.00         0.99 
TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C 
       17.95        41.98        12.00         9.99        12.00         1.02 
TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A4 TCGA-A8-A0A9 
       25.02         8.98        14.01        12.00        13.02        13.02 
TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2QJ TCGA-AC-A3HN TCGA-AC-A62V TCGA-AC-A8OP 
        2.37        10.85         2.27         0.69         0.07         1.74 
TCGA-AN-A03Y TCGA-AN-A04C TCGA-AN-A0AJ TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FJ 
        0.33         1.78         8.02         0.16         0.33         7.96 
TCGA-AN-A0FK TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XO TCGA-AN-A0XU 
        7.00         0.33         0.33         0.33        12.33         0.33 
TCGA-AO-A03L TCGA-AO-A03O TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J7 TCGA-AO-A0J9 
       80.28        81.63        32.78        21.40        20.32        53.03 
TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A128 TCGA-AO-A12A 
       50.86        76.77        55.33        71.80        94.59        90.58 
TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A0Y5 
       77.56        57.30        70.39         0.53        24.79         5.65 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0TR TCGA-AR-A0TV TCGA-AR-A1AI TCGA-AR-A1AK 
        2.56        21.86         5.26        29.75        61.84        51.25 
TCGA-AR-A1AV TCGA-AR-A1AY TCGA-AR-A24R TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W 
       42.58        20.22        57.40        53.36        54.18        50.96 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LR TCGA-AR-A5QM 
       39.85        34.82        42.87         7.36        20.38        54.74 
TCGA-AR-A5QP TCGA-B6-A0I1 TCGA-B6-A0IJ TCGA-B6-A0IQ TCGA-B6-A0WV TCGA-B6-A0WY 
       20.45        77.62       176.98       140.88        79.63       113.79 
TCGA-B6-A1KI TCGA-B6-A408 TCGA-B6-A40B TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW 
       73.51        49.94        82.88        24.53        38.79        20.45 
TCGA-BH-A0AZ TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BF 
       28.50        39.55        48.36        56.98        37.22        25.71 
TCGA-BH-A0BJ TCGA-BH-A0BP TCGA-BH-A0C1 TCGA-BH-A0DI TCGA-BH-A0DP TCGA-BH-A0DS 
       21.70        48.69        44.02        22.13        15.65         2.56 
TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0H7 TCGA-BH-A0HP TCGA-BH-A0HQ 
       24.49        31.00        24.43        23.08        13.61        36.85 
TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18K TCGA-BH-A18L 
       27.25        50.79        42.35        44.81        90.84        26.66 
TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1EU 
       72.56        37.74        51.39        69.93        91.99        42.28 
TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1FM TCGA-BH-A202 
       12.00        55.69        31.53        97.48        45.63         0.72 
TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A2L8 TCGA-C8-A12L TCGA-C8-A12P TCGA-C8-A12Q 
       38.60        57.83        20.12        11.93        11.77         0.07 
TCGA-C8-A130 TCGA-C8-A135 TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A27B 
        3.12         0.62        11.34        12.03         2.30         0.99 
TCGA-D8-A142 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JE TCGA-D8-A1JG 
       13.97        21.14        14.17        17.49        18.90        12.03 
TCGA-D8-A1JH TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JT TCGA-D8-A1X6 
       14.01        20.09        20.12        20.09        13.32        17.79 
TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XY 
       27.58        18.15        16.31        12.99        12.66        16.54 
TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27V TCGA-D8-A27W 
       15.52        14.24        13.05        14.43        12.53        12.26 
TCGA-E2-A107 TCGA-E2-A10B TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14S TCGA-E2-A14T 
       34.42        37.51        44.68        40.96        33.17        33.30 
TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A158 
       28.60        17.03        27.12        23.24        21.04        14.79 
TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A1B0 TCGA-E2-A1B4 
       20.71        18.21        20.58         7.73        53.62        29.95 
TCGA-E2-A1B5 TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IN TCGA-E2-A1IU 
       32.35        17.10        33.73        33.70        22.19        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A2P5 TCGA-E2-A574 
       54.18        19.66        18.87       106.75        16.93        19.89 
TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1NA TCGA-E9-A1NI TCGA-E9-A1R3 TCGA-E9-A1R4 
       13.48        12.00        36.56         9.86         2.10         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD 
        1.38         2.76        21.21        20.81        40.24         0.66 
TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A243 TCGA-E9-A249 TCGA-E9-A295 TCGA-E9-A3HO 
       21.27        34.59        17.06         0.95         0.72        26.07 
TCGA-E9-A54Y TCGA-E9-A5FL TCGA-EW-A1IY TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1P4 
        0.23         0.26         8.48        16.57        28.77        29.82 
TCGA-EW-A1P5 TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A423 TCGA-GM-A2DC TCGA-GM-A2DH 
       23.11         6.15        13.94        10.16        53.52        42.28 
TCGA-GM-A3NW TCGA-GM-A3XN TCGA-GM-A5PV TCGA-LD-A66U TCGA-LL-A5YM TCGA-LL-A5YP 
      110.50        53.95        13.55         8.28         4.70         3.25 
TCGA-LL-A6FQ TCGA-LL-A8F5 TCGA-MS-A51U TCGA-OL-A5S0 TCGA-OL-A66N TCGA-S3-A6ZG 
        2.63         6.21         2.79         9.80        18.21         6.81 
TCGA-W8-A86G 
        5.29 

$`5P GAIN WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04N 
       20.88        31.79         7.96        28.01        18.21       104.81 
TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V 
       18.02        41.95        82.16        73.84        22.06        63.12 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO 
       55.43        36.13       125.59        64.57        24.79       112.08 
TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU 
       92.48        88.60       107.93        75.55        75.25         5.19 
TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 
       63.45        64.04        21.14        34.55        33.76        28.77 
TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EW 
       25.22       101.72       107.61        74.40        37.05        29.75 
TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SX TCGA-A2-A0SY 
       24.16        99.19        54.64        27.12        50.43        44.28 
TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 
       17.52        17.13         8.38        18.71        20.52        17.46 
TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ 
       32.55        25.28        15.42        21.67        14.50        18.61 
TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FZ TCGA-A2-A1G1 
       19.33        14.63        31.73        23.47        22.45        19.20 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A25D 
       19.56        16.47        52.47       107.70        17.19        18.15 
TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT 
       91.92        10.59        20.88        39.65        33.93        83.01 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RW 
       14.07        49.48        38.40        34.98        38.37         7.30 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH 
        8.81         8.91         3.42        35.31        34.29        35.47 
TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       37.45        35.67        10.72        23.61        29.56        31.36 
TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A3IY TCGA-A7-A3IZ 
       24.26        23.74        23.80        21.73        11.34        10.59 
TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A426 TCGA-A7-A4SE TCGA-A7-A5ZW 
       10.29        11.28        13.41        11.97        21.17        10.72 
TCGA-A7-A5ZX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06T TCGA-A8-A06X TCGA-A8-A06Y 
       11.05         8.75        13.02        41.06        31.00        26.01 
TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F 
       17.03        53.98         9.01        33.01        19.99        18.97 
TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R 
       14.01        12.00        17.03         9.99        10.98         8.98 
TCGA-A8-A07S TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A08A TCGA-A8-A08C 
        7.99        18.05        15.06        36.95         0.99        19.99 
TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X 
       37.05         9.99        31.00        19.07        93.04        33.99 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A099 TCGA-A8-A09D TCGA-A8-A09E 
       40.01        19.07        16.01         9.99        13.02        31.00 
TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09T TCGA-A8-A09V 
       33.07        29.98        15.02         1.02        19.04        15.02 
TCGA-A8-A09W TCGA-A8-A0A2 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0AB TCGA-A8-A0AD 
        0.99        19.04        21.04         0.99        17.03        38.04 
TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB 
        0.95         2.66         1.48        38.53        38.20        40.57 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH 
       55.43        36.99        38.79        26.04        50.70         1.02 
TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 
        0.92         0.99        14.83         9.40         1.12         1.81 
TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62X TCGA-AC-A62Y 
        1.68         1.55         1.32         1.55         1.12         1.81 
TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 
        1.18         0.69         0.43         0.33         0.23         0.33 
TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR 
        0.62         2.96         1.71         7.36         6.51         0.33 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        0.33         6.44         4.64         7.59         7.17         6.28 
TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XN TCGA-AN-A0XP 
        6.02         0.33         0.36         0.33         0.33         0.30 
TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03M 
        0.33         0.33         0.33         5.33         5.59        47.84 
TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V 
       66.77        84.69        68.75        47.87        59.05        29.13 
TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0JA TCGA-AO-A0JB 
       17.65        24.16        37.48        22.36        21.53        50.70 
TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A124 
       72.00        21.37        26.24        38.53        62.04       102.58 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A12G 
       99.25        93.70        96.10        64.04        48.36        41.62 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KT TCGA-AQ-A04J 
       28.37        14.73        82.62        61.87        17.79        26.93 
TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ 
      130.09        15.62        13.22         9.99        82.88        49.32 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
       37.41        56.88        24.30        64.83        55.86        76.14 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH 
       65.36        70.16        83.87        76.18        55.36        75.55 
TCGA-AR-A1AJ TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP 
       52.77        48.82        62.56        43.73        43.56        39.98 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX 
       43.07        17.23        40.83        46.32        35.24        36.26 
TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
      109.58        50.89        73.02        65.46        68.19        65.69 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24X TCGA-AR-A24Z 
        0.85        66.05        62.07        53.26        48.16        51.75 
TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH 
       56.15        45.17        40.64        93.83       128.65        20.25 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QQ 
       40.04        17.10        20.81        16.96        16.04        10.59 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC 
      143.38       149.59        12.13       220.90       129.57        50.70 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
       65.72       146.50       112.37        18.77       126.12        84.59 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
      110.14       110.93       211.56        68.45       189.01       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ 
       81.17        78.02       172.96       162.05       102.77       140.48 
TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT 
      100.70        89.46       131.21       157.41        97.48       188.68 
TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
       17.98        21.47       129.57       129.70       186.48        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU 
       68.94        58.88        43.59       101.52       139.17       170.17 
TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A40C TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0B2 
       85.35        54.28        55.00        25.55        46.95        40.83 
TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BG 
       39.16        56.94        51.68        32.02        18.21        24.85 
TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       44.05        61.68        35.67        27.19        53.69        53.95 
TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C3 
       45.57        49.94        11.67        49.05        41.75        48.13 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DK 
       42.90        45.83        31.17        23.44        38.01        13.91 
TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DQ TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       48.23        17.26         3.22        38.47        45.17        47.41 
TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 
       16.27         4.41        15.68        14.30         9.63        44.81 
TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       46.19        32.65        30.35        10.78        15.16        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI 
       35.51        24.56        41.00        52.96        26.50        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0RX TCGA-BH-A0W3 
        5.85         2.50        12.89        51.32         5.59        23.93 
TCGA-BH-A0W4 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J 
       24.95        23.05         8.81         2.01         7.23        20.12 
TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18V 
       30.28        55.63        37.55        66.05         7.36        51.16 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F5 
      113.82        82.85        49.58        17.69        25.81        89.16 
TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG 
       24.66       120.62       114.15        33.17        74.73       122.89 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU 
       36.92        63.35        55.00        72.07       144.59        72.07 
TCGA-BH-A201 TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A42T 
        6.90        83.31       130.16        10.65         6.44         0.99 
TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12U 
      109.28         8.94        11.77        11.77        12.66        12.66 
TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 
       12.66        12.66        12.66         1.78         1.45         0.69 
TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ 
        3.85         3.75        12.33        10.92        11.34         0.16 
TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y 
       10.42         3.25         0.30         0.23         0.36         0.43 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A 
        8.28         9.67         0.03         0.03         0.03        12.20 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 
        0.03         0.23        11.90        20.88        13.25        20.58 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC 
       14.17        13.48        19.20        16.50        18.71        15.78 
TCGA-D8-A1JD TCGA-D8-A1JF TCGA-D8-A1JI TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP 
       18.15        12.03        18.97        19.40        20.38        21.01 
TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 
       12.20        14.70        18.58        16.73        25.74        23.90 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK 
        2.66        17.16        15.22        14.73        21.83        14.50 
TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XT 
       19.92        17.69         7.96        16.41        15.85         6.35 
TCGA-D8-A1XV TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F 
       15.16        15.32         3.81        14.14        17.42        16.04 
TCGA-D8-A27G TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P 
       13.45         9.44        16.41        13.48         4.80         0.76 
TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 
       10.09        13.08        14.50        18.51         7.33        43.00 
TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F 
       27.52        46.59        40.41        40.11        28.44        28.87 
TCGA-E2-A14N TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W 
       47.15        38.24        38.60        43.33        34.26        32.02 
TCGA-E2-A14X TCGA-E2-A150 TCGA-E2-A154 TCGA-E2-A156 TCGA-E2-A159 TCGA-E2-A15A 
       31.96        25.41        19.43        23.87        25.05        23.34 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J 
       22.82        17.29        21.63        12.92        17.42        19.40 
TCGA-E2-A15K TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
        9.04        13.02        19.56        17.06        14.07        14.99 
TCGA-E2-A1AZ TCGA-E2-A1B1 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF 
       60.53        53.03        28.50        16.47        38.30        37.41 
TCGA-E2-A1IG TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IO TCGA-E2-A1L7 
       32.78        28.44        22.65         3.88        20.98        27.42 
TCGA-E2-A1L8 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LI TCGA-E2-A1LK 
       39.62        24.59        40.47        28.90       102.61         8.75 
TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 
       43.04         5.52        15.72         7.20        18.05        22.26 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N9 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE 
       19.20        36.82        13.12        39.55        12.59        35.77 
TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1RA 
       20.05        21.57        11.90        14.30         0.62        32.09 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 
       34.65         6.58        35.64        34.13         0.79        12.53 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H 
       13.32        39.09        22.75        12.89        23.51        24.10 
TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A2JS 
        0.69         0.85        27.22         1.94        12.56        17.75 
TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A5FK TCGA-E9-A5UO 
        0.76        18.41         0.62        15.72         0.39         0.23 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 
       15.39        12.20        39.72        18.21        18.90        13.25 
TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ 
       15.68        25.94        22.82        29.95        29.85        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 
       41.13        39.78        52.96        18.48        30.08         7.86 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH 
       18.90        19.99        10.52        14.43        34.55        19.96 
TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 
       55.00        52.73        25.91        22.09        21.27        17.49 
TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       10.59         7.40       109.87        59.57       194.27        53.13 
TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       43.04        42.71        61.91        62.33        90.84        76.64 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A4E0 
       77.33        53.36        38.20        32.28        69.30        57.63 
TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 
       18.12        11.84        11.57         6.67         4.60         0.66 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO 
        2.99         3.58         6.90         5.56         3.65         3.19 
TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 
        3.88         4.14         4.50         4.50         5.59         3.22 
TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA 
       15.91         2.10        12.66        46.55         7.53        44.61 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       27.65        24.10        26.20        16.87        14.10        10.29 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66O 
       14.76        23.70        54.51        33.90        31.07         7.23 
TCGA-OL-A66P 
        4.44 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.07              0.03 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           176.98            234.28 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            20.22             22.82 
[1] "0.1 - 177.0 (20.2)" "0.0 - 234.3 (22.8)"
[1] "hr=" "1.5"
D9V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5P GAIN MUTATED        25       17        1        3       108        59
  5P GAIN WILD-TYPE      55       60        8        6       227       165
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5P GAIN MUTATED           1         47          9         13        4
  5P GAIN WILD-TYPE         1         91         18         46       13
                   vv
clus                STAGE TIS STAGE X
  5P GAIN MUTATED           0       2
  5P GAIN WILD-TYPE         1      14
D9V3, multiclass
            clus
vv           5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                 25                55
  STAGE IA                17                60
  STAGE IB                 1                 8
  STAGE II                 3                 6
  STAGE IIA              108               227
  STAGE IIB               59               165
  STAGE III                1                 1
  STAGE IIIA              47                91
  STAGE IIIB               9                18
  STAGE IIIC              13                46
  STAGE IV                 4                13
  STAGE TIS                0                 1
  STAGE X                  2                14
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  5P GAIN MUTATED    68 173  38  11
  5P GAIN WILD-TYPE 190 408  79  25
D9V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1              68               190
  T2             173               408
  T3              38                79
  T4              11                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                 N0  N1  N2  N3
  5P GAIN MUTATED   152  78  43  13
  5P GAIN WILD-TYPE 316 252  68  57
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0             152               316
  N1              78               252
  N2              43                68
  N3              13                57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  5P GAIN MUTATED          1 260   4  25
  5P GAIN WILD-TYPE        1 585  13 106
D9V6, multiclass
          clus
vv         5P GAIN MUTATED 5P GAIN WILD-TYPE
  CM0 (I+)               1                 1
  M0                   260               585
  M1                     4                13
  MX                    25               106
[1] 4 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   285   5
  5P GAIN WILD-TYPE 699   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED    285    5
  5P GAIN WILD-TYPE  699    6
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE             285               699
  MALE                 5                 6
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  5P GAIN MUTATED                            1                           220
  5P GAIN WILD-TYPE                          0                           515
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  5P GAIN MUTATED                               47                   2
  5P GAIN WILD-TYPE                            119                   3
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  5P GAIN MUTATED                                  6                  2
  5P GAIN WILD-TYPE                               23                 12
                   vv
clus                OTHER  SPECIFY
  5P GAIN MUTATED               12
  5P GAIN WILD-TYPE             32
D9V8, multiclass
                                  clus
vv                                 5P GAIN MUTATED 5P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                220               515
  INFILTRATING LOBULAR CARCINOMA                47               119
  MEDULLARY CARCINOMA                            2                 3
  MIXED HISTOLOGY (PLEASE SPECIFY)               6                23
  MUCINOUS CARCINOMA                             2                12
  OTHER  SPECIFY                                12                32
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V9, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    88 202
  5P GAIN WILD-TYPE 194 511
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     88  202
  5P GAIN WILD-TYPE  194  511
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               88               194
  YES             202               511
[1] 2 2
[1] FALSE
D9V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P GAIN MUTATED                                  0    11
  5P GAIN WILD-TYPE                                1    45
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED                          36   208
  5P GAIN WILD-TYPE                       101   500
D9V11, multiclass
                                  clus
vv                                 5P GAIN MUTATED 5P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         11                45
  BLACK OR AFRICAN AMERICAN                     36               101
  WHITE                                        208               500
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V12, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    10 231
  5P GAIN WILD-TYPE  26 565
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     10  231
  5P GAIN WILD-TYPE   26  565
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                  10                26
  NOT HISPANIC OR LATINO             231               565
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED   171  18
  5Q GAIN WILD-TYPE 689  96
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              189               785 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               18                96 
$`5Q GAIN MUTATED`
TCGA-A1-A0SJ TCGA-A1-A0SN TCGA-A2-A0CX TCGA-A2-A0EN TCGA-A2-A0ET TCGA-A2-A0EU 
       13.68        39.32        56.81        89.36        35.05        34.29 
TCGA-A2-A0EV TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A1FW 
       31.82        18.90        20.75        18.21        21.90        17.36 
TCGA-A2-A1FX TCGA-A2-A1G0 TCGA-A2-A3XU TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A2-A4S2 
       36.79        20.25        29.98         9.01        12.00         6.74 
TCGA-A7-A0CD TCGA-A7-A0DB TCGA-A7-A13F TCGA-A7-A26J TCGA-A7-A425 TCGA-A7-A4SB 
       38.30        33.11        12.72        20.61        14.70        13.74 
TCGA-A7-A4SD TCGA-A7-A6VV TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06Z 
       14.50        10.29        13.02         1.02        17.98         1.02 
TCGA-A8-A07G TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A086 TCGA-A8-A08G TCGA-A8-A08R 
       18.97         9.99        28.04        13.02        19.96         0.99 
TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09R 
       17.95        41.98        12.00        12.00         1.02         8.98 
TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A4 TCGA-A8-A0A9 TCGA-AC-A23E TCGA-AC-A23G 
       14.01        12.00        13.02        13.02         2.37        10.85 
TCGA-AC-A2QJ TCGA-AC-A3HN TCGA-AC-A8OP TCGA-AN-A03Y TCGA-AN-A0AJ TCGA-AN-A0AM 
        2.27         0.69         1.74         0.33         8.02         0.16 
TCGA-AN-A0AS TCGA-AN-A0FK TCGA-AN-A0FX TCGA-AN-A0XO TCGA-AO-A03L TCGA-AO-A03O 
        0.33         7.00         0.33        12.33        80.28        81.63 
TCGA-AO-A0J2 TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JM 
       32.78        20.32        53.03        50.86        76.77        71.80 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A1KS TCGA-AQ-A0Y5 TCGA-AR-A0TR 
       90.58        77.56        57.30         0.53         5.65         5.26 
TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AV TCGA-AR-A24R TCGA-AR-A24V TCGA-AR-A24W 
       61.84        51.25        42.58        57.40        54.18        50.96 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A5QM TCGA-AR-A5QP 
       39.85        34.82        42.87         7.36        54.74        20.45 
TCGA-B6-A0WV TCGA-B6-A0WY TCGA-B6-A1KI TCGA-B6-A408 TCGA-B6-A40B TCGA-BH-A0AU 
       79.63       113.79        73.51        49.94        82.88        24.53 
TCGA-BH-A0AZ TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BJ TCGA-BH-A0C1 
       28.50        48.36        56.98        37.22        21.70        44.02 
TCGA-BH-A0DI TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0H7 
       22.13        15.65         2.56        24.49        31.00        23.08 
TCGA-BH-A0HQ TCGA-BH-A0HX TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18K TCGA-BH-A18L 
       36.85        27.25        42.35        44.81        90.84        26.66 
TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1EU 
       72.56        37.74        51.39        69.93        91.99        42.28 
TCGA-BH-A1F6 TCGA-BH-A202 TCGA-BH-A2L8 TCGA-C8-A12P TCGA-C8-A135 TCGA-C8-A1HG 
       97.48         0.72        20.12        11.77         0.62        11.34 
TCGA-C8-A1HI TCGA-C8-A1HK TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1JE TCGA-D8-A1JH 
       11.34        12.03        21.14        14.17        18.90        14.01 
TCGA-D8-A1JJ TCGA-D8-A1JT TCGA-D8-A1X6 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XS 
       20.09        13.32        17.79        27.58        18.15        16.31 
TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A27I TCGA-D8-A27V 
       12.99        16.54        15.52        14.24        14.43        12.53 
TCGA-D8-A27W TCGA-E2-A107 TCGA-E2-A10B TCGA-E2-A14O TCGA-E2-A14S TCGA-E2-A14T 
       12.26        34.42        37.51        44.68        33.17        33.30 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A1B4 TCGA-E2-A1B5 
       27.12        23.24        20.71        18.21        29.95        32.35 
TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L9 
       17.10        33.73        22.19        11.08        54.18        19.66 
TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A56Z TCGA-E9-A1N6 TCGA-E9-A1NI TCGA-E9-A1R3 
       18.87       106.75         7.20        13.48         9.86         2.10 
TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RG 
        6.12         1.38         2.76        40.24         0.66        21.27 
TCGA-E9-A249 TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A5FL TCGA-EW-A1IY TCGA-EW-A1J3 
        0.95         0.72        17.75         0.26         8.48        16.57 
TCGA-EW-A1J6 TCGA-EW-A1P5 TCGA-EW-A1PC TCGA-EW-A423 TCGA-GM-A2DC TCGA-GM-A3NW 
       28.77        23.11         6.15        10.16        53.52       110.50 
TCGA-GM-A3XN TCGA-GM-A5PV TCGA-LD-A66U TCGA-LL-A6FQ TCGA-LL-A8F5 TCGA-MS-A51U 
       53.95        13.55         8.28         2.63         6.21         2.79 
TCGA-OL-A66N TCGA-S3-A6ZG TCGA-W8-A86G 
       18.21         6.81         5.29 

$`5Q GAIN WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ 
       20.88        31.79         7.96        28.01        19.20        18.21 
TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U 
      104.81        18.02        41.95        82.16        73.84        22.06 
TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL 
       63.12        64.04        55.43        36.13       125.59        64.57 
TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS 
       24.79       112.08        92.48        88.60       107.93        75.55 
TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 
       75.25         5.19        63.45        64.04        21.14        34.55 
TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EO TCGA-A2-A0EP 
       33.76        28.77        25.22       101.72        80.28       107.61 
TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY 
       79.76        74.40        37.05        29.75        24.72        24.16 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY 
       99.19        54.64        27.12        44.88        50.43        44.28 
TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 
       17.52        17.13         8.38        18.71        20.52        17.46 
TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ 
       32.55        25.28        15.42        21.67        14.50        18.61 
TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FZ 
       19.33        14.63        31.73        23.77        23.47        22.45 
TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B 
       19.20        19.56        16.47        52.47       107.70        16.31 
TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD 
       17.19        18.15        91.92        10.59        20.88        39.65 
TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       33.93        83.01        14.07        49.48        38.40        34.98 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S3 
       31.99        38.37         7.30         8.81         8.91         3.42 
TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA 
       35.31        34.29        35.47        30.61        37.45        35.67 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F 
       31.73        10.72        23.61        29.56        31.36        24.26 
TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ 
       23.74        23.80        21.73        22.32        11.34        10.59 
TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SE 
       10.29        11.28        13.41        11.97        14.93        21.17 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VW 
       17.92        14.73        12.10        10.72        11.05         9.37 
TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X 
       10.42         8.75        13.02        41.06        29.03        31.00 
TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E 
       26.01        17.03        53.98         9.01        33.01        19.99 
TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P 
       18.97        14.01        12.00        17.03         9.99        10.98 
TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 
        8.98         7.99         9.96        18.05        15.06        36.95 
TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08J 
        0.99        23.08        19.99        18.05        12.00        37.05 
TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X 
        9.99        31.00        31.00        19.07        93.04        33.99 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09D 
       40.01        19.07        16.01         9.99         9.99        13.02 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q 
       31.00        33.07        29.98        15.02         1.02        25.02 
TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A2 TCGA-A8-A0A6 TCGA-A8-A0A7 
       19.04        15.02         0.99        19.04        21.04         0.99 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK 
       17.03        38.04         0.95         2.66         1.48        38.53 
TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM 
       38.20        40.57        55.43        36.99        38.79        26.04 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3OD TCGA-AC-A3QP 
       50.70         1.02         0.92         0.99        14.83         9.40 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS 
        1.12         1.81         1.68         1.55         1.32         1.55 
TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX 
        0.07         1.12         1.81         1.18         0.69         0.43 
TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C 
        0.33         0.23         0.33         0.62         2.96         1.78 
TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD 
        1.71         7.36         6.51         0.33         0.33         6.44 
TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT 
        4.64         7.96         7.59         7.17         6.28         6.02 
TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN 
        0.33         0.36         0.33         0.33         0.33         0.33 
TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV 
        0.30         0.33         0.33         0.33         0.33         5.33 
TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T 
        5.59        47.84        66.77        84.69        68.75        47.87 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       59.05        29.13        21.40        17.65        24.16        37.48 
TCGA-AO-A0J8 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JG 
       22.36        21.53        50.70        72.00        21.37        26.24 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 
       38.53        62.04        55.33       102.58        99.25        93.70 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
       94.59        96.10        64.04        48.36        41.62        28.37 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H 
       14.73        82.62        61.87        70.39        17.79        24.79 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O 
       26.93       130.09        15.62        13.22         2.56        21.86 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV 
        9.99        82.88        49.32        37.41        56.88        29.75 
TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 
       24.30        64.83        55.86        76.14        65.36        70.16 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AL 
       83.87        76.18        55.36        75.55        52.77        48.82 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR 
       62.56        43.73        43.56        39.98        43.07        17.23 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H 
       40.83        46.32        35.24        36.26        20.22       109.58 
TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
       50.89        73.02        65.46        68.19        65.69         0.85 
TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A24Z 
       66.05        62.07        53.26        53.36        48.16        51.75 
TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH 
       56.15        45.17        40.64        93.83       128.65        20.25 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QN 
       40.04        17.10        20.81        16.96        20.38        16.04 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA 
       10.59        77.62       143.38       149.59        12.13       220.90 
TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ 
      129.57        50.70        65.72       146.50       112.37       176.98 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ 
       18.77       126.12        84.59       110.14       110.93       140.88 
TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM 
      211.56        68.45       189.01       234.28        81.17        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT 
      172.96       162.05       102.77       140.48       100.70        89.46 
TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX 
      131.21       157.41        97.48       188.68        17.98        21.47 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      129.57       129.70       186.48        28.27        68.94        58.88 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 
       43.59       101.52       139.17       170.17        85.35        54.28 
TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0B2 
       55.00        38.79        20.45        25.55        46.95        40.83 
TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD 
       39.55        39.16        56.94        51.68        32.02        18.21 
TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP 
       25.71        24.85        44.05        61.68        35.67        48.69 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW 
       27.19        53.69        53.95        45.57        49.94        11.67 
TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE 
       49.05        41.75        48.13        42.90        45.83        31.17 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DQ 
       23.44        38.01        13.91        48.23        17.26         3.22 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 
       38.47        45.17        47.41        16.27         4.41        15.68 
TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EI 
       14.30         9.63        44.81        46.19        32.65        24.43 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       30.35        10.78        15.16        37.78        35.51        24.56 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       41.00        52.96        26.50        20.38         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 
       13.61        12.89        51.32        50.79         5.59        23.93 
TCGA-BH-A0W4 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J 
       24.95        23.05         8.81         2.01         7.23        20.12 
TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18V 
       30.28        55.63        37.55        66.05         7.36        51.16 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY 
      113.82        82.85        12.00        55.69        49.58        17.69 
TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC 
       25.81        31.53        89.16        24.66       120.62       114.15 
TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
       33.17        74.73       122.89        36.92        63.35        55.00 
TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A203 
       45.63        72.07       144.59        72.07         6.90        38.60 
TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A42T 
       83.31        57.83       130.16        10.65         6.44         0.99 
TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O 
      109.28         8.94        11.93        11.77        11.77        12.66 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 
        0.07        12.66        12.66        12.66        12.66         3.12 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE 
        1.78         1.45         0.69         3.85         3.75        12.33 
TCGA-C8-A1HF TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V 
       10.92         0.16        10.42         2.30         3.25         0.30 
TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 
        0.23         0.36         0.43         8.28         9.67         0.03 
TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 
        0.03         0.03        12.20         0.99         0.03         0.23 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 
       11.90        20.88        13.25        20.58        13.97        14.17 
TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC 
       13.48        19.20        17.49        16.50        18.71        15.78 
TCGA-D8-A1JD TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JI TCGA-D8-A1JK TCGA-D8-A1JL 
       18.15        12.03        12.03        18.97        20.12        20.09 
TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X5 
       19.40        20.38        21.01        12.20        14.70        18.58 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF 
       16.73        25.74        23.90         2.66        17.16        15.22 
TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO 
       14.73        21.83        14.50        19.92        17.69         7.96 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XZ 
       16.41        15.85         6.35        15.16        12.66        15.32 
TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H 
        3.81        14.14        17.42        16.04        13.45        13.05 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R 
        9.44        16.41        13.48         4.80         0.76        10.09 
TCGA-D8-A27T TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A108 
       13.08        14.50        18.51         7.33        43.00        27.52 
TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N 
       46.59        40.41        40.11        28.44        28.87        47.15 
TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W 
       40.96        38.24        38.60        43.33        34.26        32.02 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A154 TCGA-E2-A155 
       31.96        28.60        17.03        25.41        19.43        21.04 
TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D 
       23.87        14.79        25.05        23.34        22.82        17.29 
TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       21.63        12.92        17.42        19.40         9.04        20.58 
TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
        7.73        13.02        19.56        17.06        14.07        14.99 
TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE 
       60.53        53.62        53.03        28.50        16.47        38.30 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       37.41        32.78        33.70        28.44        22.65         3.88 
TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       20.98        27.42        39.62        24.59        40.47        28.90 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX 
      102.61         8.75        43.04        16.93         5.52        15.72 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 
       18.05        22.26        19.89        19.20        36.82        12.00 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF 
       13.12        36.56        39.55        12.59        35.77        20.05 
TCGA-E9-A1NG TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R7 TCGA-E9-A1RA 
       21.57        11.90        14.30         0.62        21.21        32.09 
TCGA-E9-A1RB TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 
       20.81        34.65         6.58        34.59        35.64        34.13 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E 
        0.79        12.53        13.32        39.09        22.75        12.89 
TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A247 
       23.51        24.10        17.06         0.69         0.85        27.22 
TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA 
        1.94        12.56         0.76        26.07        18.41         0.62 
TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW 
       15.72         0.23         0.39         0.23        15.39        12.20 
TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J5 TCGA-EW-A1OV 
       39.72        18.21        18.90        13.25        15.68        25.94 
TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 
       22.82        29.95        29.85        40.41        41.13        39.78 
TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA 
       52.96        29.82        18.48        30.08         7.86        18.90 
TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH 
       19.99        13.94        10.52        14.43        34.55        19.96 
TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 
       55.00        52.73        25.91        22.09        21.27        17.49 
TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       10.59         7.40       109.87        59.57       194.27        53.13 
TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       43.04        42.71        42.28        61.91        62.33        90.84 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL 
       76.64        77.33        53.36        38.20        32.28        69.30 
TCGA-GM-A4E0 TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A74U TCGA-LD-A7W6 
       57.63        18.12        11.84        11.57         6.67         4.60 
TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM 
        0.66         2.99         3.58         6.90         5.56         4.70 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z 
        3.65         3.19         3.25         3.88         4.14         4.50 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A5D6 
        4.50         5.59         3.22        15.91         2.10        12.66 
TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW 
       46.55         7.53        44.61        27.65        24.10        26.20 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I 
       16.87        14.10        10.29         9.80        14.76        23.70 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P 
       54.51        33.90        31.07         7.23         4.44 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.16              0.03 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           113.79            234.28 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            18.97             22.36 
[1] "0.2 - 113.8 (19.0)" "0.0 - 234.3 (22.4)"
[1] "hr=" "1.2"
D10V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5Q GAIN MUTATED        17       14        0        3        63        44
  5Q GAIN WILD-TYPE      63       63        9        6       272       180
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5Q GAIN MUTATED           1         34          5         10        1
  5Q GAIN WILD-TYPE         1        104         22         49       16
                   vv
clus                STAGE TIS STAGE X
  5Q GAIN MUTATED           0       1
  5Q GAIN WILD-TYPE         1      15
D10V3, multiclass
            clus
vv           5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                 17                63
  STAGE IA                14                63
  STAGE IB                 0                 9
  STAGE II                 3                 6
  STAGE IIA               63               272
  STAGE IIB               44               180
  STAGE III                1                 1
  STAGE IIIA              34               104
  STAGE IIIB               5                22
  STAGE IIIC              10                49
  STAGE IV                 1                16
  STAGE TIS                0                 1
  STAGE X                  1                15
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  5Q GAIN MUTATED    50 107  30   7
  5Q GAIN WILD-TYPE 208 474  87  29
D10V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1              50               208
  T2             107               474
  T3              30                87
  T4               7                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                 N0  N1  N2  N3
  5Q GAIN MUTATED    97  57  28  10
  5Q GAIN WILD-TYPE 371 273  83  60
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0              97               371
  N1              57               273
  N2              28                83
  N3              10                60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  5Q GAIN MUTATED          1 170   1  22
  5Q GAIN WILD-TYPE        1 675  16 109
D10V6, multiclass
          clus
vv         5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CM0 (I+)               1                 1
  M0                   170               675
  M1                     1                16
  MX                    22               109
[1] 4 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   192   2
  5Q GAIN WILD-TYPE 792   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED    192    2
  5Q GAIN WILD-TYPE  792    9
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE             192               792
  MALE                 2                 9
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  5Q GAIN MUTATED                            0                           137
  5Q GAIN WILD-TYPE                          1                           598
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  5Q GAIN MUTATED                               40                   1
  5Q GAIN WILD-TYPE                            126                   4
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  5Q GAIN MUTATED                                  5                  2
  5Q GAIN WILD-TYPE                               24                 12
                   vv
clus                OTHER  SPECIFY
  5Q GAIN MUTATED                9
  5Q GAIN WILD-TYPE             35
D10V8, multiclass
                                  clus
vv                                 5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                137               598
  INFILTRATING LOBULAR CARCINOMA                40               126
  MEDULLARY CARCINOMA                            1                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               5                24
  MUCINOUS CARCINOMA                             2                12
  OTHER  SPECIFY                                 9                35
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V9, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    59 135
  5Q GAIN WILD-TYPE 223 578
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     59  135
  5Q GAIN WILD-TYPE  223  578
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO               59               223
  YES             135               578
[1] 2 2
[1] FALSE
D10V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q GAIN MUTATED                                  0     7
  5Q GAIN WILD-TYPE                                1    49
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED                          15   148
  5Q GAIN WILD-TYPE                       122   560
D10V11, multiclass
                                  clus
vv                                 5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          7                49
  BLACK OR AFRICAN AMERICAN                     15               122
  WHITE                                        148               560
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V12, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     7 153
  5Q GAIN WILD-TYPE  29 643
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      7  153
  5Q GAIN WILD-TYPE   29  643
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                29
  NOT HISPANIC OR LATINO             153               643
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED   164  26
  6P GAIN WILD-TYPE 696  88
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              190               784 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               26                88 
$`6P GAIN MUTATED`
TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A2-A04T TCGA-A2-A04X TCGA-A2-A0CM TCGA-A2-A0D2 
       31.79        28.01        73.84        55.43        24.79        33.76 
TCGA-A2-A0EQ TCGA-A2-A0ET TCGA-A2-A0EV TCGA-A2-A0EY TCGA-A2-A0T2 TCGA-A2-A0YE 
       79.76        35.05        31.82        24.16         8.38        18.21 
TCGA-A2-A0YG TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FX TCGA-A2-A25C 
       21.90        18.61        31.73        23.77        36.79        17.19 
TCGA-A2-A3XS TCGA-A2-A3XV TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4S1 
       33.93        14.07        38.40        34.98        38.37        12.00 
TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A13F TCGA-A7-A26I TCGA-A7-A26J 
       38.30        30.61        35.67        12.72        21.73        20.61 
TCGA-A7-A425 TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A6VV TCGA-A8-A06R 
       14.70        14.50        21.17        17.92        10.29        17.98 
TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07F TCGA-A8-A07R TCGA-A8-A07U 
       31.00        17.03        53.98        18.97         8.98         9.96 
TCGA-A8-A07W TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A092 
        9.99        23.08        19.99         0.99        19.07        16.01 
TCGA-A8-A09B TCGA-A8-A09E TCGA-A8-A09Q TCGA-AC-A23E TCGA-AC-A2QH TCGA-AC-A3W5 
       12.00        31.00        25.02         2.37         1.02         1.81 
TCGA-AC-A62X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A0AJ TCGA-AN-A0AM TCGA-AN-A0FK 
        1.12         0.33         0.23         8.02         0.16         7.00 
TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0XN TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03O 
        0.36         0.33         0.33        80.28        66.77        81.63 
TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12F 
       55.33        71.80       102.58        96.10        77.56        48.36 
TCGA-AO-A1KS TCGA-AQ-A0Y5 TCGA-AQ-A7U7 TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TV 
        0.53         5.65         9.99         5.26        37.41        29.75 
TCGA-AR-A0U0 TCGA-AR-A1AV TCGA-AR-A24Q TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A255 
       65.36        42.58        66.05        51.75        56.15        34.82 
TCGA-AR-A2LL TCGA-AR-A2LR TCGA-B6-A0I2 TCGA-B6-A0I9 TCGA-B6-A0IN TCGA-B6-A0IO 
        7.36        20.38       143.38        12.13        84.59       110.14 
TCGA-B6-A0RU TCGA-B6-A0WY TCGA-B6-A0X1 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A402 
      131.21       113.79       186.48        43.59       101.52        54.28 
TCGA-B6-A408 TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0B3 
       49.94        55.00        38.79        20.45        25.55        39.55 
TCGA-BH-A0B6 TCGA-BH-A0BA TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BT TCGA-BH-A0BZ 
       56.94        37.22        24.85        44.05        45.57        49.05 
TCGA-BH-A0C1 TCGA-BH-A0DH TCGA-BH-A0EB TCGA-BH-A0HQ TCGA-BH-A0WA TCGA-BH-A18K 
       44.02        38.01        24.49        36.85        23.05        90.84 
TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1EV TCGA-BH-A1FC 
       55.63         7.36        69.93        91.99        12.00       114.15 
TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A42V TCGA-C8-A12L TCGA-C8-A12X 
       38.60        57.83       130.16         8.94        11.93        12.66 
TCGA-C8-A130 TCGA-C8-A1HJ TCGA-C8-A1HM TCGA-C8-A26X TCGA-D8-A13Z TCGA-D8-A142 
        3.12         0.16         2.30         0.36        20.88        13.97 
TCGA-D8-A143 TCGA-D8-A1J8 TCGA-D8-A1JJ TCGA-D8-A1JL TCGA-D8-A1XJ TCGA-D8-A1XK 
       14.17        14.17        20.09        20.09        21.83        14.50 
TCGA-D8-A1XL TCGA-D8-A1XQ TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y3 TCGA-D8-A27F 
       19.92        16.41        16.54        15.32        14.14        16.04 
TCGA-D8-A27R TCGA-D8-A27V TCGA-E2-A10C TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A150 
       10.09        12.53        40.11        31.96        17.03        25.41 
TCGA-E2-A159 TCGA-E2-A15M TCGA-E2-A15S TCGA-E2-A1B0 TCGA-E2-A1II TCGA-E2-A1IL 
       25.05         7.73        14.07        53.62        33.70         3.88 
TCGA-E2-A1IN TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A2P5 TCGA-E2-A56Z TCGA-E2-A573 
       22.19       106.75       102.61        16.93         7.20        22.26 
TCGA-E2-A574 TCGA-E9-A1N9 TCGA-E9-A1ND TCGA-E9-A1RF TCGA-E9-A295 TCGA-E9-A3HO 
       19.89        13.12        12.59         6.58         0.72        26.07 
TCGA-E9-A3QA TCGA-E9-A54Y TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P6 
        0.62         0.23        25.94        22.82        29.82        18.48 
TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A2FV TCGA-EW-A423 TCGA-GI-A2C9 TCGA-GM-A2DF 
       30.08         7.86        25.91        10.16       109.87        42.71 
TCGA-LL-A441 TCGA-LL-A5YN TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A740 TCGA-LL-A7T0 
        2.99         3.65         3.88         4.14         4.50         3.22 
TCGA-OL-A5DA TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-OL-A66I 
       44.61        26.20         9.80        23.70 

$`6P GAIN WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A1-A0SQ 
       20.88        13.68         7.96        39.32        19.20        18.21 
TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04U TCGA-A2-A04V 
      104.81        18.02        41.95        82.16        22.06        63.12 
TCGA-A2-A04W TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP 
       64.04        36.13       125.59        64.57       112.08        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV 
       88.60       107.93        75.55        75.25         5.19        63.45 
TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0D4 
       64.04        56.81        21.14        34.55        28.77        25.22 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES 
      101.72        89.36        80.28       107.61        74.40        37.05 
TCGA-A2-A0EU TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV 
       34.29        29.75        24.72        99.19        54.64        27.12 
TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T3 
       44.88        50.43        44.28        17.52        17.13        18.71 
TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD 
       20.52        17.46        18.90        20.75        32.55        25.28 
TCGA-A2-A0YF TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A1FV 
       15.42        21.67        14.50        19.33        14.63        23.47 
TCGA-A2-A1FW TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 
       17.36        22.45        20.25        19.20        19.56        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
       52.47       107.70        16.31        18.15        91.92        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XW TCGA-A2-A3XZ 
       20.88        39.65        83.01        29.98        49.48        31.99 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 
        7.30         9.01         8.81         8.91         6.74         3.42 
TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13D 
       35.31        34.29        35.47        37.45        33.11        31.73 
TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G 
       10.72        23.61        29.56        31.36        24.26        23.74 
TCGA-A7-A26H TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       23.80        22.32        11.34        10.59        10.29        11.28 
TCGA-A7-A3RF TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A56D TCGA-A7-A5ZV 
       13.41        11.97        14.93        13.74        14.73        12.10 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O 
       10.72        11.05         9.37        10.42         8.75        13.02 
TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A06Z 
       13.02         1.02        41.06        29.03        26.01         1.02 
TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J 
        9.01        33.01        19.99        18.97        14.01        12.00 
TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07Z TCGA-A8-A082 
       17.03         9.99        10.98         7.99        28.04        18.05 
TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08F TCGA-A8-A08G 
       15.06        36.95        13.02         0.99        18.05        19.96 
TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08T 
       12.00        37.05         9.99        31.00        31.00        93.04 
TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 
       33.99        40.01        19.07        17.95        41.98        12.00 
TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09I TCGA-A8-A09K 
        9.99         9.99         1.02        13.02        33.07        29.98 
TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
       15.02         1.02         8.98        19.04        15.02         0.99 
TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 
       14.01        12.00        19.04        13.02        21.04         0.99 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A23H 
       13.02        17.03        38.04         0.95        10.85         2.66 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG 
        1.48        38.53        38.20        40.57        55.43        36.99 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB 
       38.79        26.04        50.70         0.92         2.27         0.99 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3YI 
        0.69        14.83         9.40         1.12         1.68         1.55 
TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW 
        1.32         1.55         0.07         1.81         1.18         0.69 
TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A 
        0.43         1.74         0.33         0.33         0.62         2.96 
TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AS 
        1.78         1.71         7.36         6.51         0.33         0.33 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FN 
        0.33         6.44         4.64         7.96         7.59         7.17 
TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0FZ TCGA-AN-A0XL 
        6.28         6.02         0.33         0.33         0.33         0.33 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU 
       12.33         0.30         0.33         0.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T 
        5.33         5.59        47.84        84.69        68.75        47.87 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 
       59.05        29.13        32.78        21.40        17.65        24.16 
TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB 
       37.48        20.32        22.36        53.03        21.53        50.70 
TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI 
       50.86        72.00        76.77        21.37        26.24        38.53 
TCGA-AO-A0JJ TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12D 
       62.04        99.25        93.70        94.59        90.58        64.04 
TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ 
       57.30        41.62        28.37        14.73        82.62        61.87 
TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 
       70.39        17.79        24.79        26.93       130.09        15.62 
TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TT 
       13.22         2.56        21.86        82.88        49.32        56.88 
TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 
       24.30        64.83        55.86        76.14        70.16        83.87 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK 
       76.18        55.36        75.55        61.84        52.77        51.25 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ 
       48.82        62.56        43.73        43.56        39.98        43.07 
TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY 
       17.23        40.83        46.32        35.24        36.26        20.22 
TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
      109.58        50.89        73.02        65.46        68.19        65.69 
TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V 
        0.85        57.40        62.07        53.26        53.36        54.18 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A256 
       50.96        48.16        45.17        40.64        39.85        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
      128.65        20.25        42.87        40.04        17.10        20.81 
TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       16.96        54.74        16.04        20.45        10.59        77.62 
TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG 
      149.59       220.90       129.57        50.70        65.72       146.50 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IP TCGA-B6-A0IQ 
      112.37       176.98        18.77       126.12       110.93       140.88 
TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM 
      211.56        68.45       189.01       234.28        81.17        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT 
      172.96       162.05       102.77       140.48       100.70        89.46 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX 
      157.41        97.48       188.68        79.63        17.98        21.47 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KI 
      129.57       129.70        28.27        68.94        58.88        73.51 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A40B TCGA-BH-A0AU TCGA-BH-A0AZ 
      139.17       170.17        85.35        82.88        24.53        28.50 
TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 
       46.95        40.83        39.16        48.36        56.98        51.68 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO 
       32.02        18.21        25.71        21.70        61.68        35.67 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW 
       48.69        27.19        53.69        53.95        49.94        11.67 
TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG 
       41.75        48.13        42.90        45.83        31.17        23.44 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ 
       22.13        13.91        48.23        17.26        15.65         3.22 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
        2.56        38.47        45.17        47.41        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA 
       15.68        14.30         9.63        44.81        46.19        32.65 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       31.00        24.43        30.35        10.78        15.16        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB 
       35.51        24.56        23.08        41.00        52.96        26.50 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HU TCGA-BH-A0HW 
       20.38         5.85         2.50        13.61        12.89        51.32 
TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 
       27.25        50.79         5.59        23.93        24.95        42.35 
TCGA-BH-A0W7 TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18L 
       44.81         8.81         2.01         7.23        20.12        26.66 
TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U 
       72.56        37.74        30.28        37.55        66.05        51.39 
TCGA-BH-A18V TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EX 
       51.16       113.82        82.85        42.28        55.69        49.58 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 
       17.69        25.81        31.53        89.16        97.48        24.66 
TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
      120.62        33.17        74.73       122.89        36.92        63.35 
TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 
       55.00        45.63        72.07       144.59        72.07         6.90 
TCGA-BH-A202 TCGA-BH-A204 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T 
        0.72        83.31        10.65         6.44        20.12         0.99 
TCGA-BH-A42U TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q 
      109.28        11.77        11.77        12.66        11.77         0.07 
TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 
       12.66        12.66        12.66         1.78         1.45         0.69 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG 
        0.62         3.85         3.75        12.33        10.92        11.34 
TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W 
       11.34        12.03        10.42         3.25         0.30         0.23 
TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 
        0.43         8.28         9.67         0.03         0.03         0.03 
TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A140 
       12.20         0.99         0.03         0.23        11.90        13.25 
TCGA-D8-A141 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA 
       20.58        13.48        21.14        19.20        17.49        16.50 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG 
       18.71        15.78        18.15        18.90        12.03        12.03 
TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JK TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP 
       14.01        18.97        20.12        19.40        20.38        21.01 
TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 
       12.20        13.32        14.70        18.58        17.79        16.73 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD 
       25.74        23.90        27.58        18.15         2.66        17.16 
TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS 
       15.22        14.73        17.69         7.96        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1Y0 TCGA-D8-A1Y1 
        6.35        12.99        15.16        12.66        15.52         3.81 
TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K 
       14.24        17.42        13.45        13.05        14.43         9.44 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27W 
       16.41        13.48         4.80         0.76        13.08        12.26 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 
       14.50        18.51         7.33        43.00        34.42        27.52 
TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N 
       46.59        40.41        37.51        28.44        28.87        47.15 
TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T 
       44.68        40.96        38.24        38.60        33.17        33.30 
TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A152 TCGA-E2-A153 
       43.33        34.26        32.02        28.60        27.12        23.24 
TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15A TCGA-E2-A15C 
       19.43        21.04        23.87        14.79        23.34        22.82 
TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I 
       17.29        20.71        21.63        18.21        12.92        17.42 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R 
       19.40         9.04        20.58        13.02        19.56        17.06 
TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       14.99        60.53        53.03        29.95        32.35        28.50 
TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       16.47        17.10        38.30        37.41        32.78        33.73 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 
       28.44        22.65        20.98        11.08        54.18        27.42 
TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG 
       39.62        19.66        24.59        40.47        28.90        18.87 
TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E9-A1N4 
        8.75        43.04         5.52        15.72        18.05        19.20 
TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1NE 
       36.82        13.48        12.00        36.56        39.55        35.77 
TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       20.05        21.57         9.86        11.90        14.30         0.62 
TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA 
        2.10         6.12         1.38         2.76        21.21        32.09 
TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A1RH 
       20.81        40.24         0.66        34.65        21.27        34.59 
TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       35.64        34.13         0.79        12.53        13.32        39.09 
TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 
       22.75        12.89        23.51        24.10        17.06         0.69 
TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JS 
        0.85        27.22         1.94         0.95        12.56        17.75 
TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO 
        0.76        18.41        15.72         0.39         0.26         0.23 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 
       15.39        12.20        39.72         8.48        18.21        18.90 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OX TCGA-EW-A1OY 
       13.25        16.57        15.68        28.77        29.95        29.85 
TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1PA 
       40.41        41.13        39.78        52.96        23.11        18.90 
TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
       19.99         6.15        13.94        10.52        14.43        34.55 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 
       19.96        55.00        52.73        22.09        21.27        17.49 
TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC 
       10.59         7.40        59.57       194.27        53.13        53.52 
TCGA-GM-A2DD TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       43.04        42.28        61.91        62.33        90.84        76.64 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL 
       77.33        53.36       110.50        38.20        32.28        69.30 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX 
       53.95        57.63        13.55        18.12        11.84        11.57 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y 
        8.28         6.67         4.60         0.66         3.58         6.90 
TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A73Z 
        5.56         4.70         3.19         3.25         2.63         4.50 
TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
        5.59         6.21        15.91         2.79         2.10        12.66 
TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY 
       46.55         7.53        27.65        24.10        16.87        14.10 
TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       10.29        14.76        54.51        33.90        31.07        18.21 
TCGA-OL-A66O TCGA-OL-A66P TCGA-S3-A6ZG TCGA-W8-A86G 
        7.23         4.44         6.81         5.29 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.16              0.03 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           186.48            234.28 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           22.225            21.240 
[1] "0.2 - 186.5 (22.2)" "0.0 - 234.3 (21.2)"
[1] "hr=" "1.3"
D11V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6P GAIN MUTATED        15        8        2        1        74        45
  6P GAIN WILD-TYPE      65       69        7        8       261       179
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6P GAIN MUTATED           0         25          5          9        4
  6P GAIN WILD-TYPE         2        113         22         50       13
                   vv
clus                STAGE TIS STAGE X
  6P GAIN MUTATED           0       2
  6P GAIN WILD-TYPE         1      14
D11V3, multiclass
            clus
vv           6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                 15                65
  STAGE IA                 8                69
  STAGE IB                 2                 7
  STAGE II                 1                 8
  STAGE IIA               74               261
  STAGE IIB               45               179
  STAGE III                0                 2
  STAGE IIIA              25               113
  STAGE IIIB               5                22
  STAGE IIIC               9                50
  STAGE IV                 4                13
  STAGE TIS                0                 1
  STAGE X                  2                14
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  6P GAIN MUTATED    38 124  23   5
  6P GAIN WILD-TYPE 220 457  94  31
D11V4, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1              38               220
  T2             124               457
  T3              23                94
  T4               5                31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  6P GAIN MUTATED    95  57  24  10
  6P GAIN WILD-TYPE 373 273  87  60
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0              95               373
  N1              57               273
  N2              24                87
  N3              10                60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  6P GAIN MUTATED          0 160   4  26
  6P GAIN WILD-TYPE        2 685  13 105
D11V6, multiclass
          clus
vv         6P GAIN MUTATED 6P GAIN WILD-TYPE
  CM0 (I+)               0                 2
  M0                   160               685
  M1                     4                13
  MX                    26               105
[1] 4 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   189   1
  6P GAIN WILD-TYPE 795  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED    189    1
  6P GAIN WILD-TYPE  795   10
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE             189               795
  MALE                 1                10
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  6P GAIN MUTATED                            0                           155
  6P GAIN WILD-TYPE                          1                           580
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  6P GAIN MUTATED                               16                   4
  6P GAIN WILD-TYPE                            150                   1
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  6P GAIN MUTATED                                  3                  1
  6P GAIN WILD-TYPE                               26                 13
                   vv
clus                OTHER  SPECIFY
  6P GAIN MUTATED               10
  6P GAIN WILD-TYPE             34
D11V8, multiclass
                                  clus
vv                                 6P GAIN MUTATED 6P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                155               580
  INFILTRATING LOBULAR CARCINOMA                16               150
  MEDULLARY CARCINOMA                            4                 1
  MIXED HISTOLOGY (PLEASE SPECIFY)               3                26
  MUCINOUS CARCINOMA                             1                13
  OTHER  SPECIFY                                10                34
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V9, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    62 128
  6P GAIN WILD-TYPE 220 585
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     62  128
  6P GAIN WILD-TYPE  220  585
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO               62               220
  YES             128               585
[1] 2 2
[1] FALSE
D11V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P GAIN MUTATED                                  0     8
  6P GAIN WILD-TYPE                                1    48
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED                          37   127
  6P GAIN WILD-TYPE                       100   581
D11V11, multiclass
                                  clus
vv                                 6P GAIN MUTATED 6P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          8                48
  BLACK OR AFRICAN AMERICAN                     37               100
  WHITE                                        127               581
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V12, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     9 148
  6P GAIN WILD-TYPE  27 648
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      9  148
  6P GAIN WILD-TYPE   27  648
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   9                27
  NOT HISPANIC OR LATINO             148               648
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED   119  17
  6Q GAIN WILD-TYPE 741  97
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              136               838 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               17                97 
$`6Q GAIN MUTATED`
TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SP TCGA-A2-A04X TCGA-A2-A0CM TCGA-A2-A0D2 
       13.68        31.79        19.20        55.43        24.79        33.76 
TCGA-A2-A0EQ TCGA-A2-A0EY TCGA-A2-A0T2 TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YJ 
       79.76        24.16         8.38        18.21        21.90        18.61 
TCGA-A2-A1FX TCGA-A2-A1G1 TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A4S1 TCGA-A7-A0CD 
       36.79        19.20        38.40        34.98        12.00        38.30 
TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A425 TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF 
       30.61        35.67        14.70        14.50        21.17        17.92 
TCGA-A7-A6VV TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A07F TCGA-A8-A07R 
       10.29        17.98        31.00        17.03        18.97         8.98 
TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A09B TCGA-A8-A09Q 
       23.08        19.99         0.99        19.07        12.00        25.02 
TCGA-AC-A23E TCGA-AC-A2QH TCGA-AC-A62X TCGA-AN-A03Y TCGA-AN-A0AM TCGA-AN-A0FK 
        2.37         1.02         1.12         0.33         0.16         7.00 
TCGA-AN-A0FY TCGA-AO-A03O TCGA-AO-A124 TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12F 
        0.33        81.63       102.58        96.10        77.56        48.36 
TCGA-AO-A1KS TCGA-AQ-A0Y5 TCGA-AQ-A7U7 TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV 
        0.53         5.65         9.99        37.41        56.88        29.75 
TCGA-AR-A0U0 TCGA-AR-A1AI TCGA-AR-A1AV TCGA-AR-A24Q TCGA-AR-A24Z TCGA-AR-A2LL 
       65.36        61.84        42.58        66.05        51.75         7.36 
TCGA-AR-A2LR TCGA-B6-A0I2 TCGA-B6-A0I9 TCGA-B6-A0IO TCGA-B6-A402 TCGA-BH-A0AV 
       20.38       143.38        12.13       110.14        54.28        38.79 
TCGA-BH-A0AY TCGA-BH-A0B3 TCGA-BH-A0B6 TCGA-BH-A0BA TCGA-BH-A0BG TCGA-BH-A0BL 
       25.55        39.55        56.94        37.22        24.85        44.05 
TCGA-BH-A0BT TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0EB TCGA-BH-A0HQ TCGA-BH-A18Q 
       45.57        49.05        44.02        24.49        36.85        55.63 
TCGA-BH-A1EO TCGA-BH-A1EV TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A42V 
       91.99        12.00        38.60        57.83       130.16         8.94 
TCGA-C8-A12L TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A1HJ TCGA-C8-A1HM TCGA-C8-A26X 
       11.93        12.66         3.12         0.16         2.30         0.36 
TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A1J8 TCGA-D8-A1JJ TCGA-D8-A1JL 
       20.88        13.97        14.17        14.17        20.09        20.09 
TCGA-D8-A1JP TCGA-D8-A1X5 TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XQ TCGA-D8-A1XY 
       21.01        18.58        21.83        14.50        16.41        16.54 
TCGA-D8-A1XZ TCGA-D8-A1Y3 TCGA-D8-A27F TCGA-D8-A27V TCGA-E2-A10C TCGA-E2-A14X 
       15.32        14.14        16.04        12.53        40.11        31.96 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A159 TCGA-E2-A15M TCGA-E2-A1B0 TCGA-E2-A1II 
       17.03        25.41        25.05         7.73        53.62        33.70 
TCGA-E2-A1LH TCGA-E2-A2P5 TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N9 TCGA-E9-A1NF 
      106.75        16.93        22.26        19.89        13.12        20.05 
TCGA-E9-A3QA TCGA-E9-A54Y TCGA-EW-A1OV TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 
        0.62         0.23        25.94        29.82        18.48        30.08 
TCGA-EW-A1P8 TCGA-EW-A423 TCGA-GI-A2C9 TCGA-GM-A2DF TCGA-GM-A2DH TCGA-LL-A5YN 
        7.86        10.16       109.87        42.71        42.28         3.65 
TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A7T0 TCGA-OL-A5DA 
        3.88         4.14         3.22        44.61 

$`6Q GAIN WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04N 
       20.88         7.96        39.32        28.01        18.21       104.81 
TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V 
       18.02        41.95        82.16        73.84        22.06        63.12 
TCGA-A2-A04W TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP 
       64.04        36.13       125.59        64.57       112.08        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV 
       88.60       107.93        75.55        75.25         5.19        63.45 
TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0D4 
       64.04        56.81        21.14        34.55        28.77        25.22 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES 
      101.72        89.36        80.28       107.61        74.40        37.05 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST 
       35.05        34.29        31.82        29.75        24.72        99.19 
TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 
       54.64        27.12        44.88        50.43        44.28        17.52 
TCGA-A2-A0T1 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 
       17.13        18.71        20.52        17.46        18.90        20.75 
TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK 
       32.55        25.28        15.42        21.67        14.50        19.33 
TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FZ 
       14.63        31.73        23.77        23.47        17.36        22.45 
TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B 
       20.25        19.56        16.47        52.47       107.70        16.31 
TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD 
       17.19        18.15        91.92        10.59        20.88        39.65 
TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XZ 
       33.93        83.01        29.98        14.07        49.48        31.99 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 
       38.37         7.30         9.01         8.81         8.91         6.74 
TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB 
        3.42        35.31        34.29        35.47        37.45        33.11 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       31.73        10.72        12.72        23.61        29.56        31.36 
TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD 
       24.26        23.74        23.80        21.73        20.61        22.32 
TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A426 
       11.34        10.59        10.29        11.28        13.41        11.97 
TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX 
       14.93        13.74        14.73        12.10        10.72        11.05 
TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q 
        9.37        10.42         8.75        13.02        13.02         1.02 
TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 
       41.06        29.03        26.01         1.02        53.98         9.01 
TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
       33.01        19.99        18.97        14.01        12.00        17.03 
TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z 
        9.99        10.98         7.99         9.96         9.99        28.04 
TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08F 
       18.05        15.06        36.95        13.02         0.99        18.05 
TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P 
       19.96        12.00        37.05         9.99        31.00        31.00 
TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 
       93.04        33.99        40.01        19.07        16.01        17.95 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09D 
       41.98        12.00         9.99         9.99         1.02        13.02 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R 
       31.00        33.07        29.98        15.02         1.02         8.98 
TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 
       19.04        15.02         0.99        14.01        12.00        19.04 
TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD 
       13.02        21.04         0.99        13.02        17.03        38.04 
TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM 
        0.95        10.85         2.66         1.48        38.53        38.20 
TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO 
       40.57        55.43        36.99        38.79        26.04        50.70 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
        0.92         2.27         0.99         0.69        14.83         9.40 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS 
        1.12         1.81         1.68         1.55         1.32         1.55 
TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A8OP 
        0.07         1.81         1.18         0.69         0.43         1.74 
TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C 
        0.33         0.23         0.33         0.62         2.96         1.78 
TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AS 
        1.71         8.02         7.36         6.51         0.33         0.33 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FN 
        0.33         6.44         4.64         7.96         7.59         7.17 
TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FZ 
        6.28         6.02         0.33         0.36         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS 
        0.33         0.33        12.33         0.30         0.33         0.33 
TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M 
        0.33         0.33         5.33         5.59        80.28        47.84 
TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V 
       66.77        84.69        68.75        47.87        59.05        29.13 
TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 
       32.78        21.40        17.65        24.16        37.48        20.32 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD 
       22.36        53.03        21.53        50.70        50.86        72.00 
TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL 
       76.77        21.37        26.24        38.53        62.04        55.33 
TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12D 
       71.80        99.25        93.70        94.59        90.58        64.04 
TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ 
       57.30        41.62        28.37        14.73        82.62        61.87 
TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 
       70.39        17.79        24.79        26.93       130.09        15.62 
TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
       13.22         2.56        21.86        82.88        49.32         5.26 
TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 
       24.30        64.83        55.86        76.14        70.16        83.87 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL 
       76.18        55.36        75.55        52.77        51.25        48.82 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR 
       62.56        43.73        43.56        39.98        43.07        17.23 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H 
       40.83        46.32        35.24        36.26        20.22       109.58 
TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
       50.89        73.02        65.46        68.19        65.69         0.85 
TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W 
       57.40        62.07        53.26        53.36        54.18        50.96 
TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 
       48.16        56.15        45.17        40.64        39.85        34.82 
TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN 
       93.83       128.65        20.25        42.87        40.04        17.10 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       20.81        16.96        54.74        16.04        20.45        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
       77.62       149.59       220.90       129.57        50.70        65.72 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
      146.50       112.37       176.98        18.77       126.12        84.59 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
      110.93       140.88       211.56        68.45       189.01       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ 
       81.17        78.02       172.96       162.05       102.77       140.48 
TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT 
      100.70        89.46       131.21       157.41        97.48       188.68 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 
       79.63        17.98        21.47       113.79       129.57       129.70 
TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF 
      186.48        28.27        68.94        58.88        43.59       101.52 
TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40B 
       73.51       139.17       170.17        85.35        49.94        82.88 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 
       55.00        24.53        20.45        28.50        46.95        40.83 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD 
       39.16        48.36        56.98        51.68        32.02        18.21 
TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ 
       25.71        21.70        61.68        35.67        48.69        27.19 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0C0 TCGA-BH-A0C3 
       53.69        53.95        49.94        11.67        41.75        48.13 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI 
       42.90        45.83        31.17        23.44        38.01        22.13 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS 
       13.91        48.23        17.26        15.65         3.22         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 
       38.47        45.17        47.41        16.27         4.41        15.68 
TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EE 
       14.30         9.63        44.81        46.19        32.65        31.00 
TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       24.43        30.35        10.78        15.16        37.78        35.51 
TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI 
       24.56        23.08        41.00        52.96        26.50        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX 
        5.85         2.50        13.61        12.89        51.32        27.25 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       50.79         5.59        23.93        24.95        42.35        44.81 
TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K 
       23.05         8.81         2.01         7.23        20.12        90.84 
TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S 
       26.66        72.56        37.74        30.28        37.55        66.05 
TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1ET 
        7.36        51.39        51.16        69.93       113.82        82.85 
TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 
       42.28        55.69        49.58        17.69        25.81        31.53 
TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD 
       89.16        97.48        24.66       120.62       114.15        33.17 
TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM 
       74.73       122.89        36.92        63.35        55.00        45.63 
TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A204 
       72.07       144.59        72.07         6.90         0.72        83.31 
TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-C8-A12M 
       10.65         6.44        20.12         0.99       109.28        11.77 
TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V 
       11.77        12.66        11.77         0.07        12.66        12.66 
TCGA-C8-A12W TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 
       12.66         1.78         1.45         0.69         0.62         3.85 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK 
        3.75        12.33        10.92        11.34        11.34        12.03 
TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Y TCGA-C8-A26Z 
       10.42         3.25         0.30         0.23         0.43         8.28 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B 
        9.67         0.03         0.03         0.03        12.20         0.99 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A145 
        0.03         0.23        11.90        13.25        20.58        13.48 
TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC 
       21.14        19.20        17.49        16.50        18.71        15.78 
TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI 
       18.15        18.90        12.03        12.03        14.01        18.97 
TCGA-D8-A1JK TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU 
       20.12        19.40        20.38        12.20        13.32        14.70 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB 
       17.79        16.73        25.74        23.90        27.58        18.15 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XL TCGA-D8-A1XM 
        2.66        17.16        15.22        14.73        19.92        17.69 
TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV 
        7.96        15.85        16.31         6.35        12.99        15.16 
TCGA-D8-A1XW TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27G 
       12.66        15.52         3.81        14.24        17.42        13.45 
TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N 
       13.05        14.43         9.44        16.41        13.48         4.80 
TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 
        0.76        10.09        13.08        12.26        14.50        18.51 
TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A 
        7.33        43.00        34.42        27.52        46.59        40.41 
TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P 
       37.51        28.44        28.87        47.15        44.68        40.96 
TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V 
       38.24        38.60        33.17        33.30        43.33        34.26 
TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 
       32.02        28.60        27.12        23.24        19.43        21.04 
TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E 
       23.87        14.79        23.34        22.82        17.29        20.71 
TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       21.63        18.21        12.92        17.42        19.40         9.04 
TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
       20.58        13.02        19.56        17.06        14.07        14.99 
TCGA-E2-A1AZ TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC 
       60.53        53.03        29.95        32.35        28.50        16.47 
TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ 
       17.10        38.30        37.41        32.78        33.73        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       22.65         3.88        22.19        20.98        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       27.42        39.62        19.66        24.59        40.47        28.90 
TCGA-E2-A1LG TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX 
       18.87       102.61         8.75        43.04         5.52        15.72 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 
        7.20        18.05        19.20        36.82        13.48        12.00 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NI 
       36.56        39.55        12.59        35.77        21.57         9.86 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 
       11.90        14.30         0.62         2.10         6.12         1.38 
TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD 
        2.76        21.21        32.09        20.81        40.24         0.66 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 
       34.65         6.58        21.27        34.59        35.64        34.13 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E 
        0.79        12.53        13.32        39.09        22.75        12.89 
TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A247 
       23.51        24.10        17.06         0.69         0.85        27.22 
TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT 
        1.94         0.95        12.56         0.72        17.75         0.76 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO 
       26.07        18.41        15.72         0.39         0.26         0.23 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 
       15.39        12.20        39.72         8.48        18.21        18.90 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1OX 
       13.25        16.57        15.68        28.77        22.82        29.95 
TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P5 
       29.85        40.41        41.13        39.78        52.96        23.11 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
       18.90        19.99         6.15        13.94        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW 
       34.55        19.96        55.00        52.73        25.91        22.09 
TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA 
       21.27        17.49        10.59         7.40        59.57       194.27 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       53.13        53.52        43.04        61.91        62.33        90.84 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
       76.64        77.33        53.36       110.50        38.20        32.28 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW 
       69.30        53.95        57.63        13.55        18.12        11.84 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 
       11.57         8.28         6.67         4.60         0.66         2.99 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A5YP 
        3.58         6.90         5.56         4.70         3.19         3.25 
TCGA-LL-A6FQ TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-LQ-A4E4 
        2.63         4.50         4.50         5.59         6.21        15.91 
TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5RU 
        2.79         2.10        12.66        46.55         7.53        27.65 
TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 
       24.10        26.20        16.87        14.10        10.29         9.80 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       14.76        23.70        54.51        33.90        31.07        18.21 
TCGA-OL-A66O TCGA-OL-A66P TCGA-S3-A6ZG TCGA-W8-A86G 
        7.23         4.44         6.81         5.29 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.16              0.03 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           143.38            234.28 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            20.63             21.60 
[1] "0.2 - 143.4 (20.6)" "0.0 - 234.3 (21.6)"
[1] "hr=" "1.3"
D12V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6Q GAIN MUTATED        12        5        2        1        58        29
  6Q GAIN WILD-TYPE      68       72        7        8       277       195
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6Q GAIN MUTATED           0         16          3          7        2
  6Q GAIN WILD-TYPE         2        122         24         52       15
                   vv
clus                STAGE TIS STAGE X
  6Q GAIN MUTATED           0       1
  6Q GAIN WILD-TYPE         1      15
D12V3, multiclass
            clus
vv           6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                 12                68
  STAGE IA                 5                72
  STAGE IB                 2                 7
  STAGE II                 1                 8
  STAGE IIA               58               277
  STAGE IIB               29               195
  STAGE III                0                 2
  STAGE IIIA              16               122
  STAGE IIIB               3                24
  STAGE IIIC               7                52
  STAGE IV                 2                15
  STAGE TIS                0                 1
  STAGE X                  1                15
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  6Q GAIN MUTATED    25  90  18   3
  6Q GAIN WILD-TYPE 233 491  99  33
D12V4, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1              25               233
  T2              90               491
  T3              18                99
  T4               3                33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  6Q GAIN MUTATED    78  35  14   8
  6Q GAIN WILD-TYPE 390 295  97  62
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0              78               390
  N1              35               295
  N2              14                97
  N3               8                62
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  6Q GAIN MUTATED          0 117   2  17
  6Q GAIN WILD-TYPE        2 728  15 114
D12V6, multiclass
          clus
vv         6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CM0 (I+)               0                 2
  M0                   117               728
  M1                     2                15
  MX                    17               114
[1] 4 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   135   1
  6Q GAIN WILD-TYPE 849  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED    135    1
  6Q GAIN WILD-TYPE  849   10
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE             135               849
  MALE                 1                10
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  6Q GAIN MUTATED                            0                           110
  6Q GAIN WILD-TYPE                          1                           625
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  6Q GAIN MUTATED                               11                   4
  6Q GAIN WILD-TYPE                            155                   1
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  6Q GAIN MUTATED                                  3                  1
  6Q GAIN WILD-TYPE                               26                 13
                   vv
clus                OTHER  SPECIFY
  6Q GAIN MUTATED                7
  6Q GAIN WILD-TYPE             37
D12V8, multiclass
                                  clus
vv                                 6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                110               625
  INFILTRATING LOBULAR CARCINOMA                11               155
  MEDULLARY CARCINOMA                            4                 1
  MIXED HISTOLOGY (PLEASE SPECIFY)               3                26
  MUCINOUS CARCINOMA                             1                13
  OTHER  SPECIFY                                 7                37
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V9, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    43  93
  6Q GAIN WILD-TYPE 239 620
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     43   93
  6Q GAIN WILD-TYPE  239  620
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO               43               239
  YES              93               620
[1] 2 2
[1] FALSE
D12V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q GAIN MUTATED                                  0     7
  6Q GAIN WILD-TYPE                                1    49
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED                          26    90
  6Q GAIN WILD-TYPE                       111   618
D12V11, multiclass
                                  clus
vv                                 6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          7                49
  BLACK OR AFRICAN AMERICAN                     26               111
  WHITE                                         90               618
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V12, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     7 105
  6Q GAIN WILD-TYPE  29 691
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      7  105
  6Q GAIN WILD-TYPE   29  691
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                29
  NOT HISPANIC OR LATINO             105               691
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED   245  34
  7P GAIN WILD-TYPE 615  80
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              279               695 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               34                80 
$`7P GAIN MUTATED`
TCGA-A1-A0SF TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SN TCGA-A2-A04W TCGA-A2-A0CV 
       48.10        20.88        13.68        39.32        64.04        63.45 
TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0EV TCGA-A2-A0EY TCGA-A2-A0SW TCGA-A2-A0T1 
       64.04        21.14        31.82        24.16        44.88        17.13 
TCGA-A2-A0T2 TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YJ TCGA-A2-A1FV TCGA-A2-A1G0 
        8.38        18.21        21.90        18.61        23.47        20.25 
TCGA-A2-A1G4 TCGA-A2-A25B TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XZ TCGA-A2-A4S1 
       19.56        16.31        33.93        83.01        31.99        12.00 
TCGA-A7-A0CE TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E 
       35.31        37.45        35.67        33.11        31.73        10.72 
TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A425 TCGA-A7-A4SB 
       12.72        23.61        24.26        23.80        14.70        13.74 
TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A6VV TCGA-A8-A06Q 
       14.50        21.17        17.92        12.10        10.29         1.02 
TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A07F 
       17.98        31.00        26.01         1.02        53.98        18.97 
TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08P 
        8.98         9.96         9.99        19.99        19.96        31.00 
TCGA-A8-A08X TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09B 
       33.99        17.95        41.98        12.00         9.99        12.00 
TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09X TCGA-A8-A0A1 TCGA-AC-A23G TCGA-AC-A23H 
       29.98        15.02        14.01        12.00        10.85         2.66 
TCGA-AC-A2FM TCGA-AC-A2QJ TCGA-AC-A3W5 TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A8OP 
       26.04         2.27         1.81         0.07         1.81         1.74 
TCGA-AN-A049 TCGA-AN-A0AL TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0XL 
        0.62         6.51         6.02         0.36         0.33         0.33 
TCGA-AO-A03N TCGA-AO-A0J3 TCGA-AO-A0J6 TCGA-AO-A0JB TCGA-AO-A0JD TCGA-AO-A0JL 
       66.77        21.40        37.48        50.70        72.00        55.33 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A128 TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
      102.58        99.25        94.59        77.56        64.04        57.30 
TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AR-A0TR 
       61.87        70.39        15.62        13.22        21.86         5.26 
TCGA-AR-A0U0 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AR TCGA-AR-A1AV TCGA-AR-A24H 
       65.36        83.87        76.18        17.23        42.58       109.58 
TCGA-AR-A24K TCGA-AR-A24Q TCGA-AR-A24W TCGA-AR-A250 TCGA-AR-A2LR TCGA-AR-A5QM 
       50.89        66.05        50.96        56.15        20.38        54.74 
TCGA-AR-A5QP TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IB TCGA-B6-A0IC 
       20.45       143.38       149.59        12.13       129.57        50.70 
TCGA-B6-A0IH TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0RE TCGA-B6-A0RI TCGA-B6-A0RV 
      112.37       126.12        84.59       211.56       234.28       157.41 
TCGA-B6-A0WV TCGA-B6-A0WZ TCGA-B6-A401 TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AY 
       79.63       129.57        85.35        24.53        20.45        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B4 TCGA-BH-A0BA TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BP 
       28.50        39.16        37.22        21.70        44.05        48.69 
TCGA-BH-A0BT TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0DL TCGA-BH-A0DO 
       45.57        49.05        44.02        45.83        48.23        17.26 
TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0E9 
       15.65         2.56        38.47         4.41         9.63        46.19 
TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0GY TCGA-BH-A0H7 TCGA-BH-A0HP TCGA-BH-A0HQ 
       32.65        24.49        30.35        23.08        13.61        36.85 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W7 TCGA-BH-A18K TCGA-BH-A18V TCGA-BH-A1EN 
       50.79         5.59        44.81        90.84        51.16        69.93 
TCGA-BH-A1EO TCGA-BH-A1EV TCGA-BH-A1EX TCGA-BH-A1F6 TCGA-BH-A1FD TCGA-BH-A1FN 
       91.99        12.00        49.58        97.48        33.17        72.07 
TCGA-BH-A202 TCGA-C8-A12L TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12V TCGA-C8-A131 
        0.72        11.93        11.77         0.07        12.66         1.78 
TCGA-C8-A138 TCGA-C8-A1HI TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 
        3.75        11.34         0.36         0.43         8.28         9.67 
TCGA-C8-A3M7 TCGA-D8-A143 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1JF TCGA-D8-A1JG 
        0.03        14.17        21.14        14.17        12.03        12.03 
TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1X9 TCGA-D8-A1XF TCGA-D8-A1XL TCGA-D8-A1XR 
       20.12        20.09        23.90        15.22        19.92        15.85 
TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A27K TCGA-D8-A3Z5 
       12.99        16.54        15.32         3.81         9.44        14.50 
TCGA-D8-A3Z6 TCGA-E2-A107 TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A14P TCGA-E2-A14R 
       18.51        34.42        37.51        40.11        40.96        38.60 
TCGA-E2-A14T TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 
       33.30        34.26        32.02        27.12        23.24        19.43 
TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15I 
       25.05        23.34        17.29        20.71        18.21        17.42 
TCGA-E2-A15M TCGA-E2-A15R TCGA-E2-A1AZ TCGA-E2-A1B5 TCGA-E2-A1BD TCGA-E2-A1IH 
        7.73        17.06        60.53        32.35        17.10        33.73 
TCGA-E2-A1II TCGA-E2-A1IO TCGA-E2-A1L9 TCGA-E2-A1LE TCGA-E2-A1LI TCGA-E2-A1LL 
       33.70        20.98        19.66        28.90       102.61        43.04 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1ND 
        7.20        18.05        22.26        12.00        13.12        12.59 
TCGA-E9-A1NF TCGA-E9-A1QZ TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R7 TCGA-E9-A1RA 
       20.05        11.90         2.10         6.12        21.21        32.09 
TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A226 TCGA-E9-A22E TCGA-E9-A247 TCGA-E9-A249 
       20.81        40.24        34.13        12.89        27.22         0.95 
TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A3HO TCGA-E9-A3X8 TCGA-EW-A1IY TCGA-EW-A1J6 
       12.56         0.72        26.07        15.72         8.48        28.77 
TCGA-EW-A1OW TCGA-EW-A1P0 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P8 
       22.82        41.13        52.96        29.82        23.11         7.86 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A423 TCGA-GI-A2C8 TCGA-GM-A2DB TCGA-GM-A2DC 
       18.90        19.99        10.16         7.40        53.13        53.52 
TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DL TCGA-GM-A3XN TCGA-JL-A3YW TCGA-LL-A440 
       43.04        42.71        90.84        53.95        11.84         0.66 
TCGA-LL-A441 TCGA-LL-A5YM TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A740 TCGA-OL-A5D7 
        2.99         4.70         2.63         3.88         4.50        46.55 
TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66K 
       24.10        26.20        16.87        10.29        14.76        33.90 
TCGA-OL-A66N TCGA-OL-A66P TCGA-W8-A86G 
       18.21         4.44         5.29 

$`7P GAIN WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SK 
        8.52        14.37        43.43        14.27        47.24        31.79 
TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P 
        7.96        28.01        19.20        18.21       104.81        18.02 
TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04X 
       41.95        82.16        73.84        22.06        63.12        55.43 
TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
       36.13       125.59        64.57        24.79       112.08        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CX 
       88.60       107.93        75.55        75.25         5.19        56.81 
TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN 
       34.55        33.76        28.77        25.22       101.72        89.36 
TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET 
       80.28       107.61        79.76        74.40        37.05        35.05 
TCGA-A2-A0EU TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV 
       34.29        29.75        24.72        99.19        54.64        27.12 
TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 
       50.43        44.28        17.52        18.71        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YH 
       18.90        20.75        32.55        25.28        15.42        21.67 
TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FW 
       14.50        19.33        14.63        31.73        23.77        17.36 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G1 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A 
       36.79        22.45        19.20        16.47        52.47       107.70 
TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD 
       17.19        18.15        91.92        10.59        20.88        39.65 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 
       29.98        14.07        49.48        38.40        34.98        38.37 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 
        7.30         9.01         8.81         8.91         6.74         3.42 
TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A13H TCGA-A7-A26E 
       38.30        34.29        35.47        30.61        29.56        31.36 
TCGA-A7-A26G TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ 
       23.74        21.73        20.61        22.32        11.34        10.59 
TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A56D 
       10.29        11.28        13.41        11.97        14.93        14.73 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O 
       10.72        11.05         9.37        10.42         8.75        13.02 
TCGA-A8-A06P TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A075 TCGA-A8-A079 TCGA-A8-A07B 
       13.02        41.06        29.03        17.03         9.01        33.01 
TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O 
       19.99        18.97        14.01        12.00        17.03         9.99 
TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 
       10.98         7.99        28.04        18.05        15.06        36.95 
TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08J 
       13.02         0.99        23.08        18.05        12.00        37.05 
TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z 
        9.99        31.00         0.99        19.07        93.04        40.01 
TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A099 TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E 
       19.07        16.01         9.99         1.02        13.02        31.00 
TCGA-A8-A09I TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       33.07         1.02        25.02         8.98        19.04        15.02 
TCGA-A8-A09W TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 
        0.99        19.04        13.02        21.04         0.99        13.02 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A2B8 TCGA-AC-A2BK 
       17.03        38.04         0.95         2.37         1.48        38.53 
TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO 
       38.20        40.57        55.43        36.99        38.79        50.70 
TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
        1.02         0.92         0.99         0.69        14.83         9.40 
TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62X 
        1.12         1.68         1.55         1.32         1.55         1.12 
TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 
        1.18         0.69         0.43         0.33         0.33         0.23 
TCGA-AN-A046 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK 
        0.33         2.96         1.78         1.71         8.02         7.36 
TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF 
        0.16         0.33         0.33         0.33         6.44         4.64 
TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FV 
        7.96         7.00         7.59         7.17         6.28         0.33 
TCGA-AN-A0FX TCGA-AN-A0FZ TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR 
        0.33         0.33         0.33        12.33         0.30         0.33 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L 
        0.33         0.33         0.33         5.33         5.59        80.28 
TCGA-AO-A03M TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U 
       47.84        81.63        84.69        68.75        47.87        59.05 
TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J7 TCGA-AO-A0J8 
       29.13        32.78        17.65        24.16        20.32        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG 
       53.03        21.53        50.86        76.77        21.37        26.24 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12A 
       38.53        62.04        71.80        93.70        96.10        90.58 
TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KS 
       48.36        41.62        28.37        14.73        82.62         0.53 
TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A54N 
       17.79        24.79        26.93       130.09         5.65         2.56 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV 
        9.99        82.88        49.32        37.41        56.88        29.75 
TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U4 
       24.30        64.83        55.86        76.14        70.16        55.36 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM 
       75.55        61.84        52.77        51.25        48.82        62.56 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU 
       43.73        43.56        39.98        43.07        40.83        46.32 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       35.24        36.26        20.22        73.02        65.46        68.19 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U 
       65.69         0.85        57.40        62.07        53.26        53.36 
TCGA-AR-A24V TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 
       54.18        48.16        51.75        45.17        40.64        39.85 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LL 
       34.82        93.83       128.65        20.25        42.87         7.36 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QQ 
       40.04        17.10        20.81        16.96        16.04        10.59 
TCGA-B6-A0I1 TCGA-B6-A0IA TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IJ TCGA-B6-A0IK 
       77.62       220.90        65.72       146.50       176.98        18.77 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RL 
      110.14       110.93       140.88        68.45       189.01        81.17 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS 
       78.02       172.96       162.05       102.77       140.48       100.70 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX 
       89.46       131.21        97.48       188.68        17.98        21.47 
TCGA-B6-A0WY TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      113.79       129.70       186.48        28.27        68.94        58.88 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A402 
       43.59       101.52        73.51       139.17       170.17        54.28 
TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0B0 TCGA-BH-A0B2 
       49.94        82.88        55.00        38.79        46.95        40.83 
TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC 
       39.55        48.36        56.94        56.98        51.68        32.02 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ 
       18.21        25.71        24.85        61.68        35.67        27.19 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0C0 TCGA-BH-A0C3 
       53.69        53.95        49.94        11.67        41.75        48.13 
TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       42.90        31.17        23.44        38.01        22.13        13.91 
TCGA-BH-A0DQ TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 
        3.22        45.17        47.41        16.27        15.68        14.30 
TCGA-BH-A0E7 TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       44.81        31.00        24.43        10.78        15.16        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI 
       35.51        24.56        41.00        52.96        26.50        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0W3 
        5.85         2.50        12.89        51.32        27.25        23.93 
TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I 
       24.95        42.35        23.05         8.81         2.01         7.23 
TCGA-BH-A18J TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q 
       20.12        26.66        72.56        37.74        30.28        55.63 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1ES TCGA-BH-A1ET 
       37.55        66.05         7.36        51.39       113.82        82.85 
TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 
       42.28        55.69        17.69        25.81        31.53        89.16 
TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH 
       24.66       120.62       114.15        74.73       122.89        36.92 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 
       63.35        55.00        45.63       144.59        72.07         6.90 
TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q 
       38.60        83.31        57.83       130.16        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12M TCGA-C8-A12N 
       20.12         0.99       109.28         8.94        11.77        11.77 
TCGA-C8-A12O TCGA-C8-A12U TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A132 
       12.66        12.66        12.66        12.66         3.12         1.45 
TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG 
        0.69         0.62         3.85        12.33        10.92        11.34 
TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V 
        0.16        12.03        10.42         2.30         3.25         0.30 
TCGA-C8-A26W TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B 
        0.23         0.03         0.03         0.03        12.20         0.99 
TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 
        0.23        11.90        20.88        13.25        20.58        13.97 
TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC 
       13.48        19.20        17.49        16.50        18.71        15.78 
TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JM 
       18.15        18.90        14.01        18.97        20.09        19.40 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 
       20.38        21.01        12.20        13.32        14.70        18.58 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC 
       17.79        16.73        25.74        27.58        18.15         2.66 
TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XM TCGA-D8-A1XO 
       17.16        14.73        21.83        14.50        17.69         7.96 
TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1Y0 
       16.41        16.31         6.35        15.16        12.66        15.52 
TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H 
       14.24        14.14        17.42        16.04        13.45        13.05 
TCGA-D8-A27I TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R 
       14.43        16.41        13.48         4.80         0.76        10.09 
TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A108 
       13.08        12.53        12.26         7.33        43.00        27.52 
TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O 
       46.59        40.41        28.44        28.87        47.15        44.68 
TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z 
       38.24        33.17        43.33        31.96        28.60        17.03 
TCGA-E2-A150 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15C TCGA-E2-A15F 
       25.41        21.04        23.87        14.79        22.82        21.63 
TCGA-E2-A15H TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15P 
       12.92        19.40         9.04        20.58        13.02        19.56 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B6 
       14.07        14.99        53.62        53.03        29.95        28.50 
TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IJ TCGA-E2-A1IK 
       16.47        38.30        37.41        32.78        28.44        22.65 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 
        3.88        22.19        11.08        54.18        27.42        39.62 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LK TCGA-E2-A2P5 
       24.59        40.47        18.87       106.75         8.75        16.93 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A574 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 
        5.52        15.72        19.89        19.20        36.82        13.48 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1R0 
       36.56        39.55        35.77        21.57         9.86        14.30 
TCGA-E9-A1R2 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF 
        0.62         1.38         2.76         0.66        34.65         6.58 
TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
       21.27        34.59        35.64         0.79        12.53        13.32 
TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 
       39.09        22.75        23.51        24.10        17.06         0.69 
TCGA-E9-A245 TCGA-E9-A248 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA 
        0.85         1.94        17.75         0.76        18.41         0.62 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW 
        0.23         0.39         0.26         0.23        15.39        12.20 
TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
       39.72        18.21        18.90        13.25        16.57        15.68 
TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P1 TCGA-EW-A1P6 
       25.94        29.95        29.85        40.41        39.78        18.48 
TCGA-EW-A1P7 TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
       30.08         6.15        13.94        10.52        14.43        34.55 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 
       19.96        55.00        52.73        25.91        22.09        21.27 
TCGA-EW-A3U0 TCGA-EW-A424 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DH 
       17.49        10.59       109.87        59.57       194.27        42.28 
TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
       61.91        62.33        76.64        77.33        53.36       110.50 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX 
       38.20        32.28        69.30        57.63        13.55        18.12 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A442 TCGA-LL-A50Y 
       11.57         8.28         6.67         4.60         3.58         6.90 
TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A73Y TCGA-LL-A73Z 
        5.56         3.65         3.19         3.25         4.14         4.50 
TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 
        5.59         3.22         6.21        15.91         2.79         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RY TCGA-OL-A5S0 
       12.66         7.53        44.61        27.65        14.10         9.80 
TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66O TCGA-S3-A6ZG 
       23.70        54.51        31.07         7.23         6.81 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.03              0.03 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           234.28            220.90 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            21.21             21.53 
[1] "0.0 - 234.3 (21.2)" "0.0 - 220.9 (21.5)"
[1] "hr=" "1.1"
D13V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7P GAIN MUTATED        18       18        3        2       103        59
  7P GAIN WILD-TYPE      62       59        6        7       232       165
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7P GAIN MUTATED           0         41          8         20        6
  7P GAIN WILD-TYPE         2         97         19         39       11
                   vv
clus                STAGE TIS STAGE X
  7P GAIN MUTATED           0       4
  7P GAIN WILD-TYPE         1      12
D13V3, multiclass
            clus
vv           7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                 18                62
  STAGE IA                18                59
  STAGE IB                 3                 6
  STAGE II                 2                 7
  STAGE IIA              103               232
  STAGE IIB               59               165
  STAGE III                0                 2
  STAGE IIIA              41                97
  STAGE IIIB               8                19
  STAGE IIIC              20                39
  STAGE IV                 6                11
  STAGE TIS                0                 1
  STAGE X                  4                12
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  7P GAIN MUTATED    68 168  35  11
  7P GAIN WILD-TYPE 190 413  82  25
D13V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1              68               190
  T2             168               413
  T3              35                82
  T4              11                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                 N0  N1  N2  N3
  7P GAIN MUTATED   131  91  31  22
  7P GAIN WILD-TYPE 337 239  80  48
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0             131               337
  N1              91               239
  N2              31                80
  N3              22                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  7P GAIN MUTATED          1 235   6  41
  7P GAIN WILD-TYPE        1 610  11  90
D13V6, multiclass
          clus
vv         7P GAIN MUTATED 7P GAIN WILD-TYPE
  CM0 (I+)               1                 1
  M0                   235               610
  M1                     6                11
  MX                    41                90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   276   7
  7P GAIN WILD-TYPE 708   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    276    7
  7P GAIN WILD-TYPE  708    4
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE             276               708
  MALE                 7                 4
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  7P GAIN MUTATED                            1                           223
  7P GAIN WILD-TYPE                          0                           512
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  7P GAIN MUTATED                               35                   1
  7P GAIN WILD-TYPE                            131                   4
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  7P GAIN MUTATED                                  8                  2
  7P GAIN WILD-TYPE                               21                 12
                   vv
clus                OTHER  SPECIFY
  7P GAIN MUTATED               13
  7P GAIN WILD-TYPE             31
D13V8, multiclass
                                  clus
vv                                 7P GAIN MUTATED 7P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                223               512
  INFILTRATING LOBULAR CARCINOMA                35               131
  MEDULLARY CARCINOMA                            1                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               8                21
  MUCINOUS CARCINOMA                             2                12
  OTHER  SPECIFY                                13                31
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V9, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    88 195
  7P GAIN WILD-TYPE 194 518
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     88  195
  7P GAIN WILD-TYPE  194  518
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO               88               194
  YES             195               518
[1] 2 2
[1] FALSE
D13V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P GAIN MUTATED                                  1    16
  7P GAIN WILD-TYPE                                0    40
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED                          40   201
  7P GAIN WILD-TYPE                        97   507
D13V11, multiclass
                                  clus
vv                                 7P GAIN MUTATED 7P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         16                40
  BLACK OR AFRICAN AMERICAN                     40                97
  WHITE                                        201               507
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V12, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     9 223
  7P GAIN WILD-TYPE  27 573
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      9  223
  7P GAIN WILD-TYPE   27  573
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   9                27
  NOT HISPANIC OR LATINO             223               573
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED   210  25
  7Q GAIN WILD-TYPE 650  89
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              235               739 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               25                89 
$`7Q GAIN MUTATED`
TCGA-A1-A0SF TCGA-A1-A0SI TCGA-A1-A0SN TCGA-A2-A04W TCGA-A2-A0CV TCGA-A2-A0CW 
       48.10        20.88        39.32        64.04        63.45        64.04 
TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0EV TCGA-A2-A0EY TCGA-A2-A0SW TCGA-A2-A0T2 
       21.14        33.76        31.82        24.16        44.88         8.38 
TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YJ TCGA-A2-A1FV TCGA-A2-A1G0 TCGA-A2-A1G4 
       18.21        21.90        18.61        23.47        20.25        19.56 
TCGA-A2-A25B TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XZ TCGA-A2-A4S1 TCGA-A7-A0CE 
       16.31        33.93        83.01        31.99        12.00        35.31 
TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F 
       37.45        35.67        33.11        31.73        10.72        12.72 
TCGA-A7-A13G TCGA-A7-A26F TCGA-A7-A425 TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE 
       23.61        24.26        14.70        13.74        14.50        21.17 
TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A6VV TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06Y 
       17.92        12.10        10.29         1.02        17.98        26.01 
TCGA-A8-A07F TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A08C 
       18.97         8.98         9.96         9.99        28.04        19.99 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08X 
       18.05        19.96        37.05        31.00         0.99        33.99 
TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09M 
       19.07        17.95        41.98         9.99        12.00        15.02 
TCGA-A8-A09Q TCGA-A8-A09X TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2FM TCGA-AC-A2QJ 
       25.02        14.01        10.85         2.66        26.04         2.27 
TCGA-AC-A3W5 TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A8OP TCGA-AN-A0FL TCGA-AN-A0FW 
        1.81         1.12         1.81         1.74         7.59         0.36 
TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AO-A03N TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J6 
        0.33         0.33        66.77        32.78        17.65        37.48 
TCGA-AO-A0JD TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
       72.00       102.58        99.25        77.56        64.04        57.30 
TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54O 
       48.36        61.87        70.39        15.62        13.22        21.86 
TCGA-AR-A0TR TCGA-AR-A1AI TCGA-AR-A1AR TCGA-AR-A1AV TCGA-AR-A24K TCGA-AR-A24Q 
        5.26        61.84        17.23        42.58        50.89        66.05 
TCGA-AR-A256 TCGA-AR-A2LO TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QP TCGA-B6-A0I2 
       93.83        20.81        20.38        54.74        20.45       143.38 
TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IM TCGA-B6-A0RE 
      149.59        12.13       112.37       176.98       126.12       211.56 
TCGA-B6-A0RI TCGA-B6-A0RV TCGA-B6-A0WV TCGA-B6-A0WZ TCGA-B6-A401 TCGA-B6-A402 
      234.28       157.41        79.63       129.57        85.35        54.28 
TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0BA TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BP 
       24.53        20.45        37.22        21.70        44.05        48.69 
TCGA-BH-A0BT TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0DL TCGA-BH-A0DO 
       45.57        49.05        44.02        45.83        48.23        17.26 
TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0E9 
       15.65         2.56        38.47         4.41         9.63        46.19 
TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0HQ TCGA-BH-A0RX TCGA-BH-A18K TCGA-BH-A18V 
       32.65        24.49        36.85         5.59        90.84        51.16 
TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1EX TCGA-BH-A1F6 TCGA-C8-A12Q TCGA-C8-A12V 
       69.93        91.99        49.58        97.48         0.07        12.66 
TCGA-C8-A134 TCGA-C8-A1HI TCGA-C8-A1HN TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z 
        0.69        11.34         3.25         0.36         0.43         8.28 
TCGA-C8-A273 TCGA-C8-A3M7 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1JF TCGA-D8-A1JG 
        9.67         0.03        21.14        14.17        12.03        12.03 
TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1XF TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y1 
       20.12        20.09        15.22        16.54        15.32         3.81 
TCGA-D8-A27K TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-E2-A107 TCGA-E2-A10B TCGA-E2-A10C 
        9.44        14.50        18.51        34.42        37.51        40.11 
TCGA-E2-A14P TCGA-E2-A14R TCGA-E2-A14T TCGA-E2-A14V TCGA-E2-A152 TCGA-E2-A153 
       40.96        38.60        33.30        34.26        27.12        23.24 
TCGA-E2-A154 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15G 
       19.43        25.05        23.34        17.29        20.71        18.21 
TCGA-E2-A15I TCGA-E2-A15R TCGA-E2-A1AZ TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1II 
       17.42        17.06        60.53        17.10        33.73        33.70 
TCGA-E2-A1L9 TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E9-A1N8 TCGA-E9-A1NC 
       19.66         7.20        18.05        22.26        12.00        39.55 
TCGA-E9-A1ND TCGA-E9-A1QZ TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A226 
       12.59        11.90        32.09        20.81        40.24        34.13 
TCGA-E9-A22E TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A295 TCGA-E9-A3X8 TCGA-EW-A1IY 
       12.89        27.22         0.95         0.72        15.72         8.48 
TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PA 
       28.77        22.82        52.96        23.11         7.86        18.90 
TCGA-EW-A1PB TCGA-EW-A423 TCGA-GI-A2C8 TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD 
       19.99        10.16         7.40        53.13        53.52        43.04 
TCGA-GM-A2DF TCGA-GM-A3XL TCGA-GM-A3XN TCGA-JL-A3YW TCGA-LL-A440 TCGA-LL-A441 
       42.71        69.30        53.95        11.84         0.66         2.99 
TCGA-LL-A5YM TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A740 TCGA-OL-A5D7 TCGA-OL-A5RV 
        4.70         2.63         3.88         4.50        46.55        24.10 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66K TCGA-OL-A66N 
       26.20        16.87        10.29        14.76        33.90        18.21 
TCGA-W8-A86G 
        5.29 

$`7Q GAIN WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SJ 
        8.52        14.37        43.43        14.27        47.24        13.68 
TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N 
       31.79         7.96        28.01        19.20        18.21       104.81 
TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V 
       18.02        41.95        82.16        73.84        22.06        63.12 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO 
       55.43        36.13       125.59        64.57        24.79       112.08 
TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU 
       92.48        88.60       107.93        75.55        75.25         5.19 
TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN 
       56.81        34.55        28.77        25.22       101.72        89.36 
TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET 
       80.28       107.61        79.76        74.40        37.05        35.05 
TCGA-A2-A0EU TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV 
       34.29        29.75        24.72        99.19        54.64        27.12 
TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T3 TCGA-A2-A0T4 
       50.43        44.28        17.52        17.13        18.71        20.52 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF 
       17.46        18.90        20.75        32.55        25.28        15.42 
TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT 
       21.67        14.50        19.33        14.63        31.73        23.77 
TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G1 TCGA-A2-A1G6 TCGA-A2-A259 
       17.36        36.79        22.45        19.20        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
      107.70        17.19        18.15        91.92        10.59        20.88 
TCGA-A2-A3KD TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       39.65        29.98        14.07        49.48        38.40        34.98 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 
       38.37         7.30         9.01         8.81         8.91         6.74 
TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A13H 
        3.42        38.30        34.29        35.47        30.61        29.56 
TCGA-A7-A26E TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD 
       31.36        23.74        23.80        21.73        20.61        22.32 
TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A426 
       11.34        10.59        10.29        11.28        13.41        11.97 
TCGA-A7-A4SA TCGA-A7-A56D TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A7-A6VX 
       14.93        14.73        10.72        11.05         9.37        10.42 
TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X 
        8.75        13.02        13.02        41.06        29.03        31.00 
TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E 
        1.02        17.03        53.98         9.01        33.01        19.99 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P 
       18.97        14.01        12.00        17.03         9.99        10.98 
TCGA-A8-A07S TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A 
        7.99        18.05        15.06        36.95        13.02         0.99 
TCGA-A8-A08B TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08S TCGA-A8-A08T 
       23.08        12.00         9.99        31.00        19.07        93.04 
TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09C TCGA-A8-A09D 
       40.01        16.01        12.00         9.99         1.02        13.02 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T 
       31.00        33.07        29.98         1.02         8.98        19.04 
TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 
       15.02         0.99        12.00        19.04        13.02        21.04 
TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E 
        0.99        13.02        17.03        38.04         0.95         2.37 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG 
        1.48        38.53        38.20        40.57        55.43        36.99 
TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3HN 
       38.79        50.70         1.02         0.92         0.99         0.69 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ 
       14.83         9.40         1.12         1.68         1.55         1.32 
TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AN-A03X 
        1.55         0.07         1.18         0.69         0.43         0.33 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C 
        0.33         0.23         0.33         0.62         2.96         1.78 
TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR 
        1.71         8.02         7.36         6.51         0.16         0.33 
TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK 
        0.33         0.33         6.44         4.64         7.96         7.00 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0FZ 
        7.17         6.28         6.02         0.33         0.33         0.33 
TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT 
        0.33        12.33         0.30         0.33         0.33         0.33 
TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03O 
        0.33         5.33         5.59        80.28        47.84        81.63 
TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J3 
       84.69        68.75        47.87        59.05        29.13        21.40 
TCGA-AO-A0J5 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB 
       24.16        20.32        22.36        53.03        21.53        50.70 
TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ 
       50.86        76.77        21.37        26.24        38.53        62.04 
TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A 
       55.33        71.80        93.70        94.59        96.10        90.58 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KS TCGA-AO-A1KT 
       41.62        28.37        14.73        82.62         0.53        17.79 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AQ-A7U7 
       24.79        26.93       130.09         5.65         2.56         9.99 
TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW 
       82.88        49.32        37.41        56.88        29.75        24.30 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 
       64.83        55.86        76.14        65.36        70.16        83.87 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL 
       76.18        55.36        75.55        52.77        51.25        48.82 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS 
       62.56        43.73        43.56        39.98        43.07        40.83 
TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L 
       46.32        35.24        36.26        20.22       109.58        73.02 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S 
       65.46        68.19        65.69         0.85        57.40        62.07 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
       53.26        53.36        54.18        50.96        48.16        51.75 
TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LE 
       56.15        45.17        40.64        39.85        34.82       128.65 
TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ 
       20.25        42.87         7.36        40.04        17.10        16.96 
TCGA-AR-A5QN TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC 
       16.04        10.59        77.62       220.90       129.57        50.70 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP 
       65.72       146.50        18.77        84.59       110.14       110.93 
TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN 
      140.88        68.45       189.01        81.17        78.02       172.96 
TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU 
      162.05       102.77       140.48       100.70        89.46       131.21 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0X0 
       97.48       188.68        17.98        21.47       113.79       129.70 
TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF 
      186.48        28.27        68.94        58.88        43.59       101.52 
TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C 
       73.51       139.17       170.17        49.94        82.88        55.00 
TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 
       38.79        25.55        28.50        46.95        40.83        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC 
       39.16        48.36        56.94        56.98        51.68        32.02 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ 
       18.21        25.71        24.85        61.68        35.67        27.19 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0C0 TCGA-BH-A0C3 
       53.69        53.95        49.94        11.67        41.75        48.13 
TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       42.90        31.17        23.44        38.01        22.13        13.91 
TCGA-BH-A0DQ TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 
        3.22        45.17        47.41        16.27        15.68        14.30 
TCGA-BH-A0E7 TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 
       44.81        31.00        24.43        30.35        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA 
       37.78        35.51        24.56        23.08        41.00        52.96 
TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HU 
       26.50        20.38         5.85         2.50        13.61        12.89 
TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 
       51.32        27.25        50.79        23.93        24.95        42.35 
TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J 
       44.81        23.05         8.81         2.01         7.23        20.12 
TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R 
       26.66        72.56        37.74        30.28        55.63        37.55 
TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU 
       66.05         7.36        51.39       113.82        82.85        42.28 
TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 
       12.00        55.69        17.69        25.81        31.53        89.16 
TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG 
       24.66       120.62       114.15        33.17        74.73       122.89 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR 
       36.92        63.35        55.00        45.63        72.07       144.59 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 
       72.07         6.90         0.72        38.60        83.31        57.83 
TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
      130.16        10.65         6.44        20.12         0.99       109.28 
TCGA-BH-A42V TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P 
        8.94        11.93        11.77        11.77        12.66        11.77 
TCGA-C8-A12U TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 
       12.66        12.66        12.66         3.12         1.78         1.45 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG 
        0.62         3.85         3.75        12.33        10.92        11.34 
TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A26V TCGA-C8-A26W 
        0.16        12.03        10.42         2.30         0.30         0.23 
TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M8 
        0.03         0.03         0.03        12.20         0.99         0.23 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 
       11.90        20.88        13.25        20.58        13.97        14.17 
TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC 
       13.48        19.20        17.49        16.50        18.71        15.78 
TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JM 
       18.15        18.90        14.01        18.97        20.09        19.40 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 
       20.38        21.01        12.20        13.32        14.70        18.58 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB 
       17.79        16.73        25.74        23.90        27.58        18.15 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL 
        2.66        17.16        14.73        21.83        14.50        19.92 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT 
       17.69         7.96        16.41        15.85        16.31         6.35 
TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A1Y3 
       12.99        15.16        12.66        15.52        14.24        14.14 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27L 
       17.42        16.04        13.45        13.05        14.43        16.41 
TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V 
       13.48         4.80         0.76        10.09        13.08        12.53 
TCGA-D8-A27W TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A 
       12.26         7.33        43.00        27.52        46.59        40.41 
TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14S 
       28.44        28.87        47.15        44.68        38.24        33.17 
TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 
       43.33        32.02        31.96        28.60        17.03        25.41 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15C TCGA-E2-A15F TCGA-E2-A15H 
       21.04        23.87        14.79        22.82        21.63        12.92 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P 
       19.40         9.04        20.58         7.73        13.02        19.56 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       14.07        14.99        53.62        53.03        29.95        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IJ 
       28.50        16.47        38.30        37.41        32.78        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       22.65         3.88        22.19        20.98        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG 
       27.42        39.62        24.59        40.47        28.90        18.87 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 
      106.75       102.61         8.75        43.04        16.93         5.52 
TCGA-E2-A3DX TCGA-E2-A574 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 
       15.72        19.89        19.20        36.82        13.48        13.12 
TCGA-E9-A1NA TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1R0 
       36.56        35.77        20.05        21.57         9.86        14.30 
TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 
        0.62         2.10         6.12         1.38         2.76        21.21 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI 
        0.66        34.65         6.58        21.27        34.59        35.64 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22G 
        0.79        12.53        13.32        39.09        22.75        23.51 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A248 TCGA-E9-A24A 
       24.10        17.06         0.69         0.85         1.94        12.56 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54Y 
       17.75         0.76        26.07        18.41         0.62         0.23 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
        0.39         0.26         0.23        15.39        12.20        39.72 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV 
       18.21        18.90        13.25        16.57        15.68        25.94 
TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 
       29.95        29.85        40.41        41.13        39.78        29.82 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
       18.48        30.08         6.15        13.94        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW 
       34.55        19.96        55.00        52.73        25.91        22.09 
TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       21.27        17.49        10.59       109.87        59.57       194.27 
TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       42.28        61.91        62.33        90.84        76.64        77.33 
TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A4E0 TCGA-GM-A5PV 
       53.36       110.50        38.20        32.28        57.63        13.55 
TCGA-GM-A5PX TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A442 
       18.12        11.57         8.28         6.67         4.60         3.58 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A73Y 
        6.90         5.56         3.65         3.19         3.25         4.14 
TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-MS-A51U 
        4.50         5.59         3.22         6.21        15.91         2.79 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RY 
        2.10        12.66         7.53        44.61        27.65        14.10 
TCGA-OL-A5S0 TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P 
        9.80        23.70        54.51        31.07         7.23         4.44 
TCGA-S3-A6ZG 
        6.81 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.03              0.03 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           234.28            220.90 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            21.14             21.57 
[1] "0.0 - 234.3 (21.1)" "0.0 - 220.9 (21.6)"
[1] "hr=" "1.1"
D14V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7Q GAIN MUTATED        14       18        3        1        91        49
  7Q GAIN WILD-TYPE      66       59        6        8       244       175
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7Q GAIN MUTATED           0         29          8         18        5
  7Q GAIN WILD-TYPE         2        109         19         41       12
                   vv
clus                STAGE TIS STAGE X
  7Q GAIN MUTATED           0       2
  7Q GAIN WILD-TYPE         1      14
D14V3, multiclass
            clus
vv           7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                 14                66
  STAGE IA                18                59
  STAGE IB                 3                 6
  STAGE II                 1                 8
  STAGE IIA               91               244
  STAGE IIB               49               175
  STAGE III                0                 2
  STAGE IIIA              29               109
  STAGE IIIB               8                19
  STAGE IIIC              18                41
  STAGE IV                 5                12
  STAGE TIS                0                 1
  STAGE X                  2                14
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  7Q GAIN MUTATED    59 141  26  12
  7Q GAIN WILD-TYPE 199 440  91  24
D14V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1              59               199
  T2             141               440
  T3              26                91
  T4              12                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                 N0  N1  N2  N3
  7Q GAIN MUTATED   116  73  24  20
  7Q GAIN WILD-TYPE 352 257  87  50
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0             116               352
  N1              73               257
  N2              24                87
  N3              20                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  7Q GAIN MUTATED          0 198   5  36
  7Q GAIN WILD-TYPE        2 647  12  95
D14V6, multiclass
          clus
vv         7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CM0 (I+)               0                 2
  M0                   198               647
  M1                     5                12
  MX                    36                95
[1] 4 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   235   4
  7Q GAIN WILD-TYPE 749   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    235    4
  7Q GAIN WILD-TYPE  749    7
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE             235               749
  MALE                 4                 7
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  7Q GAIN MUTATED                            1                           189
  7Q GAIN WILD-TYPE                          0                           546
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  7Q GAIN MUTATED                               30                   1
  7Q GAIN WILD-TYPE                            136                   4
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  7Q GAIN MUTATED                                  6                  2
  7Q GAIN WILD-TYPE                               23                 12
                   vv
clus                OTHER  SPECIFY
  7Q GAIN MUTATED               10
  7Q GAIN WILD-TYPE             34
D14V8, multiclass
                                  clus
vv                                 7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                189               546
  INFILTRATING LOBULAR CARCINOMA                30               136
  MEDULLARY CARCINOMA                            1                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               6                23
  MUCINOUS CARCINOMA                             2                12
  OTHER  SPECIFY                                10                34
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V9, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    67 172
  7Q GAIN WILD-TYPE 215 541
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     67  172
  7Q GAIN WILD-TYPE  215  541
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO               67               215
  YES             172               541
[1] 2 2
[1] FALSE
D14V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q GAIN MUTATED                                  0    14
  7Q GAIN WILD-TYPE                                1    42
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED                          41   159
  7Q GAIN WILD-TYPE                        96   549
D14V11, multiclass
                                  clus
vv                                 7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         14                42
  BLACK OR AFRICAN AMERICAN                     41                96
  WHITE                                        159               549
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V12, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     7 187
  7Q GAIN WILD-TYPE  29 609
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      7  187
  7Q GAIN WILD-TYPE   29  609
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                29
  NOT HISPANIC OR LATINO             187               609
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED   234  31
  8P GAIN WILD-TYPE 626  83
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              265               709 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               31                83 
$`8P GAIN MUTATED`
TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SJ TCGA-A2-A04N TCGA-A2-A04R TCGA-A2-A0CM 
       43.43        14.27        13.68       104.81        82.16        24.79 
TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0D3 
       75.25        63.45        56.81        21.14        33.76        28.77 
TCGA-A2-A0EO TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0T2 
       80.28        79.76        74.40        27.12        44.88         8.38 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YE TCGA-A2-A0YJ TCGA-A2-A1G0 
       17.46        18.90        20.75        18.21        18.61        20.25 
TCGA-A2-A1G1 TCGA-A2-A259 TCGA-A2-A3XS TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 
       19.20        52.47        33.93        38.40        34.98        38.37 
TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A0DA 
        9.01        12.00         6.74        38.30        30.61        35.67 
TCGA-A7-A13F TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A3J0 
       12.72        24.26        23.74        23.80        21.73        10.29 
TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SD TCGA-A7-A5ZW TCGA-A7-A6VV TCGA-A7-A6VX 
       11.97        14.93        14.50        10.72        10.29        10.42 
TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 
        8.75        13.02        26.01         1.02        53.98         9.01 
TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A082 TCGA-A8-A086 TCGA-A8-A08C TCGA-A8-A08R 
       33.01        18.97        18.05        13.02        19.99         0.99 
TCGA-A8-A08T TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C 
       93.04        16.01        17.95         9.99        12.00         1.02 
TCGA-A8-A09E TCGA-A8-A09M TCGA-A8-A09X TCGA-A8-A0A2 TCGA-A8-A0A9 TCGA-A8-A0AB 
       31.00        15.02        14.01        19.04        13.02        17.03 
TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2BM TCGA-AC-A2FM TCGA-AC-A2QJ TCGA-AC-A3YI 
        2.37        10.85        38.20        26.04         2.27         1.55 
TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IW TCGA-AN-A03X TCGA-AN-A0AJ TCGA-AN-A0FK 
        0.07         1.12         0.69         0.33         8.02         7.00 
TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AO-A03R TCGA-AO-A03T 
        6.02         0.36         0.33         0.33        68.75        47.87 
TCGA-AO-A0J7 TCGA-AO-A0JI TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12F 
       20.32        38.53        96.10        77.56        57.30        48.36 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O 
       82.62        61.87         0.53        13.22         2.56        21.86 
TCGA-AR-A0U0 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AQ TCGA-AR-A1AY 
       65.36        55.36        75.55        61.84        43.07        20.22 
TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24W TCGA-AR-A251 TCGA-AR-A254 
       66.05        57.40        62.07        50.96        45.17        39.85 
TCGA-AR-A255 TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LR TCGA-AR-A5QN 
       34.82        20.25        42.87         7.36        20.38        16.04 
TCGA-AR-A5QP TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IH TCGA-B6-A0RE 
       20.45       149.59       220.90       129.57       112.37       211.56 
TCGA-B6-A0RH TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RP TCGA-B6-A0RV TCGA-B6-A0WX 
      189.01        81.17        78.02       102.77       157.41        21.47 
TCGA-B6-A0X1 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 
      186.48        43.59       101.52       170.17        85.35        54.28 
TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0BA TCGA-BH-A0BD 
       24.53        20.45        39.55        39.16        37.22        18.21 
TCGA-BH-A0BG TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT 
       24.85        49.05        44.02        15.65         2.56        38.47 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 
       15.68        14.30        44.81        30.35        10.78        15.16 
TCGA-BH-A0H6 TCGA-BH-A0HB TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0RX TCGA-BH-A0W5 
       24.56        26.50        36.85        12.89         5.59        42.35 
TCGA-BH-A0W7 TCGA-BH-A18L TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1EU TCGA-BH-A1EV 
       44.81        26.66        91.99       113.82        42.28        12.00 
TCGA-BH-A1EX TCGA-BH-A1F5 TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FM 
       49.58        89.16       114.15        74.73       122.89        45.63 
TCGA-BH-A202 TCGA-BH-A204 TCGA-C8-A12O TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W 
        0.72        83.31        12.66        12.66        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A135 TCGA-C8-A26X TCGA-C8-A273 TCGA-C8-A275 
       12.66         3.12         0.62         0.36         9.67         0.03 
TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JP TCGA-D8-A1JU 
       20.58        13.97        12.03        14.01        21.01        14.70 
TCGA-D8-A1X6 TCGA-D8-A1XB TCGA-D8-A1XF TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XU 
       17.79        18.15        15.22        14.50        19.92        12.99 
TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27I 
       12.66        16.54        15.32         3.81        14.14        14.43 
TCGA-D8-A27V TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A14O TCGA-E2-A14U TCGA-E2-A14Y 
       12.53        34.42        46.59        44.68        43.33        28.60 
TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15D TCGA-E2-A15F 
       27.12        19.43        14.79        25.05        17.29        21.63 
TCGA-E2-A15S TCGA-E2-A1AZ TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IN TCGA-E2-A2P5 
       14.07        60.53        28.50        17.10        22.19        16.93 
TCGA-E2-A573 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1NE TCGA-E9-A1R2 TCGA-E9-A1R3 
       22.26        36.82        13.48        35.77         0.62         2.10 
TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A228 TCGA-E9-A22G 
        2.76        32.09        20.81        40.24        12.53        23.51 
TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A3X8 TCGA-E9-A5FK 
       17.06        27.22         0.72        17.75        15.72         0.39 
TCGA-EW-A1IY TCGA-EW-A1J1 TCGA-EW-A1J6 TCGA-EW-A1P0 TCGA-EW-A1P3 TCGA-EW-A1P5 
        8.48        18.90        28.77        41.13        52.96        23.11 
TCGA-EW-A1P6 TCGA-EW-A1PB TCGA-EW-A1PC TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF 
       18.48        19.99         6.15        53.52        43.04        42.71 
TCGA-GM-A2DO TCGA-LL-A5YO TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ 
       53.36         3.19         4.14         4.50         4.50         5.59 
TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A66I TCGA-OL-A66N TCGA-S3-A6ZG 
       46.55         7.53        44.61        23.70        18.21         6.81 
TCGA-W8-A86G 
        5.29 

$`8P GAIN WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SF TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK 
        8.52        14.37        48.10        47.24        20.88        31.79 
TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04P 
        7.96        39.32        28.01        19.20        18.21        18.02 
TCGA-A2-A04Q TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X 
       41.95        73.84        22.06        63.12        64.04        55.43 
TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
       36.13       125.59        64.57       112.08        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0D1 TCGA-A2-A0D4 
      107.93        75.55         5.19        64.04        34.55        25.22 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU 
      101.72        89.36       107.61        37.05        35.05        34.29 
TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU 
       31.82        29.75        24.72        24.16        99.19        54.64 
TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T3 TCGA-A2-A0T4 
       50.43        44.28        17.52        17.13        18.71        20.52 
TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI 
       32.55        25.28        15.42        21.90        21.67        14.50 
TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW 
       19.33        14.63        31.73        23.77        23.47        17.36 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A25A TCGA-A2-A25B 
       36.79        22.45        19.56        16.47       107.70        16.31 
TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD 
       17.19        18.15        91.92        10.59        20.88        39.65 
TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XZ TCGA-A2-A4RW 
       83.01        29.98        14.07        49.48        31.99         7.30 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH 
        8.81         8.91         3.42        35.31        34.29        35.47 
TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H 
       37.45        33.11        31.73        10.72        23.61        29.56 
TCGA-A7-A26E TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J1 
       31.36        20.61        22.32        11.34        10.59        11.28 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D 
       13.41        14.70        13.74        21.17        17.92        14.73 
TCGA-A7-A5ZV TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A06R 
       12.10        11.05         9.37        13.02         1.02        17.98 
TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A07E TCGA-A8-A07G 
       41.06        29.03        31.00        17.03        19.99        18.97 
TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R 
       14.01        12.00        17.03         9.99        10.98         8.98 
TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A085 
        7.99         9.96         9.99        28.04        15.06        36.95 
TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J 
        0.99        23.08        18.05        19.96        12.00        37.05 
TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08X TCGA-A8-A08Z 
        9.99        31.00        31.00        19.07        33.99        40.01 
TCGA-A8-A091 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09D TCGA-A8-A09I 
       19.07        41.98        12.00         9.99        13.02        33.07 
TCGA-A8-A09K TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       29.98         1.02        25.02         8.98        19.04        15.02 
TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0AD 
        0.99        12.00        13.02        21.04         0.99        38.04 
TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2FB TCGA-AC-A2FF 
        0.95         2.66         1.48        38.53        40.57        55.43 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3BB 
       36.99        38.79        50.70         1.02         0.92         0.99 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 
        0.69        14.83         9.40         1.12         1.81         1.68 
TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A8OP 
        1.32         1.55         1.81         1.18         0.43         1.74 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C 
        0.33         0.23         0.33         0.62         2.96         1.78 
TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS 
        1.71         7.36         6.51         0.16         0.33         0.33 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FN 
        0.33         6.44         4.64         7.96         7.59         7.17 
TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO 
        6.28         0.33         0.33         0.33         0.33        12.33 
TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV 
        0.30         0.33         0.33         0.33         0.33         5.33 
TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P 
        5.59        80.28        47.84        66.77        81.63        84.69 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 
       59.05        29.13        32.78        21.40        17.65        24.16 
TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC 
       37.48        22.36        53.03        21.53        50.70        50.86 
TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A0JL 
       72.00        76.77        21.37        26.24        62.04        55.33 
TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A 
       71.80       102.58        99.25        93.70        94.59        90.58 
TCGA-AO-A12D TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KR TCGA-AO-A1KT 
       64.04        41.62        28.37        14.73        70.39        17.79 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A7U7 
       24.79        26.93       130.09         5.65        15.62         9.99 
TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV 
       82.88        49.32         5.26        37.41        56.88        29.75 
TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 
       24.30        64.83        55.86        76.14        70.16        83.87 
TCGA-AR-A0U3 TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
       76.18        52.77        51.25        48.82        62.56        43.73 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
       43.56        39.98        17.23        40.83        46.32        42.58 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M 
       35.24        36.26       109.58        50.89        73.02        65.46 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V 
       68.19        65.69         0.85        53.26        53.36        54.18 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A256 TCGA-AR-A2LE 
       48.16        51.75        56.15        40.64        93.83       128.65 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QQ 
       40.04        17.10        20.81        16.96        54.74        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I9 TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG 
       77.62       143.38        12.13        50.70        65.72       146.50 
TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP 
      176.98        18.77       126.12        84.59       110.14       110.93 
TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RI TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ 
      140.88        68.45       234.28       172.96       162.05       140.48 
TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV 
      100.70        89.46       131.21        97.48       188.68        79.63 
TCGA-B6-A0WW TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 
       17.98       113.79       129.57       129.70        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C 
       58.88        73.51       139.17        49.94        82.88        55.00 
TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B5 
       38.79        25.55        28.50        46.95        40.83        48.36 
TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BF TCGA-BH-A0BJ 
       56.94        56.98        51.68        32.02        25.71        21.70 
TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR 
       44.05        61.68        35.67        48.69        27.19        53.69 
TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0C0 TCGA-BH-A0C3 
       53.95        45.57        49.94        11.67        41.75        48.13 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI 
       42.90        45.83        31.17        23.44        38.01        22.13 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DQ TCGA-BH-A0DV TCGA-BH-A0DX 
       13.91        48.23        17.26         3.22        45.17        47.41 
TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB 
       16.27         4.41         9.63        46.19        32.65        24.49 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H7 TCGA-BH-A0H9 
       31.00        24.43        37.78        35.51        23.08        41.00 
TCGA-BH-A0HA TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HW 
       52.96        20.38         5.85         2.50        13.61        51.32 
TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0WA TCGA-BH-A18F 
       27.25        50.79        23.93        24.95        23.05         8.81 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18N 
        2.01         7.23        20.12        90.84        72.56        37.74 
TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U 
       30.28        55.63        37.55        66.05         7.36        51.39 
TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1ET TCGA-BH-A1EW TCGA-BH-A1EY TCGA-BH-A1F0 
       51.16        69.93        82.85        55.69        17.69        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FH 
       31.53        97.48        24.66       120.62        33.17        36.92 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 
       63.35        55.00        72.07       144.59        72.07         6.90 
TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
       38.60        57.83       130.16        10.65         6.44        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N 
        0.99       109.28         8.94        11.93        11.77        11.77 
TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 
       11.77         0.07         1.78         1.45         0.69         3.85 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ 
        3.75        12.33        10.92        11.34        11.34         0.16 
TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W 
       12.03        10.42         2.30         3.25         0.30         0.23 
TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A274 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B 
        0.43         8.28         0.03         0.03        12.20         0.99 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A143 
        0.03         0.23        11.90        20.88        13.25        14.17 
TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA 
       13.48        21.14        19.20        14.17        17.49        16.50 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JI 
       18.71        15.78        18.15        18.90        12.03        18.97 
TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JS 
       20.09        20.12        20.09        19.40        20.38        12.20 
TCGA-D8-A1JT TCGA-D8-A1X5 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA 
       13.32        18.58        16.73        25.74        23.90        27.58 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XM TCGA-D8-A1XO 
        2.66        17.16        14.73        21.83        17.69         7.96 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1Y0 
       16.41        15.85        16.31         6.35        15.16        15.52 
TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27K 
       14.24        17.42        16.04        13.45        13.05         9.44 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T 
       16.41        13.48         4.80         0.76        10.09        13.08 
TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A108 
       12.26        14.50        18.51         7.33        43.00        27.52 
TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N 
       40.41        37.51        40.11        28.44        28.87        47.15 
TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14V 
       40.96        38.24        38.60        33.17        33.30        34.26 
TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A155 
       32.02        31.96        17.03        25.41        23.24        21.04 
TCGA-E2-A156 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15H 
       23.87        23.34        22.82        20.71        18.21        12.92 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O 
       17.42        19.40         9.04        20.58         7.73        13.02 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 
       19.56        17.06        14.99        53.62        53.03        29.95 
TCGA-E2-A1B5 TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       32.35        16.47        38.30        37.41        32.78        33.73 
TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IO TCGA-E2-A1IU 
       33.70        28.44        22.65         3.88        20.98        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB 
       54.18        27.42        39.62        19.66        24.59        40.47 
TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL 
       28.90        18.87       106.75       102.61         8.75        43.04 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A574 TCGA-E9-A1N4 
        5.52        15.72         7.20        18.05        19.89        19.20 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NF 
       12.00        13.12        36.56        39.55        12.59        20.05 
TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R4 TCGA-E9-A1R5 
       21.57         9.86        11.90        14.30         6.12         1.38 
TCGA-E9-A1R7 TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH 
       21.21         0.66        34.65         6.58        21.27        34.59 
TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       35.64        34.13         0.79        13.32        39.09        22.75 
TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A248 TCGA-E9-A249 
       12.89        24.10         0.69         0.85         1.94         0.95 
TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54Y 
       12.56         0.76        26.07        18.41         0.62         0.23 
TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ 
        0.26         0.23        15.39        12.20        39.72        18.21 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX 
       13.25        16.57        15.68        25.94        22.82        29.95 
TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P7 TCGA-EW-A1P8 
       29.85        40.41        39.78        29.82        30.08         7.86 
TCGA-EW-A1PA TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH 
       18.90        13.94        10.52        14.43        34.55        19.96 
TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 
       55.00        52.73        25.91        22.09        21.27        17.49 
TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       10.16        10.59         7.40       109.87        59.57       194.27 
TCGA-GM-A2DB TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       53.13        42.28        61.91        62.33        90.84        76.64 
TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN 
       77.33       110.50        38.20        32.28        69.30        53.95 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U 
       57.63        13.55        18.12        11.84        11.57         8.28 
TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y 
        6.67         4.60         0.66         2.99         3.58         6.90 
TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A6FR 
        5.56         4.70         3.65         3.25         2.63         3.88 
TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
        3.22         6.21        15.91         2.79         2.10        12.66 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       27.65        24.10        26.20        16.87        14.10        10.29 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66O 
        9.80        14.76        54.51        33.90        31.07         7.23 
TCGA-OL-A66P 
        4.44 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.03              0.03 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           220.90            234.28 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            20.58             21.83 
[1] "0.0 - 220.9 (20.6)" "0.0 - 234.3 (21.8)"
[1] "hr=" "1.1"
D15V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8P GAIN MUTATED        21       20        2        3        93        62
  8P GAIN WILD-TYPE      59       57        7        6       242       162
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8P GAIN MUTATED           2         33          8         13        8
  8P GAIN WILD-TYPE         0        105         19         46        9
                   vv
clus                STAGE TIS STAGE X
  8P GAIN MUTATED           0       5
  8P GAIN WILD-TYPE         1      11
D15V3, multiclass
            clus
vv           8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 21                59
  STAGE IA                20                57
  STAGE IB                 2                 7
  STAGE II                 3                 6
  STAGE IIA               93               242
  STAGE IIB               62               162
  STAGE III                2                 0
  STAGE IIIA              33               105
  STAGE IIIB               8                19
  STAGE IIIC              13                46
  STAGE IV                 8                 9
  STAGE TIS                0                 1
  STAGE X                  5                11
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  8P GAIN MUTATED    73 153  34   8
  8P GAIN WILD-TYPE 185 428  83  28
D15V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1              73               185
  T2             153               428
  T3              34                83
  T4               8                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                 N0  N1  N2  N3
  8P GAIN MUTATED   125  96  27  17
  8P GAIN WILD-TYPE 343 234  84  53
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0             125               343
  N1              96               234
  N2              27                84
  N3              17                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  8P GAIN MUTATED          0 229   8  33
  8P GAIN WILD-TYPE        2 616   9  98
D15V6, multiclass
          clus
vv         8P GAIN MUTATED 8P GAIN WILD-TYPE
  CM0 (I+)               0                 2
  M0                   229               616
  M1                     8                 9
  MX                    33                98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED   266   4
  8P GAIN WILD-TYPE 718   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED    266    4
  8P GAIN WILD-TYPE  718    7
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE             266               718
  MALE                 4                 7
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  8P GAIN MUTATED                            0                           212
  8P GAIN WILD-TYPE                          1                           523
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  8P GAIN MUTATED                               34                   2
  8P GAIN WILD-TYPE                            132                   3
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  8P GAIN MUTATED                                  7                  3
  8P GAIN WILD-TYPE                               22                 11
                   vv
clus                OTHER  SPECIFY
  8P GAIN MUTATED               12
  8P GAIN WILD-TYPE             32
D15V8, multiclass
                                  clus
vv                                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                212               523
  INFILTRATING LOBULAR CARCINOMA                34               132
  MEDULLARY CARCINOMA                            2                 3
  MIXED HISTOLOGY (PLEASE SPECIFY)               7                22
  MUCINOUS CARCINOMA                             3                11
  OTHER  SPECIFY                                12                32
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V9, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    77 193
  8P GAIN WILD-TYPE 205 520
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     77  193
  8P GAIN WILD-TYPE  205  520
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO               77               205
  YES             193               520
[1] 2 2
[1] FALSE
D15V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P GAIN MUTATED                                  0    13
  8P GAIN WILD-TYPE                                1    43
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED                          47   184
  8P GAIN WILD-TYPE                        90   524
D15V11, multiclass
                                  clus
vv                                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         13                43
  BLACK OR AFRICAN AMERICAN                     47                90
  WHITE                                        184               524
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V12, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     9 211
  8P GAIN WILD-TYPE  27 585
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      9  211
  8P GAIN WILD-TYPE   27  585
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   9                27
  NOT HISPANIC OR LATINO             211               585
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED   425  58
  8Q GAIN WILD-TYPE 435  56
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              483               491 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               58                56 
$`8Q GAIN MUTATED`
TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SJ TCGA-A1-A0SK 
       14.37        43.43        48.10        14.27        13.68        31.79 
TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04Y 
       39.32        19.20       104.81        41.95        82.16        36.13 
TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CP TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CX 
       64.57        24.79        92.48        75.25        63.45        56.81 
TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EO 
       21.14        34.55        33.76        28.77        25.22        80.28 
TCGA-A2-A0EQ TCGA-A2-A0EU TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0SV TCGA-A2-A0SW 
       79.76        34.29        24.72        24.16        27.12        44.88 
TCGA-A2-A0SX TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T5 
       50.43        17.52        17.13         8.38        18.71        17.46 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YJ 
       18.90        20.75        18.21        21.90        21.67        18.61 
TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1G0 
       31.73        23.77        23.47        17.36        36.79        20.25 
TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25D TCGA-A2-A25E 
       19.20        19.56        52.47        16.31        18.15        91.92 
TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 
       39.65        33.93        29.98        38.40        34.98        38.37 
TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CJ 
        9.01        12.00         6.74         3.42        38.30        30.61 
TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H 
       35.67        31.73        12.72        24.26        23.74        23.80 
TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3J0 TCGA-A7-A426 TCGA-A7-A4SA 
       21.73        20.61        22.32        10.29        11.97        14.93 
TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VV TCGA-A7-A6VX 
       14.50        21.17        12.10        10.72        10.29        10.42 
TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06Y 
        8.75        13.02        13.02        17.98        41.06        26.01 
TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07F 
        1.02        17.03        53.98         9.01        33.01        18.97 
TCGA-A8-A07I TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A07W 
       14.01         9.99        10.98         8.98         9.96         9.99 
TCGA-A8-A082 TCGA-A8-A086 TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I 
       18.05        13.02        19.99        18.05        19.96        12.00 
TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X 
       37.05        31.00         0.99        19.07        93.04        33.99 
TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C 
       19.07        16.01        17.95         9.99        12.00         1.02 
TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R 
       31.00        29.98        15.02         1.02        25.02         8.98 
TCGA-A8-A09T TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A2 TCGA-A8-A0A7 TCGA-A8-A0A9 
       19.04         0.99        14.01        19.04         0.99        13.02 
TCGA-A8-A0AB TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2BK TCGA-AC-A2BM 
       17.03         2.37        10.85         2.66        38.53        38.20 
TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A3YI TCGA-AC-A62V TCGA-AC-A62X 
       26.04         1.02         2.27         1.55         0.07         1.12 
TCGA-AC-A6IW TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A049 TCGA-AN-A04C 
        0.69         1.74         0.33         0.33         0.62         1.78 
TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FK TCGA-AN-A0FL 
        1.71         8.02         0.16         0.33         7.00         7.59 
TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL 
        6.02         0.36         0.33         0.33         0.33         0.33 
TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XS TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T 
        0.33        12.33         0.33        81.63        68.75        47.87 
TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J7 TCGA-AO-A0JI 
       29.13        21.40        17.65        24.16        20.32        38.53 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F 
       94.59        96.10        77.56        64.04        57.30        48.36 
TCGA-AO-A12G TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT 
       41.62        82.62        61.87        70.39         0.53        17.79 
TCGA-AQ-A04H TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O 
       24.79       130.09        15.62        13.22         2.56        21.86 
TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0U0 
       82.88        49.32        37.41        56.88        24.30        65.36 
TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AP TCGA-AR-A1AQ 
       55.36        61.84        52.77        51.25        39.98        43.07 
TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24Q TCGA-AR-A24R 
       46.32        35.24        36.26        20.22        66.05        57.40 
TCGA-AR-A24S TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24Z TCGA-AR-A251 
       62.07        53.36        54.18        50.96        51.75        45.17 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LL 
       39.85        34.82        93.83        20.25        42.87         7.36 
TCGA-AR-A2LO TCGA-AR-A2LR TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       20.81        20.38        16.04        20.45        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IH TCGA-B6-A0IM 
      143.38       149.59       220.90       129.57       112.37       126.12 
TCGA-B6-A0IN TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RP 
       84.59       211.56       189.01        81.17        78.02       102.77 
TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0X1 
      131.21       157.41        17.98        21.47       113.79       186.48 
TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 
       58.88        43.59       101.52       170.17        85.35        54.28 
TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0B2 TCGA-BH-A0B3 
       24.53        38.79        20.45        25.55        40.83        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0BA TCGA-BH-A0BD TCGA-BH-A0BG TCGA-BH-A0BL 
       39.16        56.94        37.22        18.21        24.85        44.05 
TCGA-BH-A0BP TCGA-BH-A0BT TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0DD 
       48.69        45.57        49.05        41.75        44.02        45.83 
TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DZ TCGA-BH-A0E1 
       48.23        15.65         2.56        38.47        16.27        15.68 
TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H6 TCGA-BH-A0H7 
       14.30        44.81        10.78        15.16        24.56        23.08 
TCGA-BH-A0HB TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX 
       26.50        36.85        12.89        27.25        50.79         5.59 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18I TCGA-BH-A18L TCGA-BH-A18N 
       42.35        44.81        23.05         7.23        26.66        37.74 
TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1EU TCGA-BH-A1EV 
       51.39        51.16        91.99       113.82        42.28        12.00 
TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1FB 
       55.69        49.58        31.53        89.16        97.48       120.62 
TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FM TCGA-BH-A1FU TCGA-BH-A202 
      114.15        74.73       122.89        45.63        72.07         0.72 
TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A42V TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O 
       83.31       130.16         8.94        11.77        11.77        12.66 
TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A131 
       12.66        12.66        12.66        12.66         3.12         1.78 
TCGA-C8-A135 TCGA-C8-A1HG TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26X 
        0.62        11.34        12.03         2.30         3.25         0.36 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A27A TCGA-D8-A141 TCGA-D8-A142 
        8.28         9.67         0.03        12.20        20.58        13.97 
TCGA-D8-A143 TCGA-D8-A147 TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JF TCGA-D8-A1JG 
       14.17        19.20        15.78        18.15        12.03        12.03 
TCGA-D8-A1JH TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JP TCGA-D8-A1JT 
       14.01        20.09        20.12        20.09        21.01        13.32 
TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1XB TCGA-D8-A1XF TCGA-D8-A1XK 
       14.70        18.58        17.79        18.15        15.22        14.50 
TCGA-D8-A1XL TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XY 
       19.92        16.41        16.31        12.99        12.66        16.54 
TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27H 
       15.32        15.52         3.81        14.24        14.14        13.05 
TCGA-D8-A27I TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27R TCGA-D8-A27V TCGA-E2-A107 
       14.43        16.41        13.48        10.09        12.53        34.42 
TCGA-E2-A108 TCGA-E2-A10C TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14R TCGA-E2-A14S 
       27.52        40.11        47.15        44.68        38.60        33.17 
TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A152 
       33.30        43.33        31.96        28.60        17.03        27.12 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C 
       23.24        19.43        14.79        25.05        23.34        22.82 
TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15J TCGA-E2-A15M TCGA-E2-A15O 
       17.29        20.71        21.63        19.40         7.73        13.02 
TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B5 
       17.06        14.07        14.99        60.53        53.62        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1II TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1L7 
       28.50        17.10        33.70        22.19        20.98        27.42 
TCGA-E2-A1LA TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A56Z 
       24.59       106.75       102.61         8.75        16.93         7.20 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NE 
       22.26        19.89        36.82        13.48        13.12        35.77 
TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R6 TCGA-E9-A1RA 
       20.05         9.86         0.62         2.10         2.76        32.09 
TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A22A TCGA-E9-A22B 
       20.81        40.24        34.65        21.27        39.09        22.75 
TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A295 
       12.89        23.51        17.06        27.22         1.94         0.72 
TCGA-E9-A2JS TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FK TCGA-EW-A1IY 
       17.75         0.62        15.72         0.23         0.39         8.48 
TCGA-EW-A1J1 TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 
       18.90        28.77        22.82        29.85        40.41        41.13 
TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A1PC 
       52.96        23.11        18.48         7.86        19.99         6.15 
TCGA-EW-A1PD TCGA-EW-A1PH TCGA-EW-A2FV TCGA-GI-A2C9 TCGA-GM-A2DC TCGA-GM-A2DD 
       13.94        19.96        25.91       109.87        53.52        43.04 
TCGA-GM-A2DF TCGA-GM-A2DO TCGA-GM-A3XL TCGA-GM-A5PV TCGA-JL-A3YW TCGA-LL-A5YM 
       42.71        53.36        69.30        13.55        11.84         4.70 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 
        3.65         3.19         3.88         4.14         4.50         4.50 
TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A66I 
        5.59         3.22        46.55         7.53        44.61        23.70 
TCGA-OL-A66N TCGA-S3-A6ZG TCGA-W8-A86G 
       18.21         6.81         5.29 

$`8Q GAIN WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SQ 
        8.52        47.24        20.88         7.96        28.01        18.21 
TCGA-A2-A04P TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X 
       18.02        73.84        22.06        63.12        64.04        55.43 
TCGA-A2-A0CK TCGA-A2-A0CO TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CU 
      125.59       112.08        88.60       107.93        75.55         5.19 
TCGA-A2-A0CW TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES 
       64.04       101.72        89.36       107.61        74.40        37.05 
TCGA-A2-A0ET TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SY 
       35.05        31.82        29.75        99.19        54.64        44.28 
TCGA-A2-A0T4 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YI TCGA-A2-A0YK 
       20.52        32.55        25.28        15.42        14.50        19.33 
TCGA-A2-A0YL TCGA-A2-A1FZ TCGA-A2-A1G6 TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A25F 
       14.63        22.45        16.47       107.70        17.19        10.59 
TCGA-A2-A3KC TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XZ TCGA-A2-A4RW 
       20.88        83.01        14.07        49.48        31.99         7.30 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 
        8.81         8.91        35.31        34.29        35.47        37.45 
TCGA-A7-A0DB TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A3IY 
       33.11        10.72        23.61        29.56        31.36        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SB TCGA-A7-A4SF 
       10.59        11.28        13.41        14.70        13.74        17.92 
TCGA-A7-A56D TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A8-A06Q TCGA-A8-A06U TCGA-A8-A06X 
       14.73        11.05         9.37         1.02        29.03        31.00 
TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07S TCGA-A8-A07Z 
       19.99        18.97        12.00        17.03         7.99        28.04 
TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08L TCGA-A8-A08O 
       15.06        36.95         0.99        23.08         9.99        31.00 
TCGA-A8-A08Z TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09D TCGA-A8-A09I 
       40.01        41.98        12.00         9.99        13.02        33.07 
TCGA-A8-A09V TCGA-A8-A0A1 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0AD TCGA-AC-A23C 
       15.02        12.00        13.02        21.04        38.04         0.95 
TCGA-AC-A2B8 TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO 
        1.48        40.57        55.43        36.99        38.79        50.70 
TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN 
        0.92         0.99         0.69        14.83         9.40         1.12 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62Y TCGA-AC-A6IV 
        1.81         1.68         1.32         1.55         1.81         1.18 
TCGA-AC-A6IX TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A04A TCGA-AN-A0AK TCGA-AN-A0AL 
        0.43         0.23         0.33         2.96         7.36         6.51 
TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FN 
        0.33         0.33         6.44         4.64         7.96         7.17 
TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XT TCGA-AN-A0XU 
        6.28         0.33         0.30         0.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03P 
        5.33         5.59        80.28        47.84        66.77        84.69 
TCGA-AO-A03U TCGA-AO-A0J2 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA 
       59.05        32.78        37.48        22.36        53.03        21.53 
TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG 
       50.70        50.86        72.00        76.77        21.37        26.24 
TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 
       62.04        55.33        71.80       102.58        99.25        93.70 
TCGA-AO-A12A TCGA-AO-A12H TCGA-AO-A1KO TCGA-AQ-A04J TCGA-AQ-A0Y5 TCGA-AQ-A7U7 
       90.58        28.37        14.73        26.93         5.65         9.99 
TCGA-AR-A0TR TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 
        5.26        29.75        64.83        55.86        76.14        70.16 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
       83.87        76.18        75.55        48.82        62.56        43.73 
TCGA-AR-A1AO TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AV TCGA-AR-A24H TCGA-AR-A24K 
       43.56        17.23        40.83        42.58       109.58        50.89 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24T 
       73.02        65.46        68.19        65.69         0.85        53.26 
TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A2LE TCGA-AR-A2LM TCGA-AR-A2LN 
       48.16        56.15        40.64       128.65        40.04        17.10 
TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-B6-A0I9 TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG 
       16.96        54.74        12.13        50.70        65.72       146.50 
TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG 
      176.98        18.77       110.14       110.93       140.88        68.45 
TCGA-B6-A0RI TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT 
      234.28       172.96       162.05       140.48       100.70        89.46 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 
       97.48       188.68        79.63       129.57       129.70        28.27 
TCGA-B6-A0X5 TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C 
       68.94        73.51       139.17        49.94        82.88        55.00 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC 
       28.50        46.95        48.36        56.98        51.68        32.02 
TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR 
       25.71        21.70        61.68        35.67        27.19        53.69 
TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DE 
       53.95        49.94        11.67        48.13        42.90        31.17 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DQ 
       23.44        38.01        22.13        13.91        17.26         3.22 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EA 
       45.17        47.41         4.41         9.63        46.19        32.65 
TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0H3 TCGA-BH-A0H5 
       24.49        31.00        24.43        30.35        37.78        35.51 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       41.00        52.96        20.38         5.85         2.50        13.61 
TCGA-BH-A0HW TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18J 
       51.32        23.93        24.95         8.81         2.01        20.12 
TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S 
       90.84        72.56        30.28        55.63        37.55        66.05 
TCGA-BH-A18T TCGA-BH-A1EN TCGA-BH-A1ET TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F8 
        7.36        69.93        82.85        17.69        25.81        24.66 
TCGA-BH-A1FD TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR 
       33.17        36.92        63.35        55.00        72.07       144.59 
TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
        6.90        38.60        57.83        10.65         6.44        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-C8-A12L TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A132 
        0.99       109.28        11.93        11.77         0.07         1.45 
TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HI 
        0.69         3.85         3.75        12.33        10.92        11.34 
TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Y TCGA-C8-A274 
        0.16        10.42         0.30         0.23         0.43         0.03 
TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A13Z 
        0.03         0.99         0.03         0.23        11.90        20.88 
TCGA-D8-A140 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA 
       13.25        13.48        21.14        14.17        17.49        16.50 
TCGA-D8-A1JB TCGA-D8-A1JE TCGA-D8-A1JI TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JS 
       18.71        18.90        18.97        19.40        20.38        12.20 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD 
       16.73        25.74        23.90        27.58         2.66        17.16 
TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XT 
       14.73        21.83        17.69         7.96        15.85         6.35 
TCGA-D8-A1XV TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27K TCGA-D8-A27N 
       15.16        17.42        16.04        13.45         9.44         4.80 
TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 
        0.76        13.08        12.26        14.50        18.51         7.33 
TCGA-E2-A105 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F 
       43.00        46.59        40.41        37.51        28.44        28.87 
TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A150 TCGA-E2-A155 
       40.96        38.24        34.26        32.02        25.41        21.04 
TCGA-E2-A156 TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15K TCGA-E2-A15L 
       23.87        18.21        12.92        17.42         9.04        20.58 
TCGA-E2-A15P TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF 
       19.56        53.03        29.95        16.47        38.30        37.41 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IU 
       32.78        33.73        28.44        22.65         3.88        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG 
       54.18        39.62        19.66        40.47        28.90        18.87 
TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E9-A1N4 TCGA-E9-A1N8 
       43.04         5.52        15.72        18.05        19.20        12.00 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NG TCGA-E9-A1QZ TCGA-E9-A1R0 
       36.56        39.55        12.59        21.57        11.90        14.30 
TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RD TCGA-E9-A1RF TCGA-E9-A1RH 
        6.12         1.38        21.21         0.66         6.58        34.59 
TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22H 
       35.64        34.13         0.79        12.53        13.32        24.10 
TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3HO 
        0.69         0.85         0.95        12.56         0.76        26.07 
TCGA-E9-A3Q9 TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
       18.41         0.26         0.23        15.39        12.20        39.72 
TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OX 
       18.21        13.25        16.57        15.68        25.94        29.95 
TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PE TCGA-EW-A1PF 
       39.78        29.82        30.08        18.90        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 
       34.55        55.00        52.73        22.09        21.27        17.49 
TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       10.16        10.59         7.40        59.57       194.27        53.13 
TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       42.28        61.91        62.33        90.84        76.64        77.33 
TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PX 
      110.50        38.20        32.28        53.95        57.63        18.12 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 
       11.57         8.28         6.67         4.60         0.66         2.99 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A8F5 
        3.58         6.90         5.56         3.25         2.63         6.21 
TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5RU TCGA-OL-A5RV 
       15.91         2.79         2.10        12.66        27.65        24.10 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H 
       26.20        16.87        14.10        10.29         9.80        14.76 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P 
       54.51        33.90        31.07         7.23         4.44 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.03              0.03 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           220.90            234.28 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            20.81             22.13 
[1] "0.0 - 220.9 (20.8)" "0.0 - 234.3 (22.1)"
[1] "hr=" "1.1"
D16V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8Q GAIN MUTATED        43       32        3        4       175        99
  8Q GAIN WILD-TYPE      37       45        6        5       160       125
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8Q GAIN MUTATED           2         72         14         28       11
  8Q GAIN WILD-TYPE         0         66         13         31        6
                   vv
clus                STAGE TIS STAGE X
  8Q GAIN MUTATED           0      10
  8Q GAIN WILD-TYPE         1       6
D16V3, multiclass
            clus
vv           8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                 43                37
  STAGE IA                32                45
  STAGE IB                 3                 6
  STAGE II                 4                 5
  STAGE IIA              175               160
  STAGE IIB               99               125
  STAGE III                2                 0
  STAGE IIIA              72                66
  STAGE IIIB              14                13
  STAGE IIIC              28                31
  STAGE IV                11                 6
  STAGE TIS                0                 1
  STAGE X                 10                 6
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  8Q GAIN MUTATED   130 292  52  18
  8Q GAIN WILD-TYPE 128 289  65  18
D16V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1             130               128
  T2             292               289
  T3              52                65
  T4              18                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  8Q GAIN MUTATED   232 155  62  34
  8Q GAIN WILD-TYPE 236 175  49  36
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0             232               236
  N1             155               175
  N2              62                49
  N3              34                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  8Q GAIN MUTATED          1 428  11  54
  8Q GAIN WILD-TYPE        1 417   6  77
D16V6, multiclass
          clus
vv         8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CM0 (I+)               1                 1
  M0                   428               417
  M1                    11                 6
  MX                    54                77
[1] 4 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   487   7
  8Q GAIN WILD-TYPE 497   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    487    7
  8Q GAIN WILD-TYPE  497    4
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE             487               497
  MALE                 7                 4
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  8Q GAIN MUTATED                            1                           400
  8Q GAIN WILD-TYPE                          0                           335
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  8Q GAIN MUTATED                               47                   4
  8Q GAIN WILD-TYPE                            119                   1
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  8Q GAIN MUTATED                                 12                  4
  8Q GAIN WILD-TYPE                               17                 10
                   vv
clus                OTHER  SPECIFY
  8Q GAIN MUTATED               25
  8Q GAIN WILD-TYPE             19
D16V8, multiclass
                                  clus
vv                                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                400               335
  INFILTRATING LOBULAR CARCINOMA                47               119
  MEDULLARY CARCINOMA                            4                 1
  MIXED HISTOLOGY (PLEASE SPECIFY)              12                17
  MUCINOUS CARCINOMA                             4                10
  OTHER  SPECIFY                                25                19
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V9, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   156 338
  8Q GAIN WILD-TYPE 126 375
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    156  338
  8Q GAIN WILD-TYPE  126  375
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO              156               126
  YES             338               375
[1] 2 2
[1] FALSE
D16V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q GAIN MUTATED                                  1    26
  8Q GAIN WILD-TYPE                                0    30
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED                          81   330
  8Q GAIN WILD-TYPE                        56   378
D16V11, multiclass
                                  clus
vv                                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         26                30
  BLACK OR AFRICAN AMERICAN                     81                56
  WHITE                                        330               378
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V12, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    13 391
  8Q GAIN WILD-TYPE  23 405
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     13  391
  8Q GAIN WILD-TYPE   23  405
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                  13                23
  NOT HISPANIC OR LATINO             391               405
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED   108  19
  9P GAIN WILD-TYPE 752  95
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
              127               847 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               19                95 
$`9P GAIN MUTATED`
TCGA-A1-A0SK TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A0CM TCGA-A2-A0CS 
       31.79        73.84        22.06        64.04        24.79        75.55 
TCGA-A2-A0CV TCGA-A2-A0SX TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0YM TCGA-A2-A1FV 
       63.45        50.43         8.38        18.71        31.73        23.47 
TCGA-A2-A25D TCGA-A2-A4S2 TCGA-A7-A0DB TCGA-A7-A13E TCGA-A7-A3J0 TCGA-A7-A425 
       18.15         6.74        33.11        10.72        10.29        14.70 
TCGA-A7-A4SD TCGA-A7-A56D TCGA-A7-A6VX TCGA-A8-A07F TCGA-A8-A07R TCGA-A8-A07U 
       14.50        14.73        10.42        18.97         8.98         9.96 
TCGA-A8-A07Z TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08X TCGA-A8-A093 TCGA-A8-A09X 
       28.04        23.08        19.99        33.99        17.95        14.01 
TCGA-AC-A23E TCGA-AC-A23H TCGA-AC-A2BK TCGA-AC-A2FM TCGA-AC-A3W5 TCGA-AC-A62X 
        2.37         2.66        38.53        26.04         1.81         1.12 
TCGA-AN-A0AR TCGA-AN-A0FK TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AO-A0J7 
        0.33         7.00         6.02         0.33         0.33        20.32 
TCGA-AO-A0J9 TCGA-AO-A0JL TCGA-AO-A128 TCGA-AQ-A54N TCGA-AR-A1AY TCGA-AR-A24H 
       53.03        55.33        94.59         2.56        20.22       109.58 
TCGA-AR-A250 TCGA-AR-A256 TCGA-B6-A0I2 TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IQ 
       56.15        93.83       143.38       112.37       176.98       140.88 
TCGA-B6-A0RE TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WZ TCGA-B6-A0X1 TCGA-B6-A1KC 
      211.56       100.70       131.21       129.57       186.48        43.59 
TCGA-B6-A1KI TCGA-BH-A0AY TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BG TCGA-BH-A0BT 
       73.51        25.55        51.68        37.22        24.85        45.57 
TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0RX TCGA-BH-A18F TCGA-BH-A18Q TCGA-BH-A18V 
       32.65        31.00         5.59         8.81        55.63        51.16 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1F0 TCGA-BH-A1F6 TCGA-BH-A1FC TCGA-BH-A202 
       42.28        12.00        25.81        97.48       114.15         0.72 
TCGA-C8-A132 TCGA-C8-A138 TCGA-C8-A26Z TCGA-D8-A141 TCGA-D8-A146 TCGA-D8-A1J8 
        1.45         3.75         8.28        20.58        21.14        14.17 
TCGA-D8-A1JA TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JT TCGA-D8-A1XB TCGA-D8-A1XF 
       16.50        18.15        18.90        13.32        18.15        15.22 
TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A27V TCGA-D8-A3Z6 
       14.50        19.92        12.99        12.66        12.53        18.51 
TCGA-E2-A10B TCGA-E2-A14N TCGA-E2-A154 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A1AZ 
       37.51        47.15        19.43        14.79        25.05        60.53 
TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1L9 TCGA-E2-A1LL TCGA-E2-A2P5 
       17.10        33.73        33.70        19.66        43.04        16.93 
TCGA-E2-A56Z TCGA-E9-A1N6 TCGA-E9-A244 TCGA-E9-A3HO TCGA-EW-A1IY TCGA-EW-A1J1 
        7.20        13.48         0.69        26.07         8.48        18.90 
TCGA-EW-A1P8 TCGA-EW-A1PC TCGA-EW-A1PG TCGA-EW-A1PH TCGA-GM-A2DF TCGA-GM-A2DH 
        7.86         6.15        34.55        19.96        42.71        42.28 
TCGA-GM-A3XL TCGA-GM-A4E0 TCGA-LL-A5YM TCGA-LL-A6FR TCGA-MS-A51U TCGA-OL-A5RW 
       69.30        57.63         4.70         3.88         2.79        26.20 
TCGA-OL-A66I 
       23.70 

$`9P GAIN WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP 
       20.88        13.68         7.96        39.32        28.01        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04V 
       18.21       104.81        18.02        41.95        82.16        63.12 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP 
       55.43        36.13       125.59        64.57       112.08        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0CX 
       88.60       107.93        75.25         5.19        64.04        56.81 
TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM 
       21.14        34.55        33.76        28.77        25.22       101.72 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES 
       89.36        80.28       107.61        79.76        74.40        37.05 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY 
       35.05        34.29        31.82        29.75        24.72        24.16 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 
       99.19        54.64        27.12        44.88        44.28        17.52 
TCGA-A2-A0T1 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC 
       17.13        20.52        17.46        18.90        20.75        32.55 
TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI 
       25.28        18.21        15.42        21.90        21.67        14.50 
TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX 
       18.61        19.33        14.63        23.77        17.36        36.79 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       22.45        20.25        19.20        19.56        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
      107.70        16.31        17.19        91.92        10.59        20.88 
TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW 
       39.65        33.93        83.01        29.98        14.07        49.48 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX 
       38.40        34.98        31.99        38.37         7.30         9.01 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE 
        8.81         8.91        12.00         3.42        38.30        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A13D 
       34.29        35.47        30.61        37.45        35.67        31.73 
TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G 
       12.72        23.61        29.56        31.36        24.26        23.74 
TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ 
       23.80        21.73        20.61        22.32        11.34        10.59 
TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SE 
       11.28        13.41        11.97        14.93        13.74        21.17 
TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW 
       17.92        12.10        10.72        11.05        10.29         9.37 
TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T 
        8.75        13.02        13.02         1.02        17.98        41.06 
TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 
       29.03        31.00        26.01         1.02        17.03        53.98 
TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J 
        9.01        33.01        19.99        18.97        14.01        12.00 
TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07W TCGA-A8-A082 
       17.03         9.99        10.98         7.99         9.99        18.05 
TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08F TCGA-A8-A08G 
       15.06        36.95        13.02         0.99        18.05        19.96 
TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R 
       12.00        37.05         9.99        31.00        31.00         0.99 
TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A095 
       19.07        93.04        40.01        19.07        16.01        41.98 
TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D 
       12.00         9.99         9.99        12.00         1.02        13.02 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q 
       31.00        33.07        29.98        15.02         1.02        25.02 
TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A2 
        8.98        19.04        15.02         0.99        12.00        19.04 
TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD 
       13.02        21.04         0.99        13.02        17.03        38.04 
TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF 
        0.95        10.85         1.48        38.20        40.57        55.43 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ 
       36.99        38.79        50.70         1.02         0.92         2.27 
TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W6 
        0.99         0.69        14.83         9.40         1.12         1.68 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV 
        1.55         1.32         1.55         0.07         1.81         1.18 
TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 
        0.69         0.43         1.74         0.33         0.33         0.23 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ 
        0.33         0.62         2.96         1.78         1.71         8.02 
TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD 
        7.36         6.51         0.16         0.33         0.33         6.44 
TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FW 
        4.64         7.96         7.59         7.17         6.28         0.36 
TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP 
        0.33         0.33         0.33         0.33        12.33         0.30 
TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW 
        0.33         0.33         0.33         0.33         5.33         5.59 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R 
       80.28        47.84        66.77        81.63        84.69        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 
       47.87        59.05        29.13        32.78        21.40        17.65 
TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC 
       24.16        37.48        22.36        21.53        50.70        50.86 
TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ 
       72.00        76.77        21.37        26.24        38.53        62.04 
TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12A 
       71.80       102.58        99.25        93.70        96.10        90.58 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
       77.56        64.04        57.30        48.36        41.62        28.37 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT 
       14.73        82.62        61.87        70.39         0.53        17.79 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       24.79        26.93       130.09         5.65        15.62        13.22 
TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS 
       21.86         9.99        82.88        49.32         5.26        37.41 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
       56.88        29.75        24.30        64.83        55.86        76.14 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH 
       65.36        70.16        83.87        76.18        55.36        75.55 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
       61.84        52.77        51.25        48.82        62.56        43.73 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU 
       43.56        39.98        43.07        17.23        40.83        46.32 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M 
       42.58        35.24        36.26        50.89        73.02        65.46 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S 
       68.19        65.69         0.85        66.05        57.40        62.07 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
       53.26        53.36        54.18        50.96        48.16        51.75 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LH 
       45.17        40.64        39.85        34.82       128.65        20.25 
TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       42.87         7.36        40.04        17.10        20.81        16.96 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       20.38        54.74        16.04        20.45        10.59        77.62 
TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
      149.59        12.13       220.90       129.57        50.70        65.72 
TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP 
      146.50        18.77       126.12        84.59       110.14       110.93 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN 
       68.45       189.01       234.28        81.17        78.02       172.96 
TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS 
      162.05       102.77       140.48        89.46       157.41        97.48 
TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0X0 
      188.68        79.63        17.98        21.47       113.79       129.70 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU 
       28.27        68.94        58.88       101.52       139.17       170.17 
TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
       85.35        54.28        49.94        82.88        55.00        24.53 
TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 
       38.79        20.45        28.50        46.95        40.83        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0BC TCGA-BH-A0BD 
       39.16        48.36        56.94        56.98        32.02        18.21 
TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP 
       25.71        21.70        44.05        61.68        35.67        48.69 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ 
       27.19        53.69        53.95        49.94        11.67        49.05 
TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE 
       41.75        44.02        48.13        42.90        45.83        31.17 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO 
       23.44        38.01        22.13        13.91        48.23        17.26 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       15.65         3.22         2.56        38.47        45.17        47.41 
TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 
       16.27         4.41        15.68        14.30         9.63        44.81 
TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 
       46.19        24.49        24.43        30.35        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA 
       37.78        35.51        24.56        23.08        41.00        52.96 
TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ 
       26.50        20.38         5.85         2.50        13.61        36.85 
TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0W3 TCGA-BH-A0W4 
       12.89        51.32        27.25        50.79        23.93        24.95 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J 
       42.35        44.81        23.05         2.01         7.23        20.12 
TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18R 
       90.84        26.66        72.56        37.74        30.28        37.55 
TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES 
       66.05         7.36        51.39        69.93        91.99       113.82 
TCGA-BH-A1ET TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F2 TCGA-BH-A1F5 
       82.85        55.69        49.58        17.69        31.53        89.16 
TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH 
       24.66       120.62        33.17        74.73       122.89        36.92 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU 
       63.35        55.00        45.63        72.07       144.59        72.07 
TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O 
        6.90        38.60        83.31        57.83       130.16        10.65 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12L 
        6.44        20.12         0.99       109.28         8.94        11.93 
TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U 
       11.77        11.77        12.66        11.77         0.07        12.66 
TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A134 
       12.66        12.66        12.66         3.12         1.78         0.69 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI 
        0.62         3.85        12.33        10.92        11.34        11.34 
TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V 
        0.16        12.03        10.42         2.30         3.25         0.30 
TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
        0.23         0.36         0.43         9.67         0.03         0.03 
TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y 
        0.03        12.20         0.99         0.03         0.23        11.90 
TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 
       20.88        13.25        13.97        14.17        13.48        19.20 
TCGA-D8-A1J9 TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH 
       17.49        18.71        15.78        12.03        12.03        14.01 
TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN 
       18.97        20.09        20.12        20.09        19.40        20.38 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 
       21.01        12.20        14.70        18.58        17.79        16.73 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG 
       25.74        23.90        27.58         2.66        17.16        14.73 
TCGA-D8-A1XJ TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS 
       21.83        17.69         7.96        16.41        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 
        6.35        15.16        16.54        15.32        15.52         3.81 
TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H 
       14.24        14.14        17.42        16.04        13.45        13.05 
TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P 
       14.43         9.44        16.41        13.48         4.80         0.76 
TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A4Z1 TCGA-E2-A105 
       10.09        13.08        12.26        14.50         7.33        43.00 
TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A10E 
       34.42        27.52        46.59        40.41        40.11        28.44 
TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S 
       28.87        44.68        40.96        38.24        38.60        33.17 
TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y 
       33.30        43.33        34.26        32.02        31.96        28.60 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 
       17.03        25.41        27.12        23.24        21.04        23.87 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G 
       23.34        22.82        17.29        20.71        21.63        18.21 
TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M 
       12.92        17.42        19.40         9.04        20.58         7.73 
TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 
       13.02        19.56        17.06        14.07        14.99        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE 
       53.03        29.95        32.35        28.50        16.47        38.30 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN 
       37.41        32.78        28.44        22.65         3.88        22.19 
TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LA 
       20.98        11.08        54.18        27.42        39.62        24.59 
TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK 
       40.47        28.90        18.87       106.75       102.61         8.75 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N4 
        5.52        15.72        18.05        22.26        19.89        19.20 
TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND 
       36.82        12.00        13.12        36.56        39.55        12.59 
TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 
       35.77        20.05        21.57         9.86        11.90        14.30 
TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 
        0.62         2.10         6.12         1.38         2.76        21.21 
TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF 
       32.09        20.81        40.24         0.66        34.65         6.58 
TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 
       21.27        34.59        35.64        34.13         0.79        12.53 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H 
       13.32        39.09        22.75        12.89        23.51        24.10 
TCGA-E9-A243 TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A 
       17.06         0.85        27.22         1.94         0.95        12.56 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
        0.72        17.75         0.76        18.41         0.62        15.72 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW 
        0.23         0.39         0.26         0.23        15.39        12.20 
TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 
       39.72        18.21        13.25        16.57        15.68        28.77 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 
       25.94        22.82        29.95        29.85        40.41        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 
       39.78        52.96        29.82        23.11        18.48        30.08 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A2FR 
       18.90        19.99        13.94        10.52        14.43        55.00 
TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 
       52.73        25.91        22.09        21.27        17.49        10.16 
TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       10.59         7.40       109.87        59.57       194.27        53.13 
TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       53.52        43.04        61.91        62.33        90.84        76.64 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN 
       77.33        53.36       110.50        38.20        32.28        53.95 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U 
       13.55        18.12        11.84        11.57         8.28         6.67 
TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL 
        4.60         0.66         2.99         3.58         6.90         5.56 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A73Z 
        3.65         3.19         3.25         2.63         4.14         4.50 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-OK-A5Q2 
        4.50         5.59         3.22         6.21        15.91         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
       12.66        46.55         7.53        44.61        27.65        24.10 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J 
       16.87        14.10        10.29         9.80        14.76        54.51 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-S3-A6ZG 
       33.90        31.07        18.21         7.23         4.44         6.81 
TCGA-W8-A86G 
        5.29 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             0.33              0.03 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           211.56            234.28 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            20.32             21.57 
[1] "0.3 - 211.6 (20.3)" "0.0 - 234.3 (21.6)"
[1] "hr=" "1.1"
D17V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9P GAIN MUTATED         9        5        1        1        53        30
  9P GAIN WILD-TYPE      71       72        8        8       282       194
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9P GAIN MUTATED           0          9          2         11        3
  9P GAIN WILD-TYPE         2        129         25         48       14
                   vv
clus                STAGE TIS STAGE X
  9P GAIN MUTATED           0       3
  9P GAIN WILD-TYPE         1      13
D17V3, multiclass
            clus
vv           9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                  9                71
  STAGE IA                 5                72
  STAGE IB                 1                 8
  STAGE II                 1                 8
  STAGE IIA               53               282
  STAGE IIB               30               194
  STAGE III                0                 2
  STAGE IIIA               9               129
  STAGE IIIB               2                25
  STAGE IIIC              11                48
  STAGE IV                 3                14
  STAGE TIS                0                 1
  STAGE X                  3                13
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  9P GAIN MUTATED    27  80  14   6
  9P GAIN WILD-TYPE 231 501 103  30
D17V4, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1              27               231
  T2              80               501
  T3              14               103
  T4               6                30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  9P GAIN MUTATED    61  43   8  13
  9P GAIN WILD-TYPE 407 287 103  57
D17V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0              61               407
  N1              43               287
  N2               8               103
  N3              13                57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  9P GAIN MUTATED          0 108   3  17
  9P GAIN WILD-TYPE        2 737  14 114
D17V6, multiclass
          clus
vv         9P GAIN MUTATED 9P GAIN WILD-TYPE
  CM0 (I+)               0                 2
  M0                   108               737
  M1                     3                14
  MX                    17               114
[1] 4 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   128   0
  9P GAIN WILD-TYPE 856  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED    128    0
  9P GAIN WILD-TYPE  856   11
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE             128               856
  MALE                 0                11
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  9P GAIN MUTATED                            0                           102
  9P GAIN WILD-TYPE                          1                           633
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  9P GAIN MUTATED                               18                   1
  9P GAIN WILD-TYPE                            148                   4
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  9P GAIN MUTATED                                  1                  1
  9P GAIN WILD-TYPE                               28                 13
                   vv
clus                OTHER  SPECIFY
  9P GAIN MUTATED                5
  9P GAIN WILD-TYPE             39
D17V8, multiclass
                                  clus
vv                                 9P GAIN MUTATED 9P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                102               633
  INFILTRATING LOBULAR CARCINOMA                18               148
  MEDULLARY CARCINOMA                            1                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               1                28
  MUCINOUS CARCINOMA                             1                13
  OTHER  SPECIFY                                 5                39
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V9, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    36  92
  9P GAIN WILD-TYPE 246 621
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     36   92
  9P GAIN WILD-TYPE  246  621
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO               36               246
  YES              92               621
[1] 2 2
[1] FALSE
D17V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P GAIN MUTATED                                  0     7
  9P GAIN WILD-TYPE                                1    49
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED                          22    90
  9P GAIN WILD-TYPE                       115   618
D17V11, multiclass
                                  clus
vv                                 9P GAIN MUTATED 9P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          7                49
  BLACK OR AFRICAN AMERICAN                     22               115
  WHITE                                         90               618
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V12, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     5 104
  9P GAIN WILD-TYPE  31 692
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      5  104
  9P GAIN WILD-TYPE   31  692
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                31
  NOT HISPANIC OR LATINO             104               692
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    89  18
  9Q GAIN WILD-TYPE 771  96
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              107               867 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               18                96 
$`9Q GAIN MUTATED`
TCGA-A1-A0SK TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0T2 
       31.79        73.84        22.06        75.55        63.45         8.38 
TCGA-A2-A0T3 TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A25B TCGA-A2-A4S2 TCGA-A7-A0DB 
       18.71        31.73        23.47        16.31         6.74        33.11 
TCGA-A7-A13E TCGA-A7-A3J0 TCGA-A7-A425 TCGA-A7-A6VX TCGA-A8-A07F TCGA-A8-A07Z 
       10.72        10.29        14.70        10.42        18.97        28.04 
TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A093 TCGA-A8-A09X TCGA-AC-A23E TCGA-AC-A23H 
       23.08        19.99        17.95        14.01         2.37         2.66 
TCGA-AC-A2FM TCGA-AN-A0FK TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0XR 
       26.04         7.00         6.02         0.33         0.33         0.33 
TCGA-AO-A0J7 TCGA-AO-A128 TCGA-AQ-A04H TCGA-AR-A0TR TCGA-AR-A1AJ TCGA-AR-A24H 
       20.32        94.59        24.79         5.26        52.77       109.58 
TCGA-AR-A250 TCGA-AR-A256 TCGA-AR-A5QM TCGA-B6-A0I2 TCGA-B6-A0IH TCGA-B6-A0IJ 
       56.15        93.83        54.74       143.38       112.37       176.98 
TCGA-B6-A0IK TCGA-B6-A0IQ TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WZ TCGA-B6-A1KI 
       18.77       140.88       100.70       131.21       129.57        73.51 
TCGA-BH-A0AY TCGA-BH-A0BA TCGA-BH-A0BG TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A18F 
       25.55        37.22        24.85        46.19        32.65         8.81 
TCGA-BH-A18V TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1F2 TCGA-BH-A1FC TCGA-BH-A202 
       51.16        42.28        12.00        31.53       114.15         0.72 
TCGA-C8-A12M TCGA-C8-A132 TCGA-C8-A138 TCGA-C8-A1HG TCGA-C8-A1HK TCGA-C8-A26Y 
       11.77         1.45         3.75        11.34        12.03         0.43 
TCGA-C8-A275 TCGA-D8-A141 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1JD TCGA-D8-A1JE 
        0.03        20.58        21.14        14.17        18.15        18.90 
TCGA-D8-A1JG TCGA-D8-A1JT TCGA-D8-A1XB TCGA-D8-A1XF TCGA-D8-A1XL TCGA-D8-A1XU 
       12.03        13.32        18.15        15.22        19.92        12.99 
TCGA-D8-A27V TCGA-D8-A3Z6 TCGA-E2-A10B TCGA-E2-A14N TCGA-E2-A154 TCGA-E2-A1BD 
       12.53        18.51        37.51        47.15        19.43        17.10 
TCGA-E2-A1II TCGA-E2-A1L9 TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A56Z TCGA-E9-A1N6 
       33.70        19.66        43.04        16.93         7.20        13.48 
TCGA-E9-A22E TCGA-E9-A244 TCGA-E9-A3HO TCGA-EW-A1IY TCGA-EW-A1J1 TCGA-EW-A1P4 
       12.89         0.69        26.07         8.48        18.90        29.82 
TCGA-EW-A1P8 TCGA-EW-A1PC TCGA-EW-A1PG TCGA-EW-A1PH TCGA-GI-A2C8 TCGA-GM-A2DF 
        7.86         6.15        34.55        19.96         7.40        42.71 
TCGA-GM-A3XL TCGA-LL-A6FR TCGA-MS-A51U TCGA-OL-A5RW TCGA-OL-A66I 
       69.30         3.88         2.79        26.20        23.70 

$`9Q GAIN WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP 
       20.88        13.68         7.96        39.32        28.01        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04V 
       18.21       104.81        18.02        41.95        82.16        63.12 
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM 
       64.04        55.43        36.13       125.59        64.57        24.79 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CT TCGA-A2-A0CU 
      112.08        92.48        88.60       107.93        75.25         5.19 
TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 
       64.04        56.81        21.14        34.55        33.76        28.77 
TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ 
       25.22       101.72        89.36        80.28       107.61        79.76 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW 
       74.40        37.05        35.05        34.29        31.82        29.75 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW 
       24.72        24.16        99.19        54.64        27.12        44.88 
TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T4 TCGA-A2-A0T5 
       50.43        44.28        17.52        17.13        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF 
       18.90        20.75        32.55        25.28        18.21        15.42 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL 
       21.90        21.67        14.50        18.61        19.33        14.63 
TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 
       23.77        17.36        36.79        22.45        20.25        19.20 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A25D 
       19.56        16.47        52.47       107.70        17.19        18.15 
TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT 
       91.92        10.59        20.88        39.65        33.93        83.01 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ 
       29.98        14.07        49.48        38.40        34.98        31.99 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 
       38.37         7.30         9.01         8.81         8.91        12.00 
TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ 
        3.42        38.30        35.31        34.29        35.47        30.61 
TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H 
       37.45        35.67        31.73        12.72        23.61        29.56 
TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J 
       31.36        24.26        23.74        23.80        21.73        20.61 
TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A426 
       22.32        11.34        10.59        11.28        13.41        11.97 
TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D 
       14.93        13.74        14.50        21.17        17.92        14.73 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY 
       12.10        10.72        11.05        10.29         9.37         8.75 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U 
       13.02        13.02         1.02        17.98        41.06        29.03 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 
       31.00        26.01         1.02        17.03        53.98         9.01 
TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
       33.01        19.99        18.97        14.01        12.00        17.03 
TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W 
        9.99        10.98         8.98         7.99         9.96         9.99 
TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08F 
       18.05        15.06        36.95        13.02         0.99        18.05 
TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P 
       19.96        12.00        37.05         9.99        31.00        31.00 
TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 
        0.99        19.07        93.04        33.99        40.01        19.07 
TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B 
       16.01        41.98        12.00         9.99         9.99        12.00 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M 
        1.02        13.02        31.00        33.07        29.98        15.02 
TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
        1.02        25.02         8.98        19.04        15.02         0.99 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 
       12.00        19.04        13.02        21.04         0.99        13.02 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BK 
       17.03        38.04         0.95        10.85         1.48        38.53 
TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO 
       38.20        40.57        55.43        36.99        38.79        50.70 
TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD 
        1.02         0.92         2.27         0.99         0.69        14.83 
TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ 
        9.40         1.12         1.81         1.68         1.55         1.32 
TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW 
        1.55         0.07         1.12         1.81         1.18         0.69 
TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 
        0.43         1.74         0.33         0.33         0.23         0.33 
TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK 
        0.62         2.96         1.78         1.71         8.02         7.36 
TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD 
        6.51         0.16         0.33         0.33         0.33         6.44 
TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FW 
        4.64         7.96         7.59         7.17         6.28         0.36 
TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP 
        0.33         0.33         0.33         0.33        12.33         0.30 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L 
        0.33         0.33         0.33         5.33         5.59        80.28 
TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T 
       47.84        66.77        81.63        84.69        68.75        47.87 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 
       59.05        29.13        32.78        21.40        17.65        24.16 
TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC 
       37.48        22.36        53.03        21.53        50.70        50.86 
TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ 
       72.00        76.77        21.37        26.24        38.53        62.04 
TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 
       55.33        71.80       102.58        99.25        93.70        96.10 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G 
       90.58        77.56        64.04        57.30        48.36        41.62 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS 
       28.37        14.73        82.62        61.87        70.39         0.53 
TCGA-AO-A1KT TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       17.79        26.93       130.09         5.65        15.62        13.22 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS 
        2.56        21.86         9.99        82.88        49.32        37.41 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
       56.88        29.75        24.30        64.83        55.86        76.14 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH 
       65.36        70.16        83.87        76.18        55.36        75.55 
TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO 
       61.84        51.25        48.82        62.56        43.73        43.56 
TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
       39.98        43.07        17.23        40.83        46.32        42.58 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M 
       35.24        36.26        20.22        50.89        73.02        65.46 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S 
       68.19        65.69         0.85        66.05        57.40        62.07 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
       53.26        53.36        54.18        50.96        48.16        51.75 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LH 
       45.17        40.64        39.85        34.82       128.65        20.25 
TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       42.87         7.36        40.04        17.10        20.81        16.96 
TCGA-AR-A2LR TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I5 
       20.38        16.04        20.45        10.59        77.62       149.59 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG 
       12.13       220.90       129.57        50.70        65.72       146.50 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0RE TCGA-B6-A0RG 
      126.12        84.59       110.14       110.93       211.56        68.45 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
      189.01       234.28        81.17        78.02       172.96       162.05 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT 
      102.77       140.48        89.46       157.41        97.48       188.68 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0X0 TCGA-B6-A0X1 
       79.63        17.98        21.47       113.79       129.70       186.48 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KN 
       28.27        68.94        58.88        43.59       101.52       139.17 
TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C 
      170.17        85.35        54.28        49.94        82.88        55.00 
TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 
       24.53        38.79        20.45        28.50        46.95        40.83 
TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 
       39.55        39.16        48.36        56.94        56.98        51.68 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM 
       32.02        18.21        25.71        21.70        44.05        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT 
       35.67        48.69        27.19        53.69        53.95        45.57 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 
       49.94        11.67        49.05        41.75        44.02        48.13 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI 
       42.90        45.83        31.17        23.44        38.01        22.13 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS 
       13.91        48.23        17.26        15.65         3.22         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 
       38.47        45.17        47.41        16.27         4.41        15.68 
TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI 
       14.30         9.63        44.81        24.49        31.00        24.43 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       30.35        10.78        15.16        37.78        35.51        24.56 
TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK 
       23.08        41.00        52.96        26.50        20.38         5.85 
TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX 
        2.50        13.61        36.85        12.89        51.32        27.25 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       50.79         5.59        23.93        24.95        42.35        44.81 
TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L 
       23.05         2.01         7.23        20.12        90.84        26.66 
TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S 
       72.56        37.74        30.28        55.63        37.55        66.05 
TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET 
        7.36        51.39        69.93        91.99       113.82        82.85 
TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F5 TCGA-BH-A1F6 
       55.69        49.58        17.69        25.81        89.16        97.48 
TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH 
       24.66       120.62        33.17        74.73       122.89        36.92 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU 
       63.35        55.00        45.63        72.07       144.59        72.07 
TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O 
        6.90        38.60        83.31        57.83       130.16        10.65 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12L 
        6.44        20.12         0.99       109.28         8.94        11.93 
TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V 
       11.77        12.66        11.77         0.07        12.66        12.66 
TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A135 
       12.66        12.66         3.12         1.78         0.69         0.62 
TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HL 
        3.85        12.33        10.92        11.34         0.16        10.42 
TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Z 
        2.30         3.25         0.30         0.23         0.36         8.28 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 
        9.67         0.03         0.03        12.20         0.99         0.03 
TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A142 TCGA-D8-A143 
        0.23        11.90        20.88        13.25        13.97        14.17 
TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC 
       13.48        19.20        17.49        16.50        18.71        15.78 
TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL 
       12.03        14.01        18.97        20.09        20.12        20.09 
TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X5 
       19.40        20.38        21.01        12.20        14.70        18.58 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XC 
       17.79        16.73        25.74        23.90        27.58         2.66 
TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XM TCGA-D8-A1XO 
       17.16        14.73        21.83        14.50        17.69         7.96 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW 
       16.41        15.85        16.31         6.35        15.16        12.66 
TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 
       16.54        15.32        15.52         3.81        14.24        14.14 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K 
       17.42        16.04        13.45        13.05        14.43         9.44 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T 
       16.41        13.48         4.80         0.76        10.09        13.08 
TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 
       12.26        14.50         7.33        43.00        34.42        27.52 
TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14O 
       46.59        40.41        40.11        28.44        28.87        44.68 
TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U 
       40.96        38.24        38.60        33.17        33.30        43.33 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 
       34.26        32.02        31.96        28.60        17.03        25.41 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 
       27.12        23.24        21.04        23.87        14.79        25.05 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G 
       23.34        22.82        17.29        20.71        21.63        18.21 
TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M 
       12.92        17.42        19.40         9.04        20.58         7.73 
TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ 
       13.02        19.56        17.06        14.07        14.99        60.53 
TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC 
       53.62        53.03        29.95        32.35        28.50        16.47 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK 
       38.30        37.41        32.78        33.73        28.44        22.65 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 
        3.88        22.19        20.98        11.08        54.18        27.42 
TCGA-E2-A1L8 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH 
       39.62        24.59        40.47        28.90        18.87       106.75 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 
      102.61         8.75         5.52        15.72        18.05        22.26 
TCGA-E2-A574 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA 
       19.89        19.20        36.82        12.00        13.12        36.56 
TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI 
       39.55        12.59        35.77        20.05        21.57         9.86 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 
       11.90        14.30         0.62         2.10         6.12         1.38 
TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD 
        2.76        21.21        32.09        20.81        40.24         0.66 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 
       34.65         6.58        21.27        34.59        35.64        34.13 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22G 
        0.79        12.53        13.32        39.09        22.75        23.51 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 
       24.10        17.06         0.85        27.22         1.94         0.95 
TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA 
       12.56         0.72        17.75         0.76        18.41         0.62 
TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE 
       15.72         0.23         0.39         0.26         0.23        15.39 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
       12.20        39.72        18.21        13.25        16.57        15.68 
TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ 
       28.77        25.94        22.82        29.95        29.85        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 
       41.13        39.78        52.96        23.11        18.48        30.08 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A2FR 
       18.90        19.99        13.94        10.52        14.43        55.00 
TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 
       52.73        25.91        22.09        21.27        17.49        10.16 
TCGA-EW-A424 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC 
       10.59       109.87        59.57       194.27        53.13        53.52 
TCGA-GM-A2DD TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       43.04        42.28        61.91        62.33        90.84        76.64 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN 
       77.33        53.36       110.50        38.20        32.28        53.95 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U 
       57.63        13.55        18.12        11.84        11.57         8.28 
TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y 
        6.67         4.60         0.66         2.99         3.58         6.90 
TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FQ 
        5.56         4.70         3.65         3.19         3.25         2.63 
TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 
        4.14         4.50         4.50         5.59         3.22         6.21 
TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA 
       15.91         2.10        12.66        46.55         7.53        44.61 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 
       27.65        24.10        16.87        14.10        10.29         9.80 
TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O 
       14.76        54.51        33.90        31.07        18.21         7.23 
TCGA-OL-A66P TCGA-S3-A6ZG TCGA-W8-A86G 
        4.44         6.81         5.29 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.03              0.03 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           176.98            234.28 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            19.43             21.83 
[1] "0.0 - 177.0 (19.4)" "0.0 - 234.3 (21.8)"
[1] "hr=" "1.4"
D18V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9Q GAIN MUTATED         7        4        1        1        45        28
  9Q GAIN WILD-TYPE      73       73        8        8       290       196
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9Q GAIN MUTATED           0          9          4          6        2
  9Q GAIN WILD-TYPE         2        129         23         53       15
                   vv
clus                STAGE TIS STAGE X
  9Q GAIN MUTATED           0       1
  9Q GAIN WILD-TYPE         1      15
D18V3, multiclass
            clus
vv           9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                  7                73
  STAGE IA                 4                73
  STAGE IB                 1                 8
  STAGE II                 1                 8
  STAGE IIA               45               290
  STAGE IIB               28               196
  STAGE III                0                 2
  STAGE IIIA               9               129
  STAGE IIIB               4                23
  STAGE IIIC               6                53
  STAGE IV                 2                15
  STAGE TIS                0                 1
  STAGE X                  1                15
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  9Q GAIN MUTATED    22  69  12   5
  9Q GAIN WILD-TYPE 236 512 105  31
D18V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1              22               236
  T2              69               512
  T3              12               105
  T4               5                31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  9Q GAIN MUTATED    52  41   6   8
  9Q GAIN WILD-TYPE 416 289 105  62
D18V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0              52               416
  N1              41               289
  N2               6               105
  N3               8                62
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  9Q GAIN MUTATED          0  92   2  14
  9Q GAIN WILD-TYPE        2 753  15 117
D18V6, multiclass
          clus
vv         9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CM0 (I+)               0                 2
  M0                    92               753
  M1                     2                15
  MX                    14               117
[1] 4 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   108   0
  9Q GAIN WILD-TYPE 876  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED    108    0
  9Q GAIN WILD-TYPE  876   11
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE             108               876
  MALE                 0                11
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  9Q GAIN MUTATED                            0                            85
  9Q GAIN WILD-TYPE                          1                           650
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  9Q GAIN MUTATED                               15                   2
  9Q GAIN WILD-TYPE                            151                   3
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  9Q GAIN MUTATED                                  1                  1
  9Q GAIN WILD-TYPE                               28                 13
                   vv
clus                OTHER  SPECIFY
  9Q GAIN MUTATED                4
  9Q GAIN WILD-TYPE             40
D18V8, multiclass
                                  clus
vv                                 9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                 85               650
  INFILTRATING LOBULAR CARCINOMA                15               151
  MEDULLARY CARCINOMA                            2                 3
  MIXED HISTOLOGY (PLEASE SPECIFY)               1                28
  MUCINOUS CARCINOMA                             1                13
  OTHER  SPECIFY                                 4                40
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V9, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    33  75
  9Q GAIN WILD-TYPE 249 638
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     33   75
  9Q GAIN WILD-TYPE  249  638
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO               33               249
  YES              75               638
[1] 2 2
[1] FALSE
D18V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q GAIN MUTATED                                  0    10
  9Q GAIN WILD-TYPE                                1    46
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED                          14    78
  9Q GAIN WILD-TYPE                       123   630
D18V11, multiclass
                                  clus
vv                                 9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         10                46
  BLACK OR AFRICAN AMERICAN                     14               123
  WHITE                                         78               630
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V12, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     4  91
  9Q GAIN WILD-TYPE  32 705
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      4   91
  9Q GAIN WILD-TYPE   32  705
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                32
  NOT HISPANIC OR LATINO              91               705
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED   171  26
  10P GAIN WILD-TYPE 689  88
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               197                777 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                26                 88 
$`10P GAIN MUTATED`
TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04U 
       43.43        48.10        28.01        18.02        41.95        22.06 
TCGA-A2-A0CM TCGA-A2-A0D2 TCGA-A2-A0EQ TCGA-A2-A0EV TCGA-A2-A0SW TCGA-A2-A0SX 
       24.79        33.76        79.76        31.82        44.88        50.43 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T7 TCGA-A2-A0YG TCGA-A2-A0YJ 
       17.13         8.38        18.71        20.75        21.90        18.61 
TCGA-A2-A0YM TCGA-A2-A1G1 TCGA-A2-A25B TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A7-A0DA 
       31.73        19.20        16.31        33.93        83.01        35.67 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A26G TCGA-A7-A26I TCGA-A7-A4SA TCGA-A7-A4SD 
       31.73        10.72        23.74        21.73        14.93        14.50 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A6VV TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A06X 
       17.92        14.73        10.29        13.02         1.02        31.00 
TCGA-A8-A075 TCGA-A8-A07B TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A07Z TCGA-A8-A08B 
       17.03        33.01         8.98         9.96        28.04        23.08 
TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08X TCGA-A8-A092 TCGA-A8-A09A 
       19.96        37.05        31.00        33.99        16.01         9.99 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09Q TCGA-A8-A09X TCGA-AC-A23E TCGA-AC-A2BK 
       13.02        31.00        25.02        14.01         2.37        38.53 
TCGA-AC-A62V TCGA-AC-A62X TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AS TCGA-AN-A0FZ 
        0.07         1.12         1.78         1.71         0.33         0.33 
TCGA-AO-A03O TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J9 TCGA-AO-A0JL 
       81.63        29.13        32.78        21.40        53.03        55.33 
TCGA-AO-A124 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04L 
      102.58        94.59        90.58        70.39         0.53       130.09 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0U4 
        2.56        21.86         9.99        37.41        56.88        55.36 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AQ TCGA-AR-A1AW TCGA-AR-A1AY 
       61.84        52.77        51.25        43.07        35.24        20.22 
TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24S TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A251 
      109.58        50.89        62.07        53.36        54.18        45.17 
TCGA-AR-A2LL TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IN 
        7.36       129.57        65.72       112.37       176.98        84.59 
TCGA-B6-A0IO TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RO TCGA-B6-A0X1 TCGA-B6-A1KC 
      110.14       140.88       211.56       162.05       186.48        43.59 
TCGA-B6-A1KF TCGA-B6-A402 TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0B6 TCGA-BH-A0BG 
      101.52        54.28        20.45        25.55        56.94        24.85 
TCGA-BH-A0BL TCGA-BH-A0C0 TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0E6 TCGA-BH-A0E7 
       44.05        41.75         2.56        38.47         9.63        44.81 
TCGA-BH-A0EA TCGA-BH-A0GY TCGA-BH-A0H7 TCGA-BH-A0HU TCGA-BH-A0HY TCGA-BH-A0RX 
       32.65        30.35        23.08        12.89        50.79         5.59 
TCGA-BH-A18L TCGA-BH-A18T TCGA-BH-A1EN TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1F2 
       26.66         7.36        69.93        12.00        55.69        31.53 
TCGA-BH-A1F6 TCGA-BH-A1FC TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12W TCGA-C8-A130 
       97.48       114.15        12.66        11.77        12.66         3.12 
TCGA-C8-A131 TCGA-C8-A1HM TCGA-C8-A26X TCGA-C8-A274 TCGA-C8-A27B TCGA-D8-A13Z 
        1.78         2.30         0.36         0.03         0.99        20.88 
TCGA-D8-A142 TCGA-D8-A147 TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JF TCGA-D8-A1JL 
       13.97        19.20        18.71        18.15        12.03        20.09 
TCGA-D8-A1X5 TCGA-D8-A1X9 TCGA-D8-A1XF TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XZ 
       18.58        23.90        15.22        12.99        12.66        15.32 
TCGA-D8-A3Z6 TCGA-E2-A107 TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14R TCGA-E2-A150 
       18.51        34.42        47.15        44.68        38.60        25.41 
TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A159 TCGA-E2-A15G TCGA-E2-A1AZ TCGA-E2-A1LH 
       27.12        19.43        25.05        18.21        60.53       106.75 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N6 
      102.61         8.75        16.93        22.26        19.89        13.48 
TCGA-E9-A1N9 TCGA-E9-A1RB TCGA-E9-A1RH TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A295 
       13.12        20.81        34.59         0.69        27.22         0.72 
TCGA-E9-A3QA TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OZ TCGA-EW-A1PB 
        0.62        28.77        25.94        22.82        40.41        19.99 
TCGA-EW-A1PC TCGA-EW-A1PH TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A423 TCGA-GI-A2C9 
        6.15        19.96        52.73        25.91        10.16       109.87 
TCGA-GM-A2DB TCGA-GM-A2DF TCGA-GM-A2DH TCGA-JL-A3YW TCGA-LL-A5YM TCGA-LL-A5YO 
       53.13        42.71        42.28        11.84         4.70         3.19 
TCGA-LL-A6FQ TCGA-LL-A73Z TCGA-LL-A8F5 TCGA-MS-A51U TCGA-OL-A5S0 
        2.63         4.50         6.21         2.79         9.80 

$`10P GAIN WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ 
        8.52        14.37        14.27        47.24        20.88        13.68 
TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N 
       31.79         7.96        39.32        19.20        18.21       104.81 
TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
       82.16        73.84        63.12        64.04        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
      125.59        64.57       112.08        92.48        88.60       107.93 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX 
       75.55        75.25         5.19        63.45        64.04        56.81 
TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN 
       21.14        34.55        28.77        25.22       101.72        89.36 
TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU 
       80.28       107.61        74.40        37.05        35.05        34.29 
TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV 
       29.75        24.72        24.16        99.19        54.64        27.12 
TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC 
       44.28        17.52        20.52        17.46        18.90        32.55 
TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK 
       25.28        18.21        15.42        21.67        14.50        19.33 
TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ 
       14.63        23.77        23.47        17.36        36.79        22.45 
TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25C 
       20.25        19.56        16.47        52.47       107.70        17.19 
TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XU 
       18.15        91.92        10.59        20.88        39.65        29.98 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 
       14.07        49.48        38.40        34.98        31.99        38.37 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 
        7.30         9.01         8.81         8.91        12.00         6.74 
TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ 
        3.42        38.30        35.31        34.29        35.47        30.61 
TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       37.45        33.11        12.72        23.61        29.56        31.36 
TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ 
       24.26        23.80        20.61        22.32        11.34        10.59 
TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SB 
       10.29        11.28        13.41        14.70        11.97        13.74 
TCGA-A7-A4SE TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A7-A6VX 
       21.17        12.10        10.72        11.05         9.37        10.42 
TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Y 
        8.75        13.02        17.98        41.06        29.03        26.01 
TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G 
        1.02        53.98         9.01        19.99        18.97        18.97 
TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S 
       14.01        12.00        17.03         9.99        10.98         7.99 
TCGA-A8-A07W TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A 
        9.99        18.05        15.06        36.95        13.02         0.99 
TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R 
       19.99        18.05        12.00         9.99        31.00         0.99 
TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 
       19.07        93.04        40.01        19.07        17.95        41.98 
TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09I TCGA-A8-A09K 
       12.00         9.99        12.00         1.02        33.07        29.98 
TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
       15.02         1.02         8.98        19.04        15.02         0.99 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 
       12.00        19.04        13.02        21.04         0.99        13.02 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 
       17.03        38.04         0.95        10.85         2.66         1.48 
TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM 
       38.20        40.57        55.43        36.99        38.79        26.04 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN 
       50.70         1.02         0.92         2.27         0.99         0.69 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI 
       14.83         9.40         1.12         1.81         1.68         1.55 
TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX 
        1.32         1.55         1.81         1.18         0.69         0.43 
TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 
        1.74         0.33         0.33         0.23         0.33         0.62 
TCGA-AN-A04A TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR 
        2.96         8.02         7.36         6.51         0.16         0.33 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL 
        0.33         6.44         4.64         7.96         7.00         7.59 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX 
        7.17         6.28         6.02         0.33         0.36         0.33 
TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR 
        0.33         0.33         0.33        12.33         0.30         0.33 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L 
        0.33         0.33         0.33         5.33         5.59        80.28 
TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U 
       47.84        66.77        84.69        68.75        47.87        59.05 
TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0JA 
       17.65        24.16        37.48        20.32        22.36        21.53 
TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG 
       50.70        50.86        72.00        76.77        21.37        26.24 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 
       38.53        62.04        71.80        99.25        93.70        96.10 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
       77.56        64.04        57.30        48.36        41.62        28.37 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J 
       14.73        82.62        61.87        17.79        24.79        26.93 
TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
        5.65        15.62        13.22        82.88        49.32         5.26 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 
       29.75        24.30        64.83        55.86        76.14        65.36 
TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AL TCGA-AR-A1AM 
       70.16        83.87        76.18        75.55        48.82        62.56 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU 
       43.73        43.56        39.98        17.23        40.83        46.32 
TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       42.58        36.26        73.02        65.46        68.19        65.69 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24W TCGA-AR-A24X 
        0.85        66.05        57.40        53.26        50.96        48.16 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
       51.75        56.15        40.64        39.85        34.82        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
      128.65        20.25        42.87        40.04        17.10        20.81 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       16.96        20.38        54.74        16.04        20.45        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC 
       77.62       143.38       149.59        12.13       220.90        50.70 
TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IP TCGA-B6-A0RG TCGA-B6-A0RH 
      146.50        18.77       126.12       110.93        68.45       189.01 
TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RQ 
      234.28        81.17        78.02       172.96       102.77       140.48 
TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT 
      100.70        89.46       131.21       157.41        97.48       188.68 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 
       79.63        17.98        21.47       113.79       129.57       129.70 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU 
       28.27        68.94        58.88        73.51       139.17       170.17 
TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV 
       85.35        49.94        82.88        55.00        24.53        38.79 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 
       28.50        46.95        40.83        39.55        39.16        48.36 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       56.98        51.68        37.22        32.02        18.21        25.71 
TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR 
       21.70        61.68        35.67        48.69        27.19        53.69 
TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 
       53.95        45.57        49.94        11.67        49.05        44.02 
TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH 
       48.13        42.90        45.83        31.17        23.44        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ 
       22.13        13.91        48.23        17.26        15.65         3.22 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 
       45.17        47.41        16.27         4.41        15.68        14.30 
TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 
       46.19        24.49        31.00        24.43        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB 
       37.78        35.51        24.56        41.00        52.96        26.50 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HW 
       20.38         5.85         2.50        13.61        36.85        51.32 
TCGA-BH-A0HX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA 
       27.25        23.93        24.95        42.35        44.81        23.05 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M 
        8.81         2.01         7.23        20.12        90.84        72.56 
TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U 
       37.74        30.28        55.63        37.55        66.05        51.39 
TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EX 
       51.16        91.99       113.82        82.85        42.28        49.58 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F5 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD 
       17.69        25.81        89.16        24.66       120.62        33.17 
TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM 
       74.73       122.89        36.92        63.35        55.00        45.63 
TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 
       72.07       144.59        72.07         6.90         0.72        38.60 
TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
       83.31        57.83       130.16        10.65         6.44        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N 
        0.99       109.28         8.94        11.93        11.77        11.77 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A132 TCGA-C8-A134 
        0.07        12.66        12.66        12.66         1.45         0.69 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG 
        0.62         3.85         3.75        12.33        10.92        11.34 
TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26V 
       11.34         0.16        12.03        10.42         3.25         0.30 
TCGA-C8-A26W TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A278 
        0.23         0.43         8.28         9.67         0.03         0.03 
TCGA-C8-A27A TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 
       12.20         0.03         0.23        11.90        13.25        20.58 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA 
       14.17        13.48        21.14        14.17        17.49        16.50 
TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ 
       15.78        18.90        12.03        14.01        18.97        20.09 
TCGA-D8-A1JK TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT 
       20.12        19.40        20.38        21.01        12.20        13.32 
TCGA-D8-A1JU TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1XA TCGA-D8-A1XB 
       14.70        17.79        16.73        25.74        27.58        18.15 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL 
        2.66        17.16        14.73        21.83        14.50        19.92 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT 
       17.69         7.96        16.41        15.85        16.31         6.35 
TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 
       15.16        16.54        15.52         3.81        14.24        14.14 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K 
       17.42        16.04        13.45        13.05        14.43         9.44 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T 
       16.41        13.48         4.80         0.76        10.09        13.08 
TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A108 
       12.53        12.26        14.50         7.33        43.00        27.52 
TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F 
       46.59        40.41        37.51        40.11        28.44        28.87 
TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V 
       40.96        38.24        33.17        33.30        43.33        34.26 
TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A153 TCGA-E2-A155 
       32.02        31.96        28.60        17.03        23.24        21.04 
TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E 
       23.87        14.79        23.34        22.82        17.29        20.71 
TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       21.63        12.92        17.42        19.40         9.04        20.58 
TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
        7.73        13.02        19.56        17.06        14.07        14.99 
TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC 
       53.62        53.03        29.95        32.35        28.50        16.47 
TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II 
       17.10        38.30        37.41        32.78        33.73        33.70 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       28.44        22.65         3.88        22.19        20.98        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB 
       54.18        27.42        39.62        19.66        24.59        40.47 
TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z 
       28.90        18.87        43.04         5.52        15.72         7.20 
TCGA-E2-A570 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1NA TCGA-E9-A1NC 
       18.05        19.20        36.82        12.00        36.56        39.55 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ 
       12.59        35.77        20.05        21.57         9.86        11.90 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 
       14.30         0.62         2.10         6.12         1.38         2.76 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF 
       21.21        32.09        40.24         0.66        34.65         6.58 
TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
       21.27        35.64        34.13         0.79        12.53        13.32 
TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 
       39.09        22.75        12.89        23.51        24.10        17.06 
TCGA-E9-A245 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JS TCGA-E9-A2JT 
        0.85         1.94         0.95        12.56        17.75         0.76 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL 
       26.07        18.41        15.72         0.23         0.39         0.26 
TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
        0.23        15.39        12.20        39.72         8.48        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OX TCGA-EW-A1OY 
       18.90        13.25        16.57        15.68        29.95        29.85 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 
       41.13        39.78        52.96        29.82        23.11        18.48 
TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
       30.08         7.86        18.90        13.94        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A2FR TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 
       34.55        55.00        22.09        21.27        17.49        10.59 
TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DI 
        7.40        59.57       194.27        53.52        43.04        61.91 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
       62.33        90.84        76.64        77.33        53.36       110.50 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV 
       38.20        32.28        69.30        53.95        57.63        13.55 
TCGA-GM-A5PX TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 
       18.12        11.57         8.28         6.67         4.60         0.66 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YP 
        2.99         3.58         6.90         5.56         3.65         3.25 
TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LQ-A4E4 
        3.88         4.14         4.50         5.59         3.22        15.91 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.10        12.66        46.55         7.53        44.61        27.65 
TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H 
       24.10        26.20        16.87        14.10        10.29        14.76 
TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O 
       23.70        54.51        33.90        31.07        18.21         7.23 
TCGA-OL-A66P TCGA-S3-A6ZG TCGA-W8-A86G 
        4.44         6.81         5.29 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.03               0.03 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            211.56             234.28 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             23.90              21.01 
[1] "0.0 - 211.6 (23.9)" "0.0 - 234.3 (21.0)"
[1] "hr=" "1"  
D19V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10P GAIN MUTATED        17       10        1        1        77        35
  10P GAIN WILD-TYPE      63       67        8        8       258       189
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10P GAIN MUTATED           0         27          6         12        7
  10P GAIN WILD-TYPE         2        111         21         47       10
                    vv
clus                 STAGE TIS STAGE X
  10P GAIN MUTATED           1       5
  10P GAIN WILD-TYPE         0      11
D19V3, multiclass
            clus
vv           10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                  17                 63
  STAGE IA                 10                 67
  STAGE IB                  1                  8
  STAGE II                  1                  8
  STAGE IIA                77                258
  STAGE IIB                35                189
  STAGE III                 0                  2
  STAGE IIIA               27                111
  STAGE IIIB                6                 21
  STAGE IIIC               12                 47
  STAGE IV                  7                 10
  STAGE TIS                 1                  0
  STAGE X                   5                 11
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  10P GAIN MUTATED    43 123  22  10
  10P GAIN WILD-TYPE 215 458  95  26
D19V4, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1               43                215
  T2              123                458
  T3               22                 95
  T4               10                 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                  N0  N1  N2  N3
  10P GAIN MUTATED   100  54  26  15
  10P GAIN WILD-TYPE 368 276  85  55
D19V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0              100                368
  N1               54                276
  N2               26                 85
  N3               15                 55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  10P GAIN MUTATED          0 172   7  21
  10P GAIN WILD-TYPE        2 673  10 110
D19V6, multiclass
          clus
vv         10P GAIN MUTATED 10P GAIN WILD-TYPE
  CM0 (I+)                0                  2
  M0                    172                673
  M1                      7                 10
  MX                     21                110
[1] 4 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   198   2
  10P GAIN WILD-TYPE 786   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED    198    2
  10P GAIN WILD-TYPE  786    9
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE              198                786
  MALE                  2                  9
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  10P GAIN MUTATED                            0                           171
  10P GAIN WILD-TYPE                          1                           564
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  10P GAIN MUTATED                               16                   3
  10P GAIN WILD-TYPE                            150                   2
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  10P GAIN MUTATED                                  4                  0
  10P GAIN WILD-TYPE                               25                 14
                    vv
clus                 OTHER  SPECIFY
  10P GAIN MUTATED                6
  10P GAIN WILD-TYPE             38
D19V8, multiclass
                                  clus
vv                                 10P GAIN MUTATED 10P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 171                564
  INFILTRATING LOBULAR CARCINOMA                 16                150
  MEDULLARY CARCINOMA                             3                  2
  MIXED HISTOLOGY (PLEASE SPECIFY)                4                 25
  MUCINOUS CARCINOMA                              0                 14
  OTHER  SPECIFY                                  6                 38
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V9, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    68 132
  10P GAIN WILD-TYPE 214 581
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     68  132
  10P GAIN WILD-TYPE  214  581
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                68                214
  YES              132                581
[1] 2 2
[1] FALSE
D19V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P GAIN MUTATED                                  1    10
  10P GAIN WILD-TYPE                                0    46
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED                          41   128
  10P GAIN WILD-TYPE                        96   580
D19V11, multiclass
                                  clus
vv                                 10P GAIN MUTATED 10P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                          10                 46
  BLACK OR AFRICAN AMERICAN                      41                 96
  WHITE                                         128                580
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V12, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     7 155
  10P GAIN WILD-TYPE  29 641
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      7  155
  10P GAIN WILD-TYPE   29  641
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    7                 29
  NOT HISPANIC OR LATINO              155                641
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    97  17
  10Q GAIN WILD-TYPE 763  97
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               114                860 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                17                 97 
$`10Q GAIN MUTATED`
TCGA-A1-A0SF TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04U TCGA-A2-A0CM 
       48.10        28.01        18.02        41.95        22.06        24.79 
TCGA-A2-A0EQ TCGA-A2-A0SX TCGA-A2-A0T1 TCGA-A2-A0T7 TCGA-A2-A3XS TCGA-A7-A13E 
       79.76        50.43        17.13        20.75        33.93        10.72 
TCGA-A7-A26G TCGA-A7-A26I TCGA-A8-A06O TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A07Z 
       23.74        21.73        13.02        31.00        17.03        28.04 
TCGA-A8-A08B TCGA-A8-A08P TCGA-A8-A092 TCGA-A8-A09A TCGA-A8-A09D TCGA-A8-A09Q 
       23.08        31.00        16.01         9.99        13.02        25.02 
TCGA-A8-A09X TCGA-AC-A23E TCGA-AC-A62V TCGA-AC-A62X TCGA-AN-A04C TCGA-AN-A0FZ 
       14.01         2.37         0.07         1.12         1.78         0.33 
TCGA-AO-A03O TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J9 TCGA-AO-A128 TCGA-AO-A12A 
       81.63        32.78        21.40        53.03        94.59        90.58 
TCGA-AO-A1KS TCGA-AQ-A04L TCGA-AQ-A54N TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A1AI 
        0.53       130.09         2.56        37.41        56.88        61.84 
TCGA-AR-A1AJ TCGA-AR-A1AQ TCGA-AR-A1AW TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24S 
       52.77        43.07        35.24       109.58        50.89        62.07 
TCGA-AR-A24U TCGA-AR-A24V TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IJ 
       53.36        54.18       129.57        65.72       112.37       176.98 
TCGA-B6-A0IO TCGA-B6-A0IQ TCGA-B6-A0RO TCGA-B6-A0WV TCGA-B6-A1KC TCGA-BH-A0AY 
      110.14       140.88       162.05        79.63        43.59        25.55 
TCGA-BH-A0B6 TCGA-BH-A0BL TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0E6 TCGA-BH-A0E7 
       56.94        44.05         2.56        38.47         9.63        44.81 
TCGA-BH-A0EA TCGA-BH-A18L TCGA-BH-A1EN TCGA-BH-A1EV TCGA-C8-A12O TCGA-C8-A12P 
       32.65        26.66        69.93        12.00        12.66        11.77 
TCGA-C8-A12W TCGA-C8-A130 TCGA-C8-A1HM TCGA-C8-A274 TCGA-D8-A13Z TCGA-D8-A147 
       12.66         3.12         2.30         0.03        20.88        19.20 
TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JF TCGA-D8-A1X9 TCGA-D8-A1XL TCGA-D8-A1XZ 
       18.71        18.15        12.03        23.90        19.92        15.32 
TCGA-E2-A107 TCGA-E2-A14O TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A15G 
       34.42        44.68        25.41        27.12        19.43        18.21 
TCGA-E2-A15S TCGA-E2-A1AZ TCGA-E2-A1LI TCGA-E2-A2P5 TCGA-E2-A573 TCGA-E9-A1N6 
       14.07        60.53       102.61        16.93        22.26        13.48 
TCGA-E9-A1N9 TCGA-E9-A1RB TCGA-E9-A1RH TCGA-E9-A247 TCGA-E9-A295 TCGA-E9-A3QA 
       13.12        20.81        34.59        27.22         0.72         0.62 
TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1PC TCGA-EW-A423 TCGA-GM-A2DB TCGA-GM-A2DH 
       28.77        25.94         6.15        10.16        53.13        42.28 
TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A6FQ TCGA-LL-A73Z TCGA-MS-A51U TCGA-OL-A5S0 
        4.70         3.19         2.63         4.50         2.79         9.80 

$`10Q GAIN WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI 
        8.52        14.37        43.43        14.27        47.24        20.88 
TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A1-A0SQ 
       13.68        31.79         7.96        39.32        19.20        18.21 
TCGA-A2-A04N TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X 
      104.81        82.16        73.84        63.12        64.04        55.43 
TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
       36.13       125.59        64.57       112.08        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW 
      107.93        75.55        75.25         5.19        63.45        64.04 
TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 
       56.81        21.14        34.55        33.76        28.77        25.22 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES 
      101.72        89.36        80.28       107.61        74.40        37.05 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY 
       35.05        34.29        31.82        29.75        24.72        24.16 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 
       99.19        54.64        27.12        44.88        44.28        17.52 
TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC 
        8.38        18.71        20.52        17.46        18.90        32.55 
TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI 
       25.28        18.21        15.42        21.90        21.67        14.50 
TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV 
       18.61        19.33        14.63        31.73        23.77        23.47 
TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 
       17.36        36.79        22.45        20.25        19.20        19.56 
TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D 
       16.47        52.47       107.70        16.31        17.19        18.15 
TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XU 
       91.92        10.59        20.88        39.65        83.01        29.98 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 
       14.07        49.48        38.40        34.98        31.99        38.37 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 
        7.30         9.01         8.81         8.91        12.00         6.74 
TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ 
        3.42        38.30        35.31        34.29        35.47        30.61 
TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A13G 
       37.45        35.67        33.11        31.73        12.72        23.61 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD 
       29.56        31.36        24.26        23.80        20.61        22.32 
TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 
       11.34        10.59        10.29        11.28        13.41        14.70 
TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF 
       11.97        14.93        13.74        14.50        21.17        17.92 
TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW 
       14.73        12.10        10.72        11.05        10.29         9.37 
TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T 
       10.42         8.75        13.02         1.02        17.98        41.06 
TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B 
       29.03        26.01         1.02        53.98         9.01        33.01 
TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
       19.99        18.97        18.97        14.01        12.00        17.03 
TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W 
        9.99        10.98         8.98         7.99         9.96         9.99 
TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C 
       18.05        15.06        36.95        13.02         0.99        19.99 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O 
       18.05        19.96        12.00        37.05         9.99        31.00 
TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 
        0.99        19.07        93.04        33.99        40.01        19.07 
TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09C 
       17.95        41.98        12.00         9.99        12.00         1.02 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R 
       31.00        33.07        29.98        15.02         1.02         8.98 
TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 
       19.04        15.02         0.99        12.00        19.04        13.02 
TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C 
       21.04         0.99        13.02        17.03        38.04         0.95 
TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB 
       10.85         2.66         1.48        38.53        38.20        40.57 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH 
       55.43        36.99        38.79        26.04        50.70         1.02 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
        0.92         2.27         0.99         0.69        14.83         9.40 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS 
        1.12         1.81         1.68         1.55         1.32         1.55 
TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AN-A03X 
        1.81         1.18         0.69         0.43         1.74         0.33 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D 
        0.33         0.23         0.33         0.62         2.96         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS 
        8.02         7.36         6.51         0.16         0.33         0.33 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL 
        0.33         6.44         4.64         7.96         7.00         7.59 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX 
        7.17         6.28         6.02         0.33         0.36         0.33 
TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR 
        0.33         0.33         0.33        12.33         0.30         0.33 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L 
        0.33         0.33         0.33         5.33         5.59        80.28 
TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U 
       47.84        66.77        84.69        68.75        47.87        59.05 
TCGA-AO-A03V TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 
       29.13        17.65        24.16        37.48        20.32        22.36 
TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF 
       21.53        50.70        50.86        72.00        76.77        21.37 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 
       26.24        38.53        62.04        55.33        71.80       102.58 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
       99.25        93.70        96.10        77.56        64.04        57.30 
TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ 
       48.36        41.62        28.37        14.73        82.62        61.87 
TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A0Y5 TCGA-AQ-A1H2 
       70.39        17.79        24.79        26.93         5.65        15.62 
TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
       13.22        21.86         9.99        82.88        49.32         5.26 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 
       29.75        24.30        64.83        55.86        76.14        65.36 
TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AK 
       70.16        83.87        76.18        55.36        75.55        51.25 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AR 
       48.82        62.56        43.73        43.56        39.98        17.23 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24L 
       40.83        46.32        42.58        36.26        20.22        73.02 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R 
       65.46        68.19        65.69         0.85        66.05        57.40 
TCGA-AR-A24T TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 
       53.26        50.96        48.16        51.75        56.15        45.17 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH 
       40.64        39.85        34.82        93.83       128.65        20.25 
TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       42.87         7.36        40.04        17.10        20.81        16.96 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       20.38        54.74        16.04        20.45        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IG 
      143.38       149.59        12.13       220.90        50.70       146.50 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0RE TCGA-B6-A0RG 
       18.77       126.12        84.59       110.93       211.56        68.45 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RP 
      189.01       234.28        81.17        78.02       172.96       102.77 
TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS 
      140.48       100.70        89.46       131.21       157.41        97.48 
TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 
      188.68        17.98        21.47       113.79       129.57       129.70 
TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KI 
      186.48        28.27        68.94        58.88       101.52        73.51 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B 
      139.17       170.17        85.35        54.28        49.94        82.88 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B0 
       55.00        24.53        38.79        20.45        28.50        46.95 
TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 
       40.83        39.55        39.16        48.36        56.98        51.68 
TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ 
       37.22        32.02        18.21        25.71        24.85        21.70 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       61.68        35.67        48.69        27.19        53.69        53.95 
TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 
       45.57        49.94        11.67        49.05        41.75        44.02 
TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH 
       48.13        42.90        45.83        31.17        23.44        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ 
       22.13        13.91        48.23        17.26        15.65         3.22 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 
       45.17        47.41        16.27         4.41        15.68        14.30 
TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ 
       46.19        24.49        31.00        24.43        30.35        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 
       15.16        37.78        35.51        24.56        23.08        41.00 
TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       52.96        26.50        20.38         5.85         2.50        13.61 
TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX 
       36.85        12.89        51.32        27.25        50.79         5.59 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F 
       23.93        24.95        42.35        44.81        23.05         8.81 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18N 
        2.01         7.23        20.12        90.84        72.56        37.74 
TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U 
       30.28        55.63        37.55        66.05         7.36        51.39 
TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW 
       51.16        91.99       113.82        82.85        42.28        55.69 
TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 
       49.58        17.69        25.81        31.53        89.16        97.48 
TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG 
       24.66       120.62       114.15        33.17        74.73       122.89 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR 
       36.92        63.35        55.00        45.63        72.07       144.59 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 
       72.07         6.90         0.72        38.60        83.31        57.83 
TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
      130.16        10.65         6.44        20.12         0.99       109.28 
TCGA-BH-A42V TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12Q TCGA-C8-A12U 
        8.94        11.93        11.77        11.77         0.07        12.66 
TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 
       12.66        12.66         1.78         1.45         0.69         0.62 
TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI 
        3.85         3.75        12.33        10.92        11.34        11.34 
TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W 
        0.16        12.03        10.42         3.25         0.30         0.23 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A278 
        0.36         0.43         8.28         9.67         0.03         0.03 
TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A140 
       12.20         0.99         0.03         0.23        11.90        13.25 
TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J8 
       20.58        13.97        14.17        13.48        21.14        14.17 
TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH 
       17.49        16.50        15.78        18.90        12.03        14.01 
TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN 
       18.97        20.09        20.12        20.09        19.40        20.38 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 
       21.01        12.20        13.32        14.70        18.58        17.79 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD 
       16.73        25.74        27.58        18.15         2.66        17.16 
TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XM TCGA-D8-A1XO 
       15.22        14.73        21.83        14.50        17.69         7.96 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV 
       16.41        15.85        16.31         6.35        12.99        15.16 
TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 
       12.66        16.54        15.52         3.81        14.24        14.14 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K 
       17.42        16.04        13.45        13.05        14.43         9.44 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T 
       16.41        13.48         4.80         0.76        10.09        13.08 
TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 
       12.53        12.26        14.50        18.51         7.33        43.00 
TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E 
       27.52        46.59        40.41        37.51        40.11        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S 
       28.87        47.15        40.96        38.24        38.60        33.17 
TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y 
       33.30        43.33        34.26        32.02        31.96        28.60 
TCGA-E2-A14Z TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 
       17.03        23.24        21.04        23.87        14.79        25.05 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15H 
       23.34        22.82        17.29        20.71        21.63        12.92 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O 
       17.42        19.40         9.04        20.58         7.73        13.02 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 
       19.56        17.06        14.99        53.62        53.03        29.95 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF 
       32.35        28.50        16.47        17.10        38.30        37.41 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       32.78        33.73        33.70        28.44        22.65         3.88 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 
       22.19        20.98        11.08        54.18        27.42        39.62 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH 
       19.66        24.59        40.47        28.90        18.87       106.75 
TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
        8.75        43.04         5.52        15.72         7.20        18.05 
TCGA-E2-A574 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1NA TCGA-E9-A1NC 
       19.89        19.20        36.82        12.00        36.56        39.55 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ 
       12.59        35.77        20.05        21.57         9.86        11.90 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 
       14.30         0.62         2.10         6.12         1.38         2.76 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF 
       21.21        32.09        40.24         0.66        34.65         6.58 
TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
       21.27        35.64        34.13         0.79        12.53        13.32 
TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 
       39.09        22.75        12.89        23.51        24.10        17.06 
TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JS 
        0.69         0.85         1.94         0.95        12.56        17.75 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FK 
        0.76        26.07        18.41        15.72         0.23         0.39 
TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
        0.26         0.23        15.39        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OW 
       18.21        18.90        13.25        16.57        15.68        22.82 
TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 
       29.95        29.85        40.41        41.13        39.78        52.96 
TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA 
       29.82        23.11        18.48        30.08         7.86        18.90 
TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH 
       19.99        13.94        10.52        14.43        34.55        19.96 
TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 
       55.00        52.73        25.91        22.09        21.27        17.49 
TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DC 
       10.59         7.40       109.87        59.57       194.27        53.52 
TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       43.04        42.71        61.91        62.33        90.84        76.64 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL 
       77.33        53.36       110.50        38.20        32.28        69.30 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX 
       53.95        57.63        13.55        18.12        11.84        11.57 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
        8.28         6.67         4.60         0.66         2.99         3.58 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y 
        6.90         5.56         3.65         3.25         3.88         4.14 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-OK-A5Q2 
        4.50         5.59         3.22         6.21        15.91         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
       12.66        46.55         7.53        44.61        27.65        24.10 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I 
       26.20        16.87        14.10        10.29        14.76        23.70 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P 
       54.51        33.90        31.07        18.21         7.23         4.44 
TCGA-S3-A6ZG TCGA-W8-A86G 
        6.81         5.29 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.03               0.03 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            176.98             234.28 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            24.345             21.140 
[1] "0.0 - 177.0 (24.3)" "0.0 - 234.3 (21.1)"
[1] "hr=" "1.1"
D20V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10Q GAIN MUTATED         9        7        0        0        43        26
  10Q GAIN WILD-TYPE      71       70        9        9       292       198
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10Q GAIN MUTATED           0         16          4          5        3
  10Q GAIN WILD-TYPE         2        122         23         54       14
                    vv
clus                 STAGE TIS STAGE X
  10Q GAIN MUTATED           1       3
  10Q GAIN WILD-TYPE         0      13
D20V3, multiclass
            clus
vv           10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                   9                 71
  STAGE IA                  7                 70
  STAGE IB                  0                  9
  STAGE II                  0                  9
  STAGE IIA                43                292
  STAGE IIB                26                198
  STAGE III                 0                  2
  STAGE IIIA               16                122
  STAGE IIIB                4                 23
  STAGE IIIC                5                 54
  STAGE IV                  3                 14
  STAGE TIS                 1                  0
  STAGE X                   3                 13
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  10Q GAIN MUTATED    23  77  12   4
  10Q GAIN WILD-TYPE 235 504 105  32
D20V4, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1               23                235
  T2               77                504
  T3               12                105
  T4                4                 32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  10Q GAIN MUTATED    58  36  13   6
  10Q GAIN WILD-TYPE 410 294  98  64
D20V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0               58                410
  N1               36                294
  N2               13                 98
  N3                6                 64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  10Q GAIN MUTATED          0 102   3  12
  10Q GAIN WILD-TYPE        2 743  14 119
D20V6, multiclass
          clus
vv         10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CM0 (I+)                0                  2
  M0                    102                743
  M1                      3                 14
  MX                     12                119
[1] 4 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   116   1
  10Q GAIN WILD-TYPE 868  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED    116    1
  10Q GAIN WILD-TYPE  868   10
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE              116                868
  MALE                  1                 10
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  10Q GAIN MUTATED                            0                            99
  10Q GAIN WILD-TYPE                          1                           636
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  10Q GAIN MUTATED                               10                   2
  10Q GAIN WILD-TYPE                            156                   3
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  10Q GAIN MUTATED                                  3                  0
  10Q GAIN WILD-TYPE                               26                 14
                    vv
clus                 OTHER  SPECIFY
  10Q GAIN MUTATED                3
  10Q GAIN WILD-TYPE             41
D20V8, multiclass
                                  clus
vv                                 10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                  99                636
  INFILTRATING LOBULAR CARCINOMA                 10                156
  MEDULLARY CARCINOMA                             2                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)                3                 26
  MUCINOUS CARCINOMA                              0                 14
  OTHER  SPECIFY                                  3                 41
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V9, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    42  75
  10Q GAIN WILD-TYPE 240 638
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     42   75
  10Q GAIN WILD-TYPE  240  638
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                42                240
  YES               75                638
[1] 2 2
[1] FALSE
D20V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q GAIN MUTATED                                  1     7
  10Q GAIN WILD-TYPE                                0    49
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED                          20    78
  10Q GAIN WILD-TYPE                       117   630
D20V11, multiclass
                                  clus
vv                                 10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           7                 49
  BLACK OR AFRICAN AMERICAN                      20                117
  WHITE                                          78                630
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V12, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     5  90
  10Q GAIN WILD-TYPE  31 706
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      5   90
  10Q GAIN WILD-TYPE   31  706
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                 31
  NOT HISPANIC OR LATINO               90                706
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED   111  17
  11P GAIN WILD-TYPE 749  97
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
               128                846 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                17                 97 
$`11P GAIN MUTATED`
TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A04X 
       20.88        31.79         7.96        22.06        64.04        55.43 
TCGA-A2-A0CM TCGA-A2-A0CT TCGA-A2-A0D0 TCGA-A2-A0EO TCGA-A2-A0EU TCGA-A2-A0T2 
       24.79        75.25        21.14        80.28        34.29         8.38 
TCGA-A2-A0T3 TCGA-A2-A0T7 TCGA-A2-A0YE TCGA-A2-A1FW TCGA-A2-A1G1 TCGA-A2-A3KD 
       18.71        20.75        18.21        17.36        19.20        39.65 
TCGA-A2-A3XT TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26J 
       83.01        38.30        30.61        24.26        23.74        20.61 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A425 TCGA-A7-A4SD TCGA-A7-A6VX TCGA-A8-A075 
       10.59        10.29        14.70        14.50        10.42        17.03 
TCGA-A8-A07F TCGA-A8-A07R TCGA-A8-A08B TCGA-A8-A08I TCGA-A8-A091 TCGA-A8-A09A 
       18.97         8.98        23.08        12.00        19.07         9.99 
TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-AC-A23C 
       29.98        15.02        25.02        21.04         0.99         0.95 
TCGA-AC-A23H TCGA-AC-A62V TCGA-AC-A62Y TCGA-AN-A04C TCGA-AN-A0AJ TCGA-AN-A0AS 
        2.66         0.07         1.81         1.78         8.02         0.33 
TCGA-AN-A0FK TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XU TCGA-AO-A03L TCGA-AO-A0J3 
        7.00         0.33         0.33         0.33        80.28        21.40 
TCGA-AO-A126 TCGA-AO-A12A TCGA-AO-A12B TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AR-A0TW 
       93.70        90.58        77.56       130.09        15.62        24.30 
TCGA-AR-A24K TCGA-AR-A24V TCGA-AR-A250 TCGA-AR-A2LR TCGA-B6-A0I2 TCGA-B6-A0IB 
       50.89        54.18        56.15        20.38       143.38       129.57 
TCGA-B6-A0IH TCGA-B6-A0RS TCGA-B6-A0X0 TCGA-B6-A1KI TCGA-B6-A408 TCGA-BH-A0AU 
      112.37       100.70       129.70        73.51        49.94        24.53 
TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BT TCGA-BH-A0DG TCGA-BH-A0DO TCGA-BH-A0DP 
       24.85        21.70        45.57        23.44        17.26        15.65 
TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A18M TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A202 
       24.43        30.35        72.56        51.16        91.99         0.72 
TCGA-BH-A208 TCGA-BH-A209 TCGA-C8-A12O TCGA-C8-A27A TCGA-D8-A140 TCGA-D8-A1JF 
       57.83       130.16        12.66        12.20        13.25        12.03 
TCGA-D8-A1XF TCGA-D8-A1XK TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y3 TCGA-E2-A14O 
       15.22        14.50        16.54        15.52        14.14        44.68 
TCGA-E2-A14V TCGA-E2-A15A TCGA-E2-A15M TCGA-E2-A15R TCGA-E2-A1AZ TCGA-E2-A1BC 
       34.26        23.34         7.73        17.06        60.53        16.47 
TCGA-E2-A1II TCGA-E2-A1IU TCGA-E2-A574 TCGA-E9-A1N8 TCGA-E9-A1R4 TCGA-E9-A1R6 
       33.70        11.08        19.89        12.00         6.12         2.76 
TCGA-E9-A1RB TCGA-E9-A1RE TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A249 
       20.81        34.65        17.06         0.69        27.22         0.95 
TCGA-E9-A5FL TCGA-EW-A1J1 TCGA-EW-A1J6 TCGA-EW-A1OY TCGA-EW-A1P5 TCGA-EW-A1P8 
        0.26        18.90        28.77        29.85        23.11         7.86 
TCGA-EW-A1PB TCGA-EW-A3U0 TCGA-EW-A423 TCGA-GM-A2DB TCGA-GM-A2DH TCGA-LL-A441 
       19.99        17.49        10.16        53.13        42.28         2.99 
TCGA-LL-A73Y TCGA-OL-A66I 
        4.14        23.70 

$`11P GAIN WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SJ TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N 
       13.68        39.32        28.01        19.20        18.21       104.81 
TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04V TCGA-A2-A04Y 
       18.02        41.95        82.16        73.84        63.12        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
      125.59        64.57       112.08        92.48        88.60       107.93 
TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D1 
       75.55         5.19        63.45        64.04        56.81        34.55 
TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP 
       33.76        28.77        25.22       101.72        89.36       107.61 
TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EV TCGA-A2-A0EW 
       79.76        74.40        37.05        35.05        31.82        29.75 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW 
       24.72        24.16        99.19        54.64        27.12        44.88 
TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T4 TCGA-A2-A0T5 
       50.43        44.28        17.52        17.13        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH 
       18.90        32.55        25.28        15.42        21.90        21.67 
TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT 
       14.50        18.61        19.33        14.63        31.73        23.77 
TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 
       23.47        36.79        22.45        20.25        19.56        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       52.47       107.70        16.31        17.19        18.15        91.92 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW 
       10.59        20.88        33.93        29.98        14.07        49.48 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX 
       38.40        34.98        31.99        38.37         7.30         9.01 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE 
        8.81         8.91        12.00         6.74         3.42        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D 
       34.29        35.47        37.45        35.67        33.11        31.73 
TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26H 
       10.72        12.72        23.61        29.56        31.36        23.80 
TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A426 
       21.73        22.32        11.34        11.28        13.41        11.97 
TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV 
       14.93        13.74        21.17        17.92        14.73        12.10 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06O 
       10.72        11.05        10.29         9.37         8.75        13.02 
TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X 
       13.02         1.02        17.98        41.06        29.03        31.00 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E 
       26.01         1.02        53.98         9.01        33.01        19.99 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P 
       18.97        14.01        12.00        17.03         9.99        10.98 
TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 
        7.99         9.96         9.99        28.04        18.05        15.06 
TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G 
       36.95        13.02         0.99        19.99        18.05        19.96 
TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S 
       37.05         9.99        31.00        31.00         0.99        19.07 
TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 
       93.04        33.99        40.01        16.01        17.95        41.98 
TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E 
       12.00         9.99        12.00         1.02        13.02        31.00 
TCGA-A8-A09I TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
       33.07         1.02         8.98        19.04        15.02         0.99 
TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A9 TCGA-A8-A0AB 
       14.01        12.00        19.04        13.02        13.02        17.03 
TCGA-A8-A0AD TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM 
       38.04         2.37        10.85         1.48        38.53        38.20 
TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO 
       40.57        55.43        36.99        38.79        26.04        50.70 
TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD 
        1.02         0.92         2.27         0.99         0.69        14.83 
TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ 
        9.40         1.12         1.81         1.68         1.55         1.32 
TCGA-AC-A5XS TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A8OP 
        1.55         1.12         1.18         0.69         0.43         1.74 
TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A 
        0.33         0.33         0.23         0.33         0.62         2.96 
TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AT 
        1.71         7.36         6.51         0.16         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        6.44         4.64         7.96         7.59         7.17         6.28 
TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FZ TCGA-AN-A0XN 
        6.02         0.33         0.36         0.33         0.33         0.33 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XV 
       12.33         0.30         0.33         0.33         0.33         5.33 
TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R 
        5.59        47.84        66.77        81.63        84.69        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J5 
       47.87        59.05        29.13        32.78        17.65        24.16 
TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB 
       37.48        20.32        22.36        53.03        21.53        50.70 
TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI 
       50.86        72.00        76.77        21.37        26.24        38.53 
TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A128 
       62.04        55.33        71.80       102.58        99.25        94.59 
TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
       96.10        64.04        57.30        48.36        41.62        28.37 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT 
       14.73        82.62        61.87        70.39         0.53        17.79 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A0Y5 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O 
       24.79        26.93         5.65        13.22         2.56        21.86 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT 
        9.99        82.88        49.32         5.26        37.41        56.88 
TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 
       29.75        64.83        55.86        76.14        65.36        70.16 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ 
       83.87        76.18        55.36        75.55        61.84        52.77 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP 
       51.25        48.82        62.56        43.73        43.56        39.98 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       43.07        17.23        40.83        46.32        42.58        35.24 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       36.26        20.22       109.58        73.02        65.46        68.19 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T 
       65.69         0.85        66.05        57.40        62.07        53.26 
TCGA-AR-A24U TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 
       53.36        50.96        48.16        51.75        45.17        40.64 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LK 
       39.85        34.82        93.83       128.65        20.25        42.87 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QM 
        7.36        40.04        17.10        20.81        16.96        54.74 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I5 TCGA-B6-A0I9 
       16.04        20.45        10.59        77.62       149.59        12.13 
TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IJ TCGA-B6-A0IK 
      220.90        50.70        65.72       146.50       176.98        18.77 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE 
      126.12        84.59       110.14       110.93       140.88       211.56 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN 
       68.45       189.01       234.28        81.17        78.02       172.96 
TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV 
      162.05       102.77       140.48        89.46       131.21       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY 
       97.48       188.68        79.63        17.98        21.47       113.79 
TCGA-B6-A0WZ TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC 
      129.57       186.48        28.27        68.94        58.88        43.59 
TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A40B 
      101.52       139.17       170.17        85.35        54.28        82.88 
TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 
       55.00        38.79        20.45        25.55        28.50        46.95 
TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 
       40.83        39.55        39.16        48.36        56.94        56.98 
TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BL 
       51.68        37.22        32.02        18.21        25.71        44.05 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       61.68        35.67        48.69        27.19        53.69        53.95 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 
       49.94        11.67        49.05        41.75        44.02        48.13 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       42.90        45.83        31.17        38.01        22.13        13.91 
TCGA-BH-A0DL TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       48.23         3.22         2.56        38.47        45.17        47.41 
TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 
       16.27         4.41        15.68        14.30         9.63        44.81 
TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0GZ TCGA-BH-A0H0 
       46.19        32.65        24.49        31.00        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA 
       37.78        35.51        24.56        23.08        41.00        52.96 
TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ 
       26.50        20.38         5.85         2.50        13.61        36.85 
TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 
       12.89        51.32        27.25        50.79         5.59        23.93 
TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G 
       24.95        42.35        44.81        23.05         8.81         2.01 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18P 
        7.23        20.12        90.84        26.66        37.74        30.28 
TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN 
       55.63        37.55        66.05         7.36        51.39        69.93 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX 
      113.82        82.85        42.28        12.00        55.69        49.58 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 
       17.69        25.81        31.53        89.16        97.48        24.66 
TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH 
      120.62       114.15        33.17        74.73       122.89        36.92 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU 
       63.35        55.00        45.63        72.07       144.59        72.07 
TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
        6.90        38.60        83.31        10.65         6.44        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N 
        0.99       109.28         8.94        11.93        11.77        11.77 
TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X 
       11.77         0.07        12.66        12.66        12.66        12.66 
TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 
        3.12         1.78         1.45         0.69         0.62         3.85 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ 
        3.75        12.33        10.92        11.34        11.34         0.16 
TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W 
       12.03        10.42         2.30         3.25         0.30         0.23 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
        0.36         0.43         8.28         9.67         0.03         0.03 
TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A13Z 
        0.03         0.99         0.03         0.23        11.90        20.88 
TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 
       20.58        13.97        14.17        13.48        21.14        19.20 
TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD 
       14.17        17.49        16.50        18.71        15.78        18.15 
TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK 
       18.90        12.03        14.01        18.97        20.09        20.12 
TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT 
       20.09        19.40        20.38        21.01        12.20        13.32 
TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 
       14.70        18.58        17.79        16.73        25.74        23.90 
TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ 
       27.58        18.15         2.66        17.16        14.73        21.83 
TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS 
       19.92        17.69         7.96        16.41        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y1 
        6.35        12.99        15.16        12.66        15.32         3.81 
TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I 
       14.24        17.42        16.04        13.45        13.05        14.43 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R 
        9.44        16.41        13.48         4.80         0.76        10.09 
TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 
       13.08        12.53        12.26        14.50        18.51         7.33 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B 
       43.00        34.42        27.52        46.59        40.41        37.51 
TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q 
       40.11        28.44        28.87        47.15        40.96        38.24 
TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14X 
       38.60        33.17        33.30        43.33        32.02        31.96 
TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 
       28.60        17.03        25.41        27.12        23.24        19.43 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15C TCGA-E2-A15D 
       21.04        23.87        14.79        25.05        22.82        17.29 
TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J 
       20.71        21.63        18.21        12.92        17.42        19.40 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15S TCGA-E2-A15T 
        9.04        20.58        13.02        19.56        14.07        14.99 
TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BD 
       53.62        53.03        29.95        32.35        28.50        17.10 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK 
       38.30        37.41        32.78        33.73        28.44        22.65 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 
        3.88        22.19        20.98        54.18        27.42        39.62 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH 
       19.66        24.59        40.47        28.90        18.87       106.75 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX 
      102.61         8.75        43.04        16.93         5.52        15.72 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 
        7.20        18.05        22.26        19.20        36.82        13.48 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF 
       13.12        36.56        39.55        12.59        35.77        20.05 
TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 
       21.57         9.86        11.90        14.30         0.62         2.10 
TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RF 
        1.38        21.21        32.09        40.24         0.66         6.58 
TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 
       21.27        34.59        35.64        34.13         0.79        12.53 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H 
       13.32        39.09        22.75        12.89        23.51        24.10 
TCGA-E9-A245 TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT 
        0.85         1.94        12.56         0.72        17.75         0.76 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FK 
       26.07        18.41         0.62        15.72         0.23         0.39 
TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
        0.23        15.39        12.20        39.72         8.48        18.21 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX 
       13.25        16.57        15.68        25.94        22.82        29.95 
TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P6 
       40.41        41.13        39.78        52.96        29.82        18.48 
TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
       30.08        18.90         6.15        13.94        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW 
       34.55        19.96        55.00        52.73        25.91        22.09 
TCGA-EW-A3E8 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       21.27        10.59         7.40       109.87        59.57       194.27 
TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       53.52        43.04        42.71        61.91        62.33        90.84 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
       76.64        77.33        53.36       110.50        38.20        32.28 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW 
       69.30        53.95        57.63        13.55        18.12        11.84 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A442 
       11.57         8.28         6.67         4.60         0.66         3.58 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP 
        6.90         5.56         4.70         3.65         3.19         3.25 
TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 
        2.63         3.88         4.50         4.50         5.59         3.22 
TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 
        6.21        15.91         2.79         2.10        12.66        46.55 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX 
        7.53        44.61        27.65        24.10        26.20        16.87 
TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K 
       14.10        10.29         9.80        14.76        54.51        33.90 
TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-S3-A6ZG TCGA-W8-A86G 
       31.07        18.21         7.23         4.44         6.81         5.29 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.07               0.03 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            143.38             234.28 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             20.68              21.78 
[1] "0.1 - 143.4 (20.7)" "0.0 - 234.3 (21.8)"
[1] "hr=" "1.2"
D21V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11P GAIN MUTATED         9       11        2        1        51        26
  11P GAIN WILD-TYPE      71       66        7        8       284       198
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11P GAIN MUTATED           0         15          3          7        3
  11P GAIN WILD-TYPE         2        123         24         52       14
                    vv
clus                 STAGE TIS STAGE X
  11P GAIN MUTATED           0       1
  11P GAIN WILD-TYPE         1      15
D21V3, multiclass
            clus
vv           11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                   9                 71
  STAGE IA                 11                 66
  STAGE IB                  2                  7
  STAGE II                  1                  8
  STAGE IIA                51                284
  STAGE IIB                26                198
  STAGE III                 0                  2
  STAGE IIIA               15                123
  STAGE IIIB                3                 24
  STAGE IIIC                7                 52
  STAGE IV                  3                 14
  STAGE TIS                 0                  1
  STAGE X                   1                 15
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  11P GAIN MUTATED    30  81  15   3
  11P GAIN WILD-TYPE 228 500 102  33
D21V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1               30                228
  T2               81                500
  T3               15                102
  T4                3                 33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  11P GAIN MUTATED    70  39   9   9
  11P GAIN WILD-TYPE 398 291 102  61
D21V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0               70                398
  N1               39                291
  N2                9                102
  N3                9                 61
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  11P GAIN MUTATED          0 111   3  15
  11P GAIN WILD-TYPE        2 734  14 116
D21V6, multiclass
          clus
vv         11P GAIN MUTATED 11P GAIN WILD-TYPE
  CM0 (I+)                0                  2
  M0                    111                734
  M1                      3                 14
  MX                     15                116
[1] 4 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   127   2
  11P GAIN WILD-TYPE 857   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED    127    2
  11P GAIN WILD-TYPE  857    9
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE              127                857
  MALE                  2                  9
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  11P GAIN MUTATED                            0                           107
  11P GAIN WILD-TYPE                          1                           628
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  11P GAIN MUTATED                                9                   1
  11P GAIN WILD-TYPE                            157                   4
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  11P GAIN MUTATED                                  1                  2
  11P GAIN WILD-TYPE                               28                 12
                    vv
clus                 OTHER  SPECIFY
  11P GAIN MUTATED                9
  11P GAIN WILD-TYPE             35
D21V8, multiclass
                                  clus
vv                                 11P GAIN MUTATED 11P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 107                628
  INFILTRATING LOBULAR CARCINOMA                  9                157
  MEDULLARY CARCINOMA                             1                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                1                 28
  MUCINOUS CARCINOMA                              2                 12
  OTHER  SPECIFY                                  9                 35
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V9, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    37  92
  11P GAIN WILD-TYPE 245 621
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     37   92
  11P GAIN WILD-TYPE  245  621
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                37                245
  YES               92                621
[1] 2 2
[1] FALSE
D21V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P GAIN MUTATED                                  0     5
  11P GAIN WILD-TYPE                                1    51
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED                          16    94
  11P GAIN WILD-TYPE                       121   614
D21V11, multiclass
                                  clus
vv                                 11P GAIN MUTATED 11P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           5                 51
  BLACK OR AFRICAN AMERICAN                      16                121
  WHITE                                          94                614
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V12, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     6 103
  11P GAIN WILD-TYPE  30 693
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      6  103
  11P GAIN WILD-TYPE   30  693
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                 30
  NOT HISPANIC OR LATINO              103                693
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    73  16
  11Q GAIN WILD-TYPE 787  98
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                89                885 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                16                 98 
$`11Q GAIN MUTATED`
TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A2-A0D0 TCGA-A2-A0EO TCGA-A2-A0EU TCGA-A2-A0EY 
       20.88        31.79        21.14        80.28        34.29        24.16 
TCGA-A2-A0YE TCGA-A2-A0YJ TCGA-A2-A1G1 TCGA-A2-A3XT TCGA-A7-A0CD TCGA-A7-A26F 
       18.21        18.61        19.20        83.01        38.30        24.26 
TCGA-A7-A26G TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A6VX TCGA-A8-A075 TCGA-A8-A07F 
       23.74        10.59        10.29        10.42        17.03        18.97 
TCGA-A8-A07G TCGA-A8-A07R TCGA-A8-A08B TCGA-A8-A08I TCGA-A8-A09A TCGA-A8-A09Q 
       18.97         8.98        23.08        12.00         9.99        25.02 
TCGA-A8-A0A7 TCGA-AC-A62V TCGA-AC-A62Y TCGA-AN-A04C TCGA-AN-A0AJ TCGA-AN-A0FK 
        0.99         0.07         1.81         1.78         8.02         7.00 
TCGA-AN-A0FY TCGA-AN-A0XU TCGA-AO-A12A TCGA-AO-A12B TCGA-AQ-A04L TCGA-AR-A0TW 
        0.33         0.33        90.58        77.56       130.09        24.30 
TCGA-AR-A24K TCGA-AR-A24V TCGA-B6-A0IE TCGA-B6-A0IO TCGA-B6-A0RS TCGA-B6-A0X0 
       50.89        54.18        65.72       110.14       100.70       129.70 
TCGA-B6-A1KI TCGA-B6-A408 TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BT TCGA-BH-A0DG 
       73.51        49.94        24.85        21.70        45.57        23.44 
TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0GY TCGA-BH-A18M TCGA-BH-A18T TCGA-BH-A18U 
       17.26        15.65        30.35        72.56         7.36        51.39 
TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1FC TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 
       51.16        91.99       114.15         0.72        38.60        57.83 
TCGA-BH-A209 TCGA-D8-A140 TCGA-D8-A1JF TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XW 
      130.16        13.25        12.03        21.83        14.50        12.66 
TCGA-D8-A1XY TCGA-D8-A1Y3 TCGA-E2-A15A TCGA-E2-A15R TCGA-E2-A1AZ TCGA-E2-A1B0 
       16.54        14.14        23.34        17.06        60.53        53.62 
TCGA-E2-A1II TCGA-E2-A574 TCGA-E9-A1N8 TCGA-E9-A1R6 TCGA-E9-A1RB TCGA-E9-A244 
       33.70        19.89        12.00         2.76        20.81         0.69 
TCGA-E9-A249 TCGA-E9-A5FL TCGA-EW-A1J6 TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A2FW 
        0.95         0.26        28.77        23.11         7.86        22.09 
TCGA-EW-A3U0 TCGA-GM-A2DB TCGA-GM-A2DH TCGA-LL-A441 TCGA-OL-A66I 
       17.49        53.13        42.28         2.99        23.70 

$`11Q GAIN WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ 
       13.68         7.96        39.32        28.01        19.20        18.21 
TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U 
      104.81        18.02        41.95        82.16        73.84        22.06 
TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL 
       63.12        64.04        55.43        36.13       125.59        64.57 
TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS 
       24.79       112.08        92.48        88.60       107.93        75.55 
TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D1 
       75.25         5.19        63.45        64.04        56.81        34.55 
TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP 
       33.76        28.77        25.22       101.72        89.36       107.61 
TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EV TCGA-A2-A0EW 
       79.76        74.40        37.05        35.05        31.82        29.75 
TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX 
       24.72        99.19        54.64        27.12        44.88        50.43 
TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 
       44.28        17.52        17.13         8.38        18.71        20.52 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF 
       17.46        18.90        20.75        32.55        25.28        15.42 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       21.90        21.67        14.50        19.33        14.63        31.73 
TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 
       23.77        23.47        17.36        36.79        22.45        20.25 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C 
       19.56        16.47        52.47       107.70        16.31        17.19 
TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS 
       18.15        91.92        10.59        20.88        39.65        33.93 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ 
       29.98        14.07        49.48        38.40        34.98        31.99 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 
       38.37         7.30         9.01         8.81         8.91        12.00 
TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ 
        6.74         3.42        35.31        34.29        35.47        30.61 
TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F 
       37.45        35.67        33.11        31.73        10.72        12.72 
TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J 
       23.61        29.56        31.36        23.80        21.73        20.61 
TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 
       22.32        11.34        11.28        13.41        14.70        11.97 
TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D 
       14.93        13.74        14.50        21.17        17.92        14.73 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY 
       12.10        10.72        11.05        10.29         9.37         8.75 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U 
       13.02        13.02         1.02        17.98        41.06        29.03 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B 
       31.00        26.01         1.02        53.98         9.01        33.01 
TCGA-A8-A07E TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P 
       19.99        14.01        12.00        17.03         9.99        10.98 
TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 
        7.99         9.96         9.99        28.04        18.05        15.06 
TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G 
       36.95        13.02         0.99        19.99        18.05        19.96 
TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S 
       37.05         9.99        31.00        31.00         0.99        19.07 
TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 
       93.04        33.99        40.01        19.07        16.01        17.95 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D 
       41.98        12.00         9.99        12.00         1.02        13.02 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R 
       31.00        33.07        29.98        15.02         1.02         8.98 
TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 
       19.04        15.02         0.99        14.01        12.00        19.04 
TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C 
       13.02        21.04        13.02        17.03        38.04         0.95 
TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM 
        2.37        10.85         2.66         1.48        38.53        38.20 
TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO 
       40.57        55.43        36.99        38.79        26.04        50.70 
TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD 
        1.02         0.92         2.27         0.99         0.69        14.83 
TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ 
        9.40         1.12         1.81         1.68         1.55         1.32 
TCGA-AC-A5XS TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A8OP 
        1.55         1.12         1.18         0.69         0.43         1.74 
TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A 
        0.33         0.33         0.23         0.33         0.62         2.96 
TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS 
        1.71         7.36         6.51         0.16         0.33         0.33 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FN 
        0.33         6.44         4.64         7.96         7.59         7.17 
TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FZ 
        6.28         6.02         0.33         0.36         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS 
        0.33         0.33        12.33         0.30         0.33         0.33 
TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N 
        0.33         5.33         5.59        80.28        47.84        66.77 
TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V 
       81.63        84.69        68.75        47.87        59.05        29.13 
TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 
       32.78        21.40        17.65        24.16        37.48        20.32 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD 
       22.36        53.03        21.53        50.70        50.86        72.00 
TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL 
       76.77        21.37        26.24        38.53        62.04        55.33 
TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 
       71.80       102.58        99.25        93.70        94.59        96.10 
TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
       64.04        57.30        48.36        41.62        28.37        14.73 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H 
       82.62        61.87        70.39         0.53        17.79        24.79 
TCGA-AQ-A04J TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O 
       26.93         5.65        15.62        13.22         2.56        21.86 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT 
        9.99        82.88        49.32         5.26        37.41        56.88 
TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 
       29.75        64.83        55.86        76.14        65.36        70.16 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ 
       83.87        76.18        55.36        75.55        61.84        52.77 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP 
       51.25        48.82        62.56        43.73        43.56        39.98 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       43.07        17.23        40.83        46.32        42.58        35.24 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       36.26        20.22       109.58        73.02        65.46        68.19 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T 
       65.69         0.85        66.05        57.40        62.07        53.26 
TCGA-AR-A24U TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 
       53.36        50.96        48.16        51.75        56.15        45.17 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH 
       40.64        39.85        34.82        93.83       128.65        20.25 
TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       42.87         7.36        40.04        17.10        20.81        16.96 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       20.38        54.74        16.04        20.45        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC 
      143.38       149.59        12.13       220.90       129.57        50.70 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
      146.50       112.37       176.98        18.77       126.12        84.59 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
      110.93       140.88       211.56        68.45       189.01       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ 
       81.17        78.02       172.96       162.05       102.77       140.48 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV 
       89.46       131.21       157.41        97.48       188.68        79.63 
TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X1 TCGA-B6-A0X4 
       17.98        21.47       113.79       129.57       186.48        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU 
       68.94        58.88        43.59       101.52       139.17       170.17 
TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV 
       85.35        54.28        82.88        55.00        24.53        38.79 
TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 
       20.45        25.55        28.50        46.95        40.83        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA 
       39.16        48.36        56.94        56.98        51.68        37.22 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO 
       32.02        18.21        25.71        44.05        61.68        35.67 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW 
       48.69        27.19        53.69        53.95        49.94        11.67 
TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD 
       49.05        41.75        44.02        48.13        42.90        45.83 
TCGA-BH-A0DE TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DQ 
       31.17        38.01        22.13        13.91        48.23         3.22 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
        2.56        38.47        45.17        47.41        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA 
       15.68        14.30         9.63        44.81        46.19        32.65 
TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       24.49        31.00        24.43        10.78        15.16        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB 
       35.51        24.56        23.08        41.00        52.96        26.50 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU 
       20.38         5.85         2.50        13.61        36.85        12.89 
TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 
       51.32        27.25        50.79         5.59        23.93        24.95 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I 
       42.35        44.81        23.05         8.81         2.01         7.23 
TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q 
       20.12        90.84        26.66        37.74        30.28        55.63 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU 
       37.55        66.05        69.93       113.82        82.85        42.28 
TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 
       12.00        55.69        49.58        17.69        25.81        31.53 
TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE 
       89.16        97.48        24.66       120.62        33.17        74.73 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN 
      122.89        36.92        63.35        55.00        45.63        72.07 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A204 TCGA-BH-A28O TCGA-BH-A28Q 
      144.59        72.07         6.90        83.31        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12L TCGA-C8-A12M 
       20.12         0.99       109.28         8.94        11.93        11.77 
TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V 
       11.77        12.66        11.77         0.07        12.66        12.66 
TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 
       12.66        12.66         3.12         1.78         1.45         0.69 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG 
        0.62         3.85         3.75        12.33        10.92        11.34 
TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN 
       11.34         0.16        12.03        10.42         2.30         3.25 
TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 
        0.30         0.23         0.36         0.43         8.28         9.67 
TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 
        0.03         0.03         0.03        12.20         0.99         0.03 
TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 
        0.23        11.90        20.88        20.58        13.97        14.17 
TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA 
       13.48        21.14        19.20        14.17        17.49        16.50 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH 
       18.71        15.78        18.15        18.90        12.03        14.01 
TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN 
       18.97        20.09        20.12        20.09        19.40        20.38 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 
       21.01        12.20        13.32        14.70        18.58        17.79 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC 
       16.73        25.74        23.90        27.58        18.15         2.66 
TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO 
       17.16        15.22        14.73        19.92        17.69         7.96 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV 
       16.41        15.85        16.31         6.35        12.99        15.16 
TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27F 
       15.32        15.52         3.81        14.24        17.42        16.04 
TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M 
       13.45        13.05        14.43         9.44        16.41        13.48 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W 
        4.80         0.76        10.09        13.08        12.53        12.26 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 
       14.50        18.51         7.33        43.00        34.42        27.52 
TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F 
       46.59        40.41        37.51        40.11        28.44        28.87 
TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S 
       47.15        44.68        40.96        38.24        38.60        33.17 
TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y 
       33.30        43.33        34.26        32.02        31.96        28.60 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 
       17.03        25.41        27.12        23.24        19.43        21.04 
TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E 
       23.87        14.79        25.05        22.82        17.29        20.71 
TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       21.63        18.21        12.92        17.42        19.40         9.04 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15S TCGA-E2-A15T 
       20.58         7.73        13.02        19.56        14.07        14.99 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD 
       53.03        29.95        32.35        28.50        16.47        17.10 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK 
       38.30        37.41        32.78        33.73        28.44        22.65 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 
        3.88        22.19        20.98        11.08        54.18        27.42 
TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG 
       39.62        19.66        24.59        40.47        28.90        18.87 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 
      106.75       102.61         8.75        43.04        16.93         5.52 
TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E9-A1N4 TCGA-E9-A1N5 
       15.72         7.20        18.05        22.26        19.20        36.82 
TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE 
       13.48        13.12        36.56        39.55        12.59        35.77 
TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       20.05        21.57         9.86        11.90        14.30         0.62 
TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RC 
        2.10         6.12         1.38        21.21        32.09        40.24 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI 
        0.66        34.65         6.58        21.27        34.59        35.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       34.13         0.79        12.53        13.32        39.09        22.75 
TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A245 TCGA-E9-A247 
       12.89        23.51        24.10        17.06         0.85        27.22 
TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO 
        1.94        12.56         0.72        17.75         0.76        26.07 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UO 
       18.41         0.62        15.72         0.23         0.39         0.23 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 
       15.39        12.20        39.72         8.48        18.21        18.90 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX 
       13.25        16.57        15.68        25.94        22.82        29.95 
TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 
       29.85        40.41        41.13        39.78        52.96        29.82 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD 
       18.48        30.08        18.90        19.99         6.15        13.94 
TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS 
       10.52        14.43        34.55        19.96        55.00        52.73 
TCGA-EW-A2FV TCGA-EW-A3E8 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 
       25.91        21.27        10.16        10.59         7.40       109.87 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DI 
       59.57       194.27        53.52        43.04        42.71        61.91 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
       62.33        90.84        76.64        77.33        53.36       110.50 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV 
       38.20        32.28        69.30        53.95        57.63        13.55 
TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 
       18.12        11.84        11.57         8.28         6.67         4.60 
TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN 
        0.66         3.58         6.90         5.56         4.70         3.65 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z 
        3.19         3.25         2.63         3.88         4.14         4.50 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-MS-A51U 
        4.50         5.59         3.22         6.21        15.91         2.79 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.10        12.66        46.55         7.53        44.61        27.65 
TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 
       24.10        26.20        16.87        14.10        10.29         9.80 
TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O 
       14.76        54.51        33.90        31.07        18.21         7.23 
TCGA-OL-A66P TCGA-S3-A6ZG TCGA-W8-A86G 
        4.44         6.81         5.29 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.07               0.03 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            130.16             234.28 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             21.83              21.37 
[1] "0.1 - 130.2 (21.8)" "0.0 - 234.3 (21.4)"
[1] "hr=" "1.5"
D22V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11Q GAIN MUTATED         8        5        1        1        34        22
  11Q GAIN WILD-TYPE      72       72        8        8       301       202
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11Q GAIN MUTATED           0          9          2          4        1
  11Q GAIN WILD-TYPE         2        129         25         55       16
                    vv
clus                 STAGE TIS STAGE X
  11Q GAIN MUTATED           1       1
  11Q GAIN WILD-TYPE         0      15
D22V3, multiclass
            clus
vv           11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                   8                 72
  STAGE IA                  5                 72
  STAGE IB                  1                  8
  STAGE II                  1                  8
  STAGE IIA                34                301
  STAGE IIB                22                202
  STAGE III                 0                  2
  STAGE IIIA                9                129
  STAGE IIIB                2                 25
  STAGE IIIC                4                 55
  STAGE IV                  1                 16
  STAGE TIS                 1                  0
  STAGE X                   1                 15
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  11Q GAIN MUTATED    21  57   8   2
  11Q GAIN WILD-TYPE 237 524 109  34
D22V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1               21                237
  T2               57                524
  T3                8                109
  T4                2                 34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  11Q GAIN MUTATED    46  32   6   4
  11Q GAIN WILD-TYPE 422 298 105  66
D22V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0               46                422
  N1               32                298
  N2                6                105
  N3                4                 66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  11Q GAIN MUTATED          0  79   1   9
  11Q GAIN WILD-TYPE        2 766  16 122
D22V6, multiclass
          clus
vv         11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CM0 (I+)                0                  2
  M0                     79                766
  M1                      1                 16
  MX                      9                122
[1] 4 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    88   1
  11Q GAIN WILD-TYPE 896  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     88    1
  11Q GAIN WILD-TYPE  896   10
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               88                896
  MALE                  1                 10
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  11Q GAIN MUTATED                            0                            72
  11Q GAIN WILD-TYPE                          1                           663
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  11Q GAIN MUTATED                                4                   2
  11Q GAIN WILD-TYPE                            162                   3
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  11Q GAIN MUTATED                                  2                  1
  11Q GAIN WILD-TYPE                               27                 13
                    vv
clus                 OTHER  SPECIFY
  11Q GAIN MUTATED                8
  11Q GAIN WILD-TYPE             36
D22V8, multiclass
                                  clus
vv                                 11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                  72                663
  INFILTRATING LOBULAR CARCINOMA                  4                162
  MEDULLARY CARCINOMA                             2                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)                2                 27
  MUCINOUS CARCINOMA                              1                 13
  OTHER  SPECIFY                                  8                 36
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V9, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    23  66
  11Q GAIN WILD-TYPE 259 647
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     23   66
  11Q GAIN WILD-TYPE  259  647
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                23                259
  YES               66                647
[1] 2 2
[1] FALSE
D22V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q GAIN MUTATED                                  0     1
  11Q GAIN WILD-TYPE                                1    55
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED                          14    65
  11Q GAIN WILD-TYPE                       123   643
D22V11, multiclass
                                  clus
vv                                 11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 55
  BLACK OR AFRICAN AMERICAN                      14                123
  WHITE                                          65                643
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V12, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     4  72
  11Q GAIN WILD-TYPE  32 724
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      4   72
  11Q GAIN WILD-TYPE   32  724
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 32
  NOT HISPANIC OR LATINO               72                724
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED   183  27
  12P GAIN WILD-TYPE 677  87
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               210                764 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                27                 87 
$`12P GAIN MUTATED`
TCGA-A1-A0SF TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A04P TCGA-A2-A04T 
       48.10        39.32        28.01        19.20        18.02        73.84 
TCGA-A2-A04U TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0ET 
       22.06        75.55         5.19        56.81        21.14        35.05 
TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EY TCGA-A2-A0YE TCGA-A2-A0YH TCGA-A2-A1FW 
       34.29        31.82        24.16        18.21        21.67        17.36 
TCGA-A2-A1G1 TCGA-A2-A3XS TCGA-A2-A3XW TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A13E 
       19.20        33.93        49.48        38.30        35.31        10.72 
TCGA-A7-A13F TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A425 TCGA-A7-A4SB TCGA-A7-A4SD 
       12.72        20.61        22.32        14.70        13.74        14.50 
TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A8-A076 
       21.17        14.73        12.10         9.37        10.42        53.98 
TCGA-A8-A079 TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A08G 
        9.01         8.98         9.96         9.99        28.04        19.96 
TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A092 TCGA-A8-A09A TCGA-A8-A09C 
       37.05        31.00        19.07        16.01         9.99         1.02 
TCGA-A8-A09N TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A9 TCGA-AC-A23E TCGA-AC-A2FM 
        1.02        14.01        12.00        13.02         2.37        26.04 
TCGA-AC-A2QH TCGA-AC-A3W5 TCGA-AC-A62X TCGA-AN-A03Y TCGA-AN-A04C TCGA-AN-A0FJ 
        1.02         1.81         1.12         0.33         1.78         7.96 
TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AO-A03L 
        6.02         0.36         0.33         0.33         0.33        80.28 
TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A0J2 TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A0JD 
       66.77        84.69        32.78        20.32        53.03        72.00 
TCGA-AO-A124 TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AQ-A0Y5 
      102.58        57.30        48.36        61.87         0.53         5.65 
TCGA-AQ-A54O TCGA-AR-A0TQ TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AK TCGA-AR-A1AQ 
       21.86        49.32        83.87        55.36        51.25        43.07 
TCGA-AR-A1AV TCGA-AR-A24H TCGA-AR-A24Q TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24Z 
       42.58       109.58        66.05        54.18        50.96        51.75 
TCGA-AR-A250 TCGA-AR-A2LM TCGA-AR-A2LR TCGA-AR-A5QM TCGA-B6-A0I2 TCGA-B6-A0IO 
       56.15        40.04        20.38        54.74       143.38       110.14 
TCGA-B6-A0RO TCGA-B6-A0WV TCGA-B6-A0WY TCGA-B6-A0X1 TCGA-B6-A1KC TCGA-B6-A1KI 
      162.05        79.63       113.79       186.48        43.59        73.51 
TCGA-B6-A402 TCGA-B6-A408 TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0B5 TCGA-BH-A0B9 
       54.28        49.94        24.53        38.79        48.36        51.68 
TCGA-BH-A0BA TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BT TCGA-BH-A0C1 TCGA-BH-A0DD 
       37.22        24.85        44.05        45.57        44.02        45.83 
TCGA-BH-A0E0 TCGA-BH-A0E7 TCGA-BH-A0EB TCGA-BH-A0GY TCGA-BH-A0HX TCGA-BH-A0WA 
        4.41        44.81        24.49        30.35        27.25        23.05 
TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18R TCGA-BH-A18V TCGA-BH-A1EO 
       90.84        26.66        37.74        37.55        51.16        91.99 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1FC TCGA-BH-A1FM TCGA-BH-A202 
       42.28        12.00        55.69       114.15        45.63         0.72 
TCGA-BH-A203 TCGA-C8-A12L TCGA-C8-A12O TCGA-C8-A12W TCGA-C8-A130 TCGA-C8-A1HI 
       38.60        11.93        12.66        12.66         3.12        11.34 
TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A26Z TCGA-C8-A278 TCGA-D8-A13Z TCGA-D8-A143 
       12.03         2.30         8.28         0.03        20.88        14.17 
TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JL TCGA-D8-A1JM 
       19.20        14.17        15.78        18.15        20.09        19.40 
TCGA-D8-A1XD TCGA-D8-A1XJ TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 
       17.16        21.83        12.99        16.54        15.32        15.52 
TCGA-D8-A27M TCGA-D8-A27R TCGA-D8-A27W TCGA-D8-A3Z6 TCGA-E2-A107 TCGA-E2-A109 
       13.48        10.09        12.26        18.51        34.42        46.59 
TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A14O TCGA-E2-A14W TCGA-E2-A152 TCGA-E2-A15A 
       37.51        40.11        44.68        32.02        27.12        23.34 
TCGA-E2-A15G TCGA-E2-A15O TCGA-E2-A15S TCGA-E2-A1AZ TCGA-E2-A1IH TCGA-E2-A1II 
       18.21        13.02        14.07        60.53        33.73        33.70 
TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A56Z TCGA-E2-A573 TCGA-E9-A1N6 TCGA-E9-A1N8 
       43.04        16.93         7.20        22.26        13.48        12.00 
TCGA-E9-A1N9 TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1R6 TCGA-E9-A1RB TCGA-E9-A1RC 
       13.12        20.05         9.86         2.76        20.81        40.24 
TCGA-E9-A1RG TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A295 TCGA-E9-A2JS TCGA-EW-A1J6 
       21.27        17.06        27.22         0.72        17.75        28.77 
TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A2FV TCGA-GI-A2C9 
       22.82        29.82        23.11         7.86        25.91       109.87 
TCGA-GM-A2DD TCGA-GM-A2DI TCGA-GM-A3XL TCGA-LD-A66U TCGA-LL-A440 TCGA-LL-A441 
       43.04        61.91        69.30         8.28         0.66         2.99 
TCGA-LL-A6FQ TCGA-LL-A7SZ TCGA-OL-A5RV TCGA-OL-A5RZ TCGA-OL-A66O TCGA-S3-A6ZG 
        2.63         5.59        24.10        10.29         7.23         6.81 

$`12P GAIN WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI 
        8.52        14.37        43.43        14.27        47.24        20.88 
TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04Q 
       13.68        31.79         7.96        18.21       104.81        41.95 
TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK 
       82.16        63.12        64.04        55.43        36.13       125.59 
TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
       64.57        24.79       112.08        92.48        88.60       107.93 
TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 
       75.25        63.45        64.04        34.55        33.76        28.77 
TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ 
       25.22       101.72        89.36        80.28       107.61        79.76 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU 
       74.40        37.05        29.75        24.72        99.19        54.64 
TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 
       27.12        44.88        50.43        44.28        17.52        17.13 
TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 
        8.38        18.71        20.52        17.46        18.90        20.75 
TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YI TCGA-A2-A0YJ 
       32.55        25.28        15.42        21.90        14.50        18.61 
TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FX 
       19.33        14.63        31.73        23.77        23.47        36.79 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A 
       22.45        20.25        19.56        16.47        52.47       107.70 
TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
       16.31        17.19        18.15        91.92        10.59        20.88 
TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XX TCGA-A2-A3XY 
       39.65        83.01        29.98        14.07        38.40        34.98 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       31.99        38.37         7.30         9.01         8.81         8.91 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ 
       12.00         6.74         3.42        34.29        35.47        30.61 
TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13G TCGA-A7-A13H 
       37.45        35.67        33.11        31.73        23.61        29.56 
TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A3IY 
       31.36        24.26        23.74        23.80        21.73        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A426 TCGA-A7-A4SA 
       10.59        10.29        11.28        13.41        11.97        14.93 
TCGA-A7-A4SF TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VY TCGA-A8-A06O 
       17.92        10.72        11.05        10.29         8.75        13.02 
TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X 
       13.02         1.02        17.98        41.06        29.03        31.00 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F 
       26.01         1.02        17.03        33.01        19.99        18.97 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P 
       18.97        14.01        12.00        17.03         9.99        10.98 
TCGA-A8-A07S TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A 
        7.99        18.05        15.06        36.95        13.02         0.99 
TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O 
       23.08        19.99        18.05        12.00         9.99        31.00 
TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A093 
        0.99        93.04        33.99        40.01        19.07        17.95 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09E 
       41.98        12.00         9.99        12.00        13.02        31.00 
TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T 
       33.07        29.98        15.02        25.02         8.98        19.04 
TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 
       15.02         0.99        19.04        13.02        21.04         0.99 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 
       17.03        38.04         0.95        10.85         2.66         1.48 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
       38.53        38.20        40.57        55.43        36.99        38.79 
TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD 
       50.70         0.92         2.27         0.99         0.69        14.83 
TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS 
        9.40         1.12         1.68         1.55         1.32         1.55 
TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A8OP 
        0.07         1.81         1.18         0.69         0.43         1.74 
TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D 
        0.33         0.23         0.33         0.62         2.96         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS 
        8.02         7.36         6.51         0.16         0.33         0.33 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN 
        0.33         6.44         4.64         7.00         7.59         7.17 
TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP 
        6.28         0.33         0.33         0.33        12.33         0.30 
TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW 
        0.33         0.33         0.33         0.33         5.33         5.59 
TCGA-AO-A03M TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V 
       47.84        81.63        68.75        47.87        59.05        29.13 
TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0JA 
       21.40        17.65        24.16        37.48        22.36        21.53 
TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI 
       50.70        50.86        76.77        21.37        26.24        38.53 
TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 
       62.04        55.33        71.80        99.25        93.70        94.59 
TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12G TCGA-AO-A12H 
       96.10        90.58        77.56        64.04        41.62        28.37 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J 
       14.73        82.62        70.39        17.79        24.79        26.93 
TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A0TP 
      130.09        15.62        13.22         2.56         9.99        82.88 
TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX 
        5.26        37.41        56.88        29.75        24.30        64.83 
TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A1AH 
       55.86        76.14        65.36        70.16        76.18        75.55 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO 
       61.84        52.77        48.82        62.56        43.73        43.56 
TCGA-AR-A1AP TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX 
       39.98        17.23        40.83        46.32        35.24        36.26 
TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       20.22        50.89        73.02        65.46        68.19        65.69 
TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X 
        0.85        57.40        62.07        53.26        53.36        48.16 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE 
       45.17        40.64        39.85        34.82        93.83       128.65 
TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       20.25        42.87         7.36        17.10        20.81        16.96 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I5 TCGA-B6-A0I9 
       16.04        20.45        10.59        77.62       149.59        12.13 
TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH 
      220.90       129.57        50.70        65.72       146.50       112.37 
TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ 
      176.98        18.77       126.12        84.59       110.93       140.88 
TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM 
      211.56        68.45       189.01       234.28        81.17        78.02 
TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU 
      172.96       102.77       140.48       100.70        89.46       131.21 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WZ 
      157.41        97.48       188.68        17.98        21.47       129.57 
TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KN 
      129.70        28.27        68.94        58.88       101.52       139.17 
TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AW TCGA-BH-A0AY 
      170.17        85.35        82.88        55.00        20.45        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B6 
       28.50        46.95        40.83        39.55        39.16        56.94 
TCGA-BH-A0B7 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BM 
       56.98        32.02        18.21        25.71        21.70        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV 
       35.67        48.69        27.19        53.69        53.95        49.94 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DE 
       11.67        49.05        41.75        48.13        42.90        31.17 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO 
       23.44        38.01        22.13        13.91        48.23        17.26 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       15.65         3.22         2.56        38.47        45.17        47.41 
TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EA 
       16.27        15.68        14.30         9.63        46.19        32.65 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       31.00        24.43        10.78        15.16        37.78        35.51 
TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI 
       24.56        23.08        41.00        52.96        26.50        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW 
        5.85         2.50        13.61        36.85        12.89        51.32 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       50.79         5.59        23.93        24.95        42.35        44.81 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18M TCGA-BH-A18P 
        8.81         2.01         7.23        20.12        72.56        30.28 
TCGA-BH-A18Q TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1ES 
       55.63        66.05         7.36        51.39        69.93       113.82 
TCGA-BH-A1ET TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 
       82.85        49.58        17.69        25.81        31.53        89.16 
TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG 
       97.48        24.66       120.62        33.17        74.73       122.89 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU 
       36.92        63.35        55.00        72.07       144.59        72.07 
TCGA-BH-A201 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q 
        6.90        83.31        57.83       130.16        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12M TCGA-C8-A12N 
       20.12         0.99       109.28         8.94        11.77        11.77 
TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A131 
       11.77         0.07        12.66        12.66        12.66         1.78 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE 
        1.45         0.69         0.62         3.85         3.75        12.33 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26V 
       10.92        11.34         0.16        10.42         3.25         0.30 
TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
        0.23         0.36         0.43         9.67         0.03         0.03 
TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A140 
       12.20         0.99         0.03         0.23        11.90        13.25 
TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J9 TCGA-D8-A1JA 
       20.58        13.97        13.48        21.14        17.49        16.50 
TCGA-D8-A1JB TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI 
       18.71        18.90        12.03        12.03        14.01        18.97 
TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT 
       20.09        20.12        20.38        21.01        12.20        13.32 
TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 
       14.70        18.58        17.79        16.73        25.74        23.90 
TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XK 
       27.58        18.15         2.66        15.22        14.73        14.50 
TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS 
       19.92        17.69         7.96        16.41        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 
        6.35        15.16        12.66         3.81        14.24        14.14 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K 
       17.42        16.04        13.45        13.05        14.43         9.44 
TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 
       16.41         4.80         0.76        13.08        12.53        14.50 
TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10E TCGA-E2-A10F 
        7.33        43.00        27.52        40.41        28.44        28.87 
TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T 
       47.15        40.96        38.24        38.60        33.17        33.30 
TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 
       43.33        34.26        31.96        28.60        17.03        25.41 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 
       23.24        19.43        21.04        23.87        14.79        25.05 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15I 
       22.82        17.29        20.71        21.63        12.92        17.42 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R 
       19.40         9.04        20.58         7.73        19.56        17.06 
TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       14.99        53.62        53.03        29.95        32.35        28.50 
TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IJ 
       16.47        17.10        38.30        37.41        32.78        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       22.65         3.88        22.19        20.98        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       27.42        39.62        19.66        24.59        40.47        28.90 
TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P6 TCGA-E2-A3DX 
       18.87       106.75       102.61         8.75         5.52        15.72 
TCGA-E2-A570 TCGA-E2-A574 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1NA TCGA-E9-A1NC 
       18.05        19.89        19.20        36.82        36.56        39.55 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       12.59        35.77        21.57        11.90        14.30         0.62 
TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RD 
        2.10         6.12         1.38        21.21        32.09         0.66 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
       34.65         6.58        34.59        35.64        34.13         0.79 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G 
       12.53        13.32        39.09        22.75        12.89        23.51 
TCGA-E9-A22H TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A 
       24.10         0.69         0.85         1.94         0.95        12.56 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54Y 
        0.76        26.07        18.41         0.62        15.72         0.23 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
        0.39         0.26         0.23        15.39        12.20        39.72 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
        8.48        18.21        18.90        13.25        16.57        15.68 
TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 
       25.94        29.95        29.85        40.41        41.13        39.78 
TCGA-EW-A1P3 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC 
       52.96        18.48        30.08        18.90        19.99         6.15 
TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR 
       13.94        10.52        14.43        34.55        19.96        55.00 
TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 
       52.73        22.09        21.27        17.49        10.16        10.59 
TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DF 
        7.40        59.57       194.27        53.13        53.52        42.71 
TCGA-GM-A2DH TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO 
       42.28        62.33        90.84        76.64        77.33        53.36 
TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV 
      110.50        38.20        32.28        53.95        57.63        13.55 
TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A442 
       18.12        11.84        11.57         6.67         4.60         3.58 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP 
        6.90         5.56         4.70         3.65         3.19         3.25 
TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7T0 TCGA-LL-A8F5 
        3.88         4.14         4.50         4.50         3.22         6.21 
TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 
       15.91         2.79         2.10        12.66        46.55         7.53 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5S0 
       44.61        27.65        26.20        16.87        14.10         9.80 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       14.76        23.70        54.51        33.90        31.07        18.21 
TCGA-OL-A66P TCGA-W8-A86G 
        4.44         5.29 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.03               0.03 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            186.48             234.28 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            22.160             21.175 
[1] "0.0 - 186.5 (22.2)" "0.0 - 234.3 (21.2)"
[1] "hr=" "1.3"
D23V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12P GAIN MUTATED        18       13        1        3        71        40
  12P GAIN WILD-TYPE      62       64        8        6       264       184
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12P GAIN MUTATED           0         36          6         17        5
  12P GAIN WILD-TYPE         2        102         21         42       12
                    vv
clus                 STAGE TIS STAGE X
  12P GAIN MUTATED           0       4
  12P GAIN WILD-TYPE         1      12
D23V3, multiclass
            clus
vv           12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                  18                 62
  STAGE IA                 13                 64
  STAGE IB                  1                  8
  STAGE II                  3                  6
  STAGE IIA                71                264
  STAGE IIB                40                184
  STAGE III                 0                  2
  STAGE IIIA               36                102
  STAGE IIIB                6                 21
  STAGE IIIC               17                 42
  STAGE IV                  5                 12
  STAGE TIS                 0                  1
  STAGE X                   4                 12
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  12P GAIN MUTATED    43 138  24   9
  12P GAIN WILD-TYPE 215 443  93  27
D23V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1               43                215
  T2              138                443
  T3               24                 93
  T4                9                 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                  N0  N1  N2  N3
  12P GAIN MUTATED   100  61  30  20
  12P GAIN WILD-TYPE 368 269  81  50
D23V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0              100                368
  N1               61                269
  N2               30                 81
  N3               20                 50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  12P GAIN MUTATED          0 183   5  26
  12P GAIN WILD-TYPE        2 662  12 105
D23V6, multiclass
          clus
vv         12P GAIN MUTATED 12P GAIN WILD-TYPE
  CM0 (I+)                0                  2
  M0                    183                662
  M1                      5                 12
  MX                     26                105
[1] 4 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   209   5
  12P GAIN WILD-TYPE 775   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED    209    5
  12P GAIN WILD-TYPE  775    6
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE              209                775
  MALE                  5                  6
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  12P GAIN MUTATED                            1                           172
  12P GAIN WILD-TYPE                          0                           563
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  12P GAIN MUTATED                               23                   2
  12P GAIN WILD-TYPE                            143                   3
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  12P GAIN MUTATED                                  7                  1
  12P GAIN WILD-TYPE                               22                 13
                    vv
clus                 OTHER  SPECIFY
  12P GAIN MUTATED                7
  12P GAIN WILD-TYPE             37
D23V8, multiclass
                                  clus
vv                                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      1                  0
  INFILTRATING DUCTAL CARCINOMA                 172                563
  INFILTRATING LOBULAR CARCINOMA                 23                143
  MEDULLARY CARCINOMA                             2                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)                7                 22
  MUCINOUS CARCINOMA                              1                 13
  OTHER  SPECIFY                                  7                 37
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V9, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    68 146
  12P GAIN WILD-TYPE 214 567
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     68  146
  12P GAIN WILD-TYPE  214  567
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                68                214
  YES              146                567
[1] 2 2
[1] FALSE
D23V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P GAIN MUTATED                                  0    10
  12P GAIN WILD-TYPE                                1    46
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED                          34   149
  12P GAIN WILD-TYPE                       103   559
D23V11, multiclass
                                  clus
vv                                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          10                 46
  BLACK OR AFRICAN AMERICAN                      34                103
  WHITE                                         149                559
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V12, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     5 172
  12P GAIN WILD-TYPE  31 624
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      5  172
  12P GAIN WILD-TYPE   31  624
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                 31
  NOT HISPANIC OR LATINO              172                624
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED   155  23
  12Q GAIN WILD-TYPE 705  91
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               178                796 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                23                 91 
$`12Q GAIN MUTATED`
TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A04P TCGA-A2-A04U TCGA-A2-A0CS 
       39.32        28.01        19.20        18.02        22.06        75.55 
TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0SW 
       56.81        21.14        35.05        34.29        31.82        44.88 
TCGA-A2-A0T7 TCGA-A2-A0YH TCGA-A2-A1FW TCGA-A2-A1G1 TCGA-A2-A25B TCGA-A2-A25E 
       20.75        21.67        17.36        19.20        16.31        91.92 
TCGA-A2-A3XW TCGA-A7-A0CD TCGA-A7-A13F TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A425 
       49.48        38.30        12.72        20.61        22.32        14.70 
TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A56D TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A076 
       13.74        21.17        14.73        17.98        41.06        53.98 
TCGA-A8-A079 TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A08G 
        9.01        10.98         8.98         9.99        28.04        19.96 
TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A092 TCGA-A8-A09A TCGA-A8-A09C 
       37.05        31.00        19.07        16.01         9.99         1.02 
TCGA-A8-A09I TCGA-A8-A09N TCGA-A8-A09X TCGA-A8-A0A1 TCGA-AC-A23E TCGA-AC-A23H 
       33.07         1.02        14.01        12.00         2.37         2.66 
TCGA-AC-A2FM TCGA-AC-A3W5 TCGA-AC-A62X TCGA-AN-A03Y TCGA-AN-A0FF TCGA-AN-A0FT 
       26.04         1.81         1.12         0.33         4.64         6.02 
TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A0J2 
        0.36         0.33        80.28        66.77        84.69        32.78 
TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A0JD TCGA-AO-A12E TCGA-AO-A1KQ TCGA-AO-A1KS 
       20.32        53.03        72.00        57.30        61.87         0.53 
TCGA-AQ-A0Y5 TCGA-AQ-A54O TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0U2 TCGA-AR-A1AK 
        5.65        21.86        49.32         5.26        83.87        51.25 
TCGA-AR-A1AV TCGA-AR-A24M TCGA-AR-A24Q TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24Z 
       42.58        65.46        66.05        54.18        50.96        51.75 
TCGA-AR-A250 TCGA-AR-A2LM TCGA-AR-A5QM TCGA-B6-A0IO TCGA-B6-A0RO TCGA-B6-A0WV 
       56.15        40.04        54.74       110.14       162.05        79.63 
TCGA-B6-A0WY TCGA-B6-A0X1 TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A408 TCGA-BH-A0AU 
      113.79       186.48        43.59        73.51        49.94        24.53 
TCGA-BH-A0B5 TCGA-BH-A0BA TCGA-BH-A0BL TCGA-BH-A0BT TCGA-BH-A0BW TCGA-BH-A0C1 
       48.36        37.22        44.05        45.57        11.67        44.02 
TCGA-BH-A0DD TCGA-BH-A0DQ TCGA-BH-A0E7 TCGA-BH-A0EB TCGA-BH-A0GY TCGA-BH-A0H7 
       45.83         3.22        44.81        24.49        30.35        23.08 
TCGA-BH-A0HX TCGA-BH-A0WA TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18R 
       27.25        23.05        90.84        26.66        37.74        37.55 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1FC TCGA-BH-A1FM TCGA-C8-A12L 
       42.28        12.00        55.69       114.15        45.63        11.93 
TCGA-C8-A12O TCGA-C8-A130 TCGA-C8-A138 TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A26Z 
       12.66         3.12         3.75        11.34        12.03         8.28 
TCGA-C8-A278 TCGA-D8-A13Z TCGA-D8-A1J8 TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE 
        0.03        20.88        14.17        15.78        18.15        18.90 
TCGA-D8-A1XD TCGA-D8-A1XJ TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A27M 
       17.16        21.83        12.99        16.54        15.32        13.48 
TCGA-D8-A27R TCGA-D8-A27W TCGA-D8-A3Z6 TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10B 
       10.09        12.26        18.51        34.42        46.59        37.51 
TCGA-E2-A10C TCGA-E2-A14O TCGA-E2-A14W TCGA-E2-A152 TCGA-E2-A15A TCGA-E2-A15G 
       40.11        44.68        32.02        27.12        23.34        18.21 
TCGA-E2-A15O TCGA-E2-A15S TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1L8 TCGA-E2-A1LL 
       13.02        14.07        33.73        33.70        39.62        43.04 
TCGA-E2-A56Z TCGA-E2-A573 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NF 
        7.20        22.26        13.48        12.00        13.12        20.05 
TCGA-E9-A1NI TCGA-E9-A1R6 TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A247 TCGA-E9-A295 
        9.86         2.76        20.81        40.24        27.22         0.72 
TCGA-E9-A2JS TCGA-E9-A54Y TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1P5 
       17.75         0.23        28.77        22.82        29.85        23.11 
TCGA-EW-A2FV TCGA-GM-A2DI TCGA-LD-A66U TCGA-LL-A5YM TCGA-LL-A6FQ TCGA-LL-A740 
       25.91        61.91         8.28         4.70         2.63         4.50 
TCGA-LL-A7SZ TCGA-OL-A5RV TCGA-OL-A66O TCGA-S3-A6ZG 
        5.59        24.10         7.23         6.81 

$`12Q GAIN WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SQ TCGA-A2-A04N 
       20.88        13.68        31.79         7.96        18.21       104.81 
TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X 
       41.95        82.16        73.84        63.12        64.04        55.43 
TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
       36.13       125.59        64.57        24.79       112.08        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW 
       88.60       107.93        75.25         5.19        63.45        64.04 
TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN 
       34.55        33.76        28.77        25.22       101.72        89.36 
TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EW 
       80.28       107.61        79.76        74.40        37.05        29.75 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SX 
       24.72        24.16        99.19        54.64        27.12        50.43 
TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 
       44.28        17.52        17.13         8.38        18.71        20.52 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF 
       17.46        18.90        32.55        25.28        18.21        15.42 
TCGA-A2-A0YG TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       21.90        14.50        18.61        19.33        14.63        31.73 
TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 
       23.77        23.47        36.79        22.45        20.25        19.56 
TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25F 
       16.47        52.47       107.70        17.19        18.15        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV 
       20.88        39.65        33.93        83.01        29.98        14.07 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX 
       38.40        34.98        31.99        38.37         7.30         9.01 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE 
        8.81         8.91        12.00         6.74         3.42        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB 
       34.29        35.47        30.61        37.45        35.67        33.11 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F 
       31.73        10.72        23.61        29.56        31.36        24.26 
TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 
       23.74        23.80        21.73        11.34        10.59        10.29 
TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SD TCGA-A7-A4SF 
       11.28        13.41        11.97        14.93        14.50        17.92 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX 
       12.10        10.72        11.05        10.29         9.37        10.42 
TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06U TCGA-A8-A06X 
        8.75        13.02        13.02         1.02        29.03        31.00 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F 
       26.01         1.02        17.03        33.01        19.99        18.97 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07S 
       18.97        14.01        12.00        17.03         9.99         7.99 
TCGA-A8-A07U TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A 
        9.96        18.05        15.06        36.95        13.02         0.99 
TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O 
       23.08        19.99        18.05        12.00         9.99        31.00 
TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A093 
        0.99        93.04        33.99        40.01        19.07        17.95 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09E 
       41.98        12.00         9.99        12.00        13.02        31.00 
TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       29.98        15.02        25.02         8.98        19.04        15.02 
TCGA-A8-A09W TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 
        0.99        19.04        13.02        21.04         0.99        13.02 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BK 
       17.03        38.04         0.95        10.85         1.48        38.53 
TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO 
       38.20        40.57        55.43        36.99        38.79        50.70 
TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD 
        1.02         0.92         2.27         0.99         0.69        14.83 
TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS 
        9.40         1.12         1.68         1.55         1.32         1.55 
TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A8OP 
        0.07         1.81         1.18         0.69         0.43         1.74 
TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C 
        0.33         0.23         0.33         0.62         2.96         1.78 
TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR 
        1.71         8.02         7.36         6.51         0.16         0.33 
TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL 
        0.33         0.33         6.44         7.96         7.00         7.59 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL 
        7.17         6.28         0.33         0.33         0.33         0.33 
TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT 
        0.33        12.33         0.30         0.33         0.33         0.33 
TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03O TCGA-AO-A03R 
        0.33         5.33         5.59        47.84        81.63        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 
       47.87        59.05        29.13        21.40        17.65        24.16 
TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE 
       37.48        22.36        21.53        50.70        50.86        76.77 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM 
       21.37        26.24        38.53        62.04        55.33        71.80 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A 
      102.58        99.25        93.70        94.59        96.10        90.58 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
       77.56        64.04        48.36        41.62        28.37        14.73 
TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       82.62        70.39        17.79        24.79        26.93       130.09 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TS 
       15.62        13.22         2.56         9.99        82.88        37.41 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
       56.88        29.75        24.30        64.83        55.86        76.14 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
       65.36        70.16        76.18        55.36        75.55        61.84 
TCGA-AR-A1AJ TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP 
       52.77        48.82        62.56        43.73        43.56        39.98 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX 
       43.07        17.23        40.83        46.32        35.24        36.26 
TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24N TCGA-AR-A24O 
       20.22       109.58        50.89        73.02        68.19        65.69 
TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X 
        0.85        57.40        62.07        53.26        53.36        48.16 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE 
       45.17        40.64        39.85        34.82        93.83       128.65 
TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       20.25        42.87         7.36        17.10        20.81        16.96 
TCGA-AR-A2LR TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 
       20.38        16.04        20.45        10.59        77.62       143.38 
TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
      149.59        12.13       220.90       129.57        50.70        65.72 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
      146.50       112.37       176.98        18.77       126.12        84.59 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
      110.93       140.88       211.56        68.45       189.01       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS 
       81.17        78.02       172.96       102.77       140.48       100.70 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW 
       89.46       131.21       157.41        97.48       188.68        17.98 
TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
       21.47       129.57       129.70        28.27        68.94        58.88 
TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A40B 
      101.52       139.17       170.17        85.35        54.28        82.88 
TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 
       55.00        38.79        20.45        25.55        28.50        46.95 
TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 
       40.83        39.55        39.16        56.94        56.98        51.68 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BM 
       32.02        18.21        25.71        24.85        21.70        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV 
       35.67        48.69        27.19        53.69        53.95        49.94 
TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DG 
       49.05        41.75        48.13        42.90        31.17        23.44 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP 
       38.01        22.13        13.91        48.23        17.26        15.65 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
        2.56        38.47        45.17        47.41        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EE 
       15.68        14.30         9.63        46.19        32.65        31.00 
TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       24.43        10.78        15.16        37.78        35.51        24.56 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       41.00        52.96        26.50        20.38         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HY TCGA-BH-A0RX 
       13.61        36.85        12.89        51.32        50.79         5.59 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18F TCGA-BH-A18G 
       23.93        24.95        42.35        44.81         8.81         2.01 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18S 
        7.23        20.12        72.56        30.28        55.63        66.05 
TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES 
        7.36        51.39        51.16        69.93        91.99       113.82 
TCGA-BH-A1ET TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 
       82.85        49.58        17.69        25.81        31.53        89.16 
TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG 
       97.48        24.66       120.62        33.17        74.73       122.89 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU 
       36.92        63.35        55.00        72.07       144.59        72.07 
TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 
        6.90         0.72        38.60        83.31        57.83       130.16 
TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V 
       10.65         6.44        20.12         0.99       109.28         8.94 
TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V 
       11.77        11.77        11.77         0.07        12.66        12.66 
TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 
       12.66        12.66         1.78         1.45         0.69         0.62 
TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HL 
        3.85        12.33        10.92        11.34         0.16        10.42 
TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y 
        2.30         3.25         0.30         0.23         0.36         0.43 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 
        9.67         0.03         0.03        12.20         0.99         0.03 
TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 
        0.23        11.90        13.25        20.58        13.97        14.17 
TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
       13.48        21.14        19.20        17.49        16.50        18.71 
TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK 
       12.03        12.03        14.01        18.97        20.09        20.12 
TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT 
       20.09        19.40        20.38        21.01        12.20        13.32 
TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 
       14.70        18.58        17.79        16.73        25.74        23.90 
TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XK 
       27.58        18.15         2.66        15.22        14.73        14.50 
TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS 
       19.92        17.69         7.96        16.41        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 
        6.35        15.16        12.66        15.52         3.81        14.24 
TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I 
       14.14        17.42        16.04        13.45        13.05        14.43 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V 
        9.44        16.41         4.80         0.76        13.08        12.53 
TCGA-D8-A3Z5 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10E 
       14.50         7.33        43.00        27.52        40.41        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S 
       28.87        47.15        40.96        38.24        38.60        33.17 
TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z 
       33.30        43.33        34.26        31.96        28.60        17.03 
TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 
       25.41        23.24        19.43        21.04        23.87        14.79 
TCGA-E2-A159 TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15H 
       25.05        22.82        17.29        20.71        21.63        12.92 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15P 
       17.42        19.40         9.04        20.58         7.73        19.56 
TCGA-E2-A15R TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 
       17.06        14.99        60.53        53.62        53.03        29.95 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF 
       32.35        28.50        16.47        17.10        38.30        37.41 
TCGA-E2-A1IG TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO 
       32.78        28.44        22.65         3.88        22.19        20.98 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB 
       11.08        54.18        27.42        19.66        24.59        40.47 
TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P5 
       28.90        18.87       106.75       102.61         8.75        16.93 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A574 TCGA-E9-A1N4 TCGA-E9-A1N5 
        5.52        15.72        18.05        19.89        19.20        36.82 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1QZ 
       36.56        39.55        12.59        35.77        21.57        11.90 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 
       14.30         0.62         2.10         6.12         1.38        21.21 
TCGA-E9-A1RA TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH 
       32.09         0.66        34.65         6.58        21.27        34.59 
TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       35.64        34.13         0.79        12.53        13.32        39.09 
TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 
       22.75        12.89        23.51        24.10        17.06         0.69 
TCGA-E9-A245 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3HO 
        0.85         1.94         0.95        12.56         0.76        26.07 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO 
       18.41         0.62        15.72         0.39         0.26         0.23 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 
       15.39        12.20        39.72         8.48        18.21        18.90 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OZ 
       13.25        16.57        15.68        25.94        29.95        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 
       41.13        39.78        52.96        29.82        18.48        30.08 
TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE 
        7.86        18.90        19.99         6.15        13.94        10.52 
TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FW 
       14.43        34.55        19.96        55.00        52.73        22.09 
TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 
       21.27        17.49        10.16        10.59         7.40       109.87 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF 
       59.57       194.27        53.13        53.52        43.04        42.71 
TCGA-GM-A2DH TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO 
       42.28        62.33        90.84        76.64        77.33        53.36 
TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 
      110.50        38.20        32.28        69.30        53.95        57.63 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A74U TCGA-LD-A7W6 
       13.55        18.12        11.84        11.57         6.67         4.60 
TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN 
        0.66         2.99         3.58         6.90         5.56         3.65 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A7T0 
        3.19         3.25         3.88         4.14         4.50         3.22 
TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 
        6.21        15.91         2.79         2.10        12.66        46.55 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY 
        7.53        44.61        27.65        26.20        16.87        14.10 
TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K 
       10.29         9.80        14.76        23.70        54.51        33.90 
TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66P TCGA-W8-A86G 
       31.07        18.21         4.44         5.29 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.03               0.03 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            186.48             234.28 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            22.290             21.175 
[1] "0.0 - 186.5 (22.3)" "0.0 - 234.3 (21.2)"
[1] "hr=" "1.4"
D24V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12Q GAIN MUTATED        14       10        0        2        54        35
  12Q GAIN WILD-TYPE      66       67        9        7       281       189
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12Q GAIN MUTATED           0         38          6         14        5
  12Q GAIN WILD-TYPE         2        100         21         45       12
                    vv
clus                 STAGE TIS STAGE X
  12Q GAIN MUTATED           0       3
  12Q GAIN WILD-TYPE         1      13
D24V3, multiclass
            clus
vv           12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                  14                 66
  STAGE IA                 10                 67
  STAGE IB                  0                  9
  STAGE II                  2                  7
  STAGE IIA                54                281
  STAGE IIB                35                189
  STAGE III                 0                  2
  STAGE IIIA               38                100
  STAGE IIIB                6                 21
  STAGE IIIC               14                 45
  STAGE IV                  5                 12
  STAGE TIS                 0                  1
  STAGE X                   3                 13
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  12Q GAIN MUTATED    33 117  22   9
  12Q GAIN WILD-TYPE 225 464  95  27
D24V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1               33                225
  T2              117                464
  T3               22                 95
  T4                9                 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                  N0  N1  N2  N3
  12Q GAIN MUTATED    69  59  31  17
  12Q GAIN WILD-TYPE 399 271  80  53
D24V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               69                399
  N1               59                271
  N2               31                 80
  N3               17                 53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  12Q GAIN MUTATED          0 155   5  21
  12Q GAIN WILD-TYPE        2 690  12 110
D24V6, multiclass
          clus
vv         12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CM0 (I+)                0                  2
  M0                    155                690
  M1                      5                 12
  MX                     21                110
[1] 4 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   176   5
  12Q GAIN WILD-TYPE 808   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED    176    5
  12Q GAIN WILD-TYPE  808    6
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE              176                808
  MALE                  5                  6
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  12Q GAIN MUTATED                            0                           145
  12Q GAIN WILD-TYPE                          1                           590
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  12Q GAIN MUTATED                               22                   1
  12Q GAIN WILD-TYPE                            144                   4
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  12Q GAIN MUTATED                                  8                  1
  12Q GAIN WILD-TYPE                               21                 13
                    vv
clus                 OTHER  SPECIFY
  12Q GAIN MUTATED                3
  12Q GAIN WILD-TYPE             41
D24V8, multiclass
                                  clus
vv                                 12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 145                590
  INFILTRATING LOBULAR CARCINOMA                 22                144
  MEDULLARY CARCINOMA                             1                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                8                 21
  MUCINOUS CARCINOMA                              1                 13
  OTHER  SPECIFY                                  3                 41
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V9, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    59 122
  12Q GAIN WILD-TYPE 223 591
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     59  122
  12Q GAIN WILD-TYPE  223  591
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                59                223
  YES              122                591
[1] 2 2
[1] FALSE
D24V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q GAIN MUTATED                                  0     9
  12Q GAIN WILD-TYPE                                1    47
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED                          28   122
  12Q GAIN WILD-TYPE                       109   586
D24V11, multiclass
                                  clus
vv                                 12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           9                 47
  BLACK OR AFRICAN AMERICAN                      28                109
  WHITE                                         122                586
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V12, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     4 142
  12Q GAIN WILD-TYPE  32 654
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      4  142
  12Q GAIN WILD-TYPE   32  654
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 32
  NOT HISPANIC OR LATINO              142                654
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    75  11
  13Q GAIN WILD-TYPE 785 103
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                86                888 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                11                103 
$`13Q GAIN MUTATED`
TCGA-A1-A0SK TCGA-A2-A04T TCGA-A2-A0ET TCGA-A2-A0EY TCGA-A2-A0YJ TCGA-A2-A1FW 
       31.79        73.84        35.05        24.16        18.61        17.36 
TCGA-A2-A1G1 TCGA-A7-A0DA TCGA-A7-A26F TCGA-A7-A3J0 TCGA-A8-A07R TCGA-A8-A08G 
       19.20        35.67        24.26        10.29         8.98        19.96 
TCGA-A8-A08J TCGA-A8-A091 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09C TCGA-AC-A2FM 
       37.05        19.07        41.98        12.00         1.02        26.04 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A0AS TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FZ 
        0.33         0.23         0.33         6.02         0.36         0.33 
TCGA-AN-A0XO TCGA-AO-A03U TCGA-AO-A0J7 TCGA-AO-A0JB TCGA-AO-A12A TCGA-AO-A12B 
       12.33        59.05        20.32        50.70        90.58        77.56 
TCGA-AO-A12D TCGA-AR-A0TT TCGA-AR-A0U3 TCGA-AR-A24U TCGA-AR-A250 TCGA-AR-A2LR 
       64.04        56.88        76.18        53.36        56.15        20.38 
TCGA-B6-A0IO TCGA-B6-A0RE TCGA-B6-A0RO TCGA-B6-A0RS TCGA-B6-A0WY TCGA-BH-A0B9 
      110.14       211.56       162.05       100.70       113.79        51.68 
TCGA-BH-A0BT TCGA-BH-A0E2 TCGA-BH-A0EB TCGA-BH-A0HQ TCGA-BH-A18N TCGA-BH-A18V 
       45.57        14.30        24.49        36.85        37.74        51.16 
TCGA-BH-A1EX TCGA-BH-A1FN TCGA-BH-A208 TCGA-C8-A12L TCGA-C8-A131 TCGA-C8-A134 
       49.58        72.07        57.83        11.93         1.78         0.69 
TCGA-C8-A275 TCGA-D8-A141 TCGA-D8-A1JF TCGA-D8-A1XF TCGA-D8-A1XJ TCGA-D8-A27R 
        0.03        20.58        12.03        15.22        21.83        10.09 
TCGA-D8-A27W TCGA-E2-A14T TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A154 TCGA-E2-A15E 
       12.26        33.30        31.96        28.60        19.43        20.71 
TCGA-E2-A1BD TCGA-E2-A1L9 TCGA-E2-A1LH TCGA-E2-A574 TCGA-E9-A1N8 TCGA-E9-A1ND 
       17.10        19.66       106.75        19.89        12.00        12.59 
TCGA-E9-A1NF TCGA-E9-A1R3 TCGA-E9-A1RF TCGA-E9-A248 TCGA-E9-A5FL TCGA-EW-A1J6 
       20.05         2.10         6.58         1.94         0.26        28.77 
TCGA-EW-A1P7 TCGA-EW-A2FV TCGA-EW-A423 TCGA-JL-A3YX TCGA-LL-A6FQ TCGA-LL-A73Y 
       30.08        25.91        10.16        11.57         2.63         4.14 
TCGA-MS-A51U TCGA-S3-A6ZG 
        2.79         6.81 

$`13Q GAIN WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP 
       20.88        13.68         7.96        39.32        28.01        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04U 
       18.21       104.81        18.02        41.95        82.16        22.06 
TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL 
       63.12        64.04        55.43        36.13       125.59        64.57 
TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS 
       24.79       112.08        92.48        88.60       107.93        75.55 
TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 
       75.25         5.19        63.45        64.04        56.81        21.14 
TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN 
       34.55        33.76        28.77        25.22       101.72        89.36 
TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EU 
       80.28       107.61        79.76        74.40        37.05        34.29 
TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV 
       31.82        29.75        24.72        99.19        54.64        27.12 
TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 
       44.88        50.43        44.28        17.52        17.13         8.38 
TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC 
       18.71        20.52        17.46        18.90        20.75        32.55 
TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI 
       25.28        18.21        15.42        21.90        21.67        14.50 
TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FX 
       19.33        14.63        31.73        23.77        23.47        36.79 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A 
       22.45        20.25        19.56        16.47        52.47       107.70 
TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
       16.31        17.19        18.15        91.92        10.59        20.88 
TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW 
       39.65        33.93        83.01        29.98        14.07        49.48 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX 
       38.40        34.98        31.99        38.37         7.30         9.01 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD 
        8.81         8.91        12.00         6.74         3.42        38.30 
TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DB 
       35.31        34.29        35.47        30.61        37.45        33.11 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       31.73        10.72        12.72        23.61        29.56        31.36 
TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY 
       23.74        23.80        21.73        20.61        22.32        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA 
       10.59        11.28        13.41        14.70        11.97        14.93 
TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV 
       13.74        14.50        21.17        17.92        14.73        12.10 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY 
       10.72        11.05        10.29         9.37        10.42         8.75 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U 
       13.02        13.02         1.02        17.98        41.06        29.03 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 
       31.00        26.01         1.02        17.03        53.98         9.01 
TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J 
       33.01        19.99        18.97        18.97        14.01        12.00 
TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W 
       17.03         9.99        10.98         7.99         9.96         9.99 
TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A 
       28.04        18.05        15.06        36.95        13.02         0.99 
TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O 
       23.08        19.99        18.05        12.00         9.99        31.00 
TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z 
       31.00         0.99        19.07        93.04        33.99        40.01 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09D 
       16.01        17.95         9.99         9.99        12.00        13.02 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q 
       31.00        33.07        29.98        15.02         1.02        25.02 
TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 
        8.98        19.04        15.02         0.99        14.01        12.00 
TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB 
       19.04        13.02        21.04         0.99        13.02        17.03 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 
       38.04         0.95         2.37        10.85         2.66         1.48 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
       38.53        38.20        40.57        55.43        36.99        38.79 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN 
       50.70         1.02         0.92         2.27         0.99         0.69 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI 
       14.83         9.40         1.12         1.81         1.68         1.55 
TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV 
        1.32         1.55         0.07         1.12         1.81         1.18 
TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A046 TCGA-AN-A049 
        0.69         0.43         1.74         0.33         0.33         0.62 
TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL 
        2.96         1.78         1.71         8.02         7.36         6.51 
TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ 
        0.16         0.33         0.33         6.44         4.64         7.96 
TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0FX 
        7.00         7.59         7.17         6.28         0.33         0.33 
TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS 
        0.33         0.33         0.33         0.30         0.33         0.33 
TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M 
        0.33         0.33         5.33         5.59        80.28        47.84 
TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03V 
       66.77        81.63        84.69        68.75        47.87        29.13 
TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 
       32.78        21.40        17.65        24.16        37.48        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF 
       53.03        21.53        50.86        72.00        76.77        21.37 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 
       26.24        38.53        62.04        55.33        71.80       102.58 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12E TCGA-AO-A12F 
       99.25        93.70        94.59        96.10        57.30        48.36 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR 
       41.62        28.37        14.73        82.62        61.87        70.39 
TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 
        0.53        17.79        24.79        26.93       130.09         5.65 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP 
       15.62        13.22         2.56        21.86         9.99        82.88 
TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX 
       49.32         5.26        37.41        29.75        24.30        64.83 
TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U4 
       55.86        76.14        65.36        70.16        83.87        55.36 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM 
       75.55        61.84        52.77        51.25        48.82        62.56 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS 
       43.73        43.56        39.98        43.07        17.23        40.83 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H 
       46.32        42.58        35.24        36.26        20.22       109.58 
TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
       50.89        73.02        65.46        68.19        65.69         0.85 
TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24V TCGA-AR-A24W 
       66.05        57.40        62.07        53.26        54.18        50.96 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 
       48.16        51.75        45.17        40.64        39.85        34.82 
TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM 
       93.83       128.65        20.25        42.87         7.36        40.04 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP 
       17.10        20.81        16.96        54.74        16.04        20.45 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA 
       10.59        77.62       143.38       149.59        12.13       220.90 
TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ 
      129.57        50.70        65.72       146.50       112.37       176.98 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG 
       18.77       126.12        84.59       110.93       140.88        68.45 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RP 
      189.01       234.28        81.17        78.02       172.96       102.77 
TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT 
      140.48        89.46       131.21       157.41        97.48       188.68 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 
       79.63        17.98        21.47       129.57       129.70       186.48 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI 
       28.27        68.94        58.88        43.59       101.52        73.51 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B 
      139.17       170.17        85.35        54.28        49.94        82.88 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ 
       55.00        24.53        38.79        20.45        25.55        28.50 
TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 
       46.95        40.83        39.55        39.16        48.36        56.94 
TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG 
       56.98        37.22        32.02        18.21        25.71        24.85 
TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ 
       21.70        44.05        61.68        35.67        48.69        27.19 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 
       53.69        53.95        49.94        11.67        49.05        41.75 
TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG 
       44.02        48.13        42.90        45.83        31.17        23.44 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP 
       38.01        22.13        13.91        48.23        17.26        15.65 
TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ 
        3.22         2.56        38.47        45.17        47.41        16.27 
TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA 
        4.41        15.68         9.63        44.81        46.19        32.65 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       31.00        24.43        30.35        10.78        15.16        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB 
       35.51        24.56        23.08        41.00        52.96        26.50 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HU TCGA-BH-A0HW 
       20.38         5.85         2.50        13.61        12.89        51.32 
TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 
       27.25        50.79         5.59        23.93        24.95        42.35 
TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J 
       44.81        23.05         8.81         2.01         7.23        20.12 
TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R 
       90.84        26.66        72.56        30.28        55.63        37.55 
TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES 
       66.05         7.36        51.39        69.93        91.99       113.82 
TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EY TCGA-BH-A1F0 
       82.85        42.28        12.00        55.69        17.69        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC 
       31.53        89.16        97.48        24.66       120.62       114.15 
TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
       33.17        74.73       122.89        36.92        63.35        55.00 
TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 
       45.63       144.59        72.07         6.90         0.72        38.60 
TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T 
       83.31       130.16        10.65         6.44        20.12         0.99 
TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P 
      109.28         8.94        11.77        11.77        12.66        11.77 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 
        0.07        12.66        12.66        12.66        12.66         3.12 
TCGA-C8-A132 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF 
        1.45         0.62         3.85         3.75        12.33        10.92 
TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM 
       11.34        11.34         0.16        12.03        10.42         2.30 
TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z 
        3.25         0.30         0.23         0.36         0.43         8.28 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 
        9.67         0.03         0.03        12.20         0.99         0.03 
TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A142 TCGA-D8-A143 
        0.23        11.90        20.88        13.25        13.97        14.17 
TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA 
       13.48        21.14        19.20        14.17        17.49        16.50 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH 
       18.71        15.78        18.15        18.90        12.03        14.01 
TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN 
       18.97        20.09        20.12        20.09        19.40        20.38 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 
       21.01        12.20        13.32        14.70        18.58        17.79 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC 
       16.73        25.74        23.90        27.58        18.15         2.66 
TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO 
       17.16        14.73        14.50        19.92        17.69         7.96 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV 
       16.41        15.85        16.31         6.35        12.99        15.16 
TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 
       12.66        16.54        15.32        15.52         3.81        14.24 
TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I 
       14.14        17.42        16.04        13.45        13.05        14.43 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T 
        9.44        16.41        13.48         4.80         0.76        13.08 
TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A107 
       12.53        14.50        18.51         7.33        43.00        34.42 
TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E 
       27.52        46.59        40.41        37.51        40.11        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R 
       28.87        47.15        44.68        40.96        38.24        38.60 
TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14Z TCGA-E2-A150 
       33.17        43.33        34.26        32.02        17.03        25.41 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 
       27.12        23.24        21.04        23.87        14.79        25.05 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H 
       23.34        22.82        17.29        21.63        18.21        12.92 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O 
       17.42        19.40         9.04        20.58         7.73        13.02 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 
       19.56        17.06        14.07        14.99        60.53        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE 
       53.03        29.95        32.35        28.50        16.47        38.30 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK 
       37.41        32.78        33.73        33.70        28.44        22.65 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 
        3.88        22.19        20.98        11.08        54.18        27.42 
TCGA-E2-A1L8 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LI 
       39.62        24.59        40.47        28.90        18.87       102.61 
TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z 
        8.75        43.04        16.93         5.52        15.72         7.20 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 
       18.05        22.26        19.20        36.82        13.48        13.12 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ 
       36.56        39.55        35.77        21.57         9.86        11.90 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 
       14.30         0.62         6.12         1.38         2.76        21.21 
TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RG 
       32.09        20.81        40.24         0.66        34.65        21.27 
TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
       34.59        35.64        34.13         0.79        12.53        13.32 
TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 
       39.09        22.75        12.89        23.51        24.10        17.06 
TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
        0.69         0.85        27.22         0.95        12.56         0.72 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
       17.75         0.76        26.07        18.41         0.62        15.72 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
        0.23         0.39         0.23        15.39        12.20        39.72 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
        8.48        18.21        18.90        13.25        16.57        15.68 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 
       25.94        22.82        29.95        29.85        40.41        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P8 
       39.78        52.96        29.82        23.11        18.48         7.86 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
       18.90        19.99         6.15        13.94        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A3E8 
       34.55        19.96        55.00        52.73        22.09        21.27 
TCGA-EW-A3U0 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       17.49        10.59         7.40       109.87        59.57       194.27 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI 
       53.13        53.52        43.04        42.71        42.28        61.91 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
       62.33        90.84        76.64        77.33        53.36       110.50 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV 
       38.20        32.28        69.30        53.95        57.63        13.55 
TCGA-GM-A5PX TCGA-JL-A3YW TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 
       18.12        11.84         8.28         6.67         4.60         0.66 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN 
        2.99         3.58         6.90         5.56         4.70         3.65 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ 
        3.19         3.25         3.88         4.50         4.50         5.59 
TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 
        3.22         6.21        15.91         2.10        12.66        46.55 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX 
        7.53        44.61        27.65        24.10        26.20        16.87 
TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J 
       14.10        10.29         9.80        14.76        23.70        54.51 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-W8-A86G 
       33.90        31.07        18.21         7.23         4.44         5.29 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.03               0.03 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            211.56             234.28 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             20.35              21.60 
[1] "0.0 - 211.6 (20.4)" "0.0 - 234.3 (21.6)"
[1] "hr=" "1.1"
D25V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  13Q GAIN MUTATED         5        5        0        0        34        15
  13Q GAIN WILD-TYPE      75       72        9        9       301       209
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  13Q GAIN MUTATED           0         17          2          4        1
  13Q GAIN WILD-TYPE         2        121         25         55       16
                    vv
clus                 STAGE TIS STAGE X
  13Q GAIN MUTATED           0       3
  13Q GAIN WILD-TYPE         1      13
D25V3, multiclass
            clus
vv           13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                   5                 75
  STAGE IA                  5                 72
  STAGE IB                  0                  9
  STAGE II                  0                  9
  STAGE IIA                34                301
  STAGE IIB                15                209
  STAGE III                 0                  2
  STAGE IIIA               17                121
  STAGE IIIB                2                 25
  STAGE IIIC                4                 55
  STAGE IV                  1                 16
  STAGE TIS                 0                  1
  STAGE X                   3                 13
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  13Q GAIN MUTATED    18  57   7   3
  13Q GAIN WILD-TYPE 240 524 110  33
D25V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1               18                240
  T2               57                524
  T3                7                110
  T4                3                 33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  13Q GAIN MUTATED    41  26  14   5
  13Q GAIN WILD-TYPE 427 304  97  65
D25V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0               41                427
  N1               26                304
  N2               14                 97
  N3                5                 65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  13Q GAIN MUTATED          0  79   1   6
  13Q GAIN WILD-TYPE        2 766  16 125
D25V6, multiclass
          clus
vv         13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CM0 (I+)                0                  2
  M0                     79                766
  M1                      1                 16
  MX                      6                125
[1] 4 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    86   0
  13Q GAIN WILD-TYPE 898  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     86    0
  13Q GAIN WILD-TYPE  898   11
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               86                898
  MALE                  0                 11
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  13Q GAIN MUTATED                            0                            71
  13Q GAIN WILD-TYPE                          1                           664
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  13Q GAIN MUTATED                                4                   0
  13Q GAIN WILD-TYPE                            162                   5
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  13Q GAIN MUTATED                                  1                  2
  13Q GAIN WILD-TYPE                               28                 12
                    vv
clus                 OTHER  SPECIFY
  13Q GAIN MUTATED                8
  13Q GAIN WILD-TYPE             36
D25V8, multiclass
                                  clus
vv                                 13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                  71                664
  INFILTRATING LOBULAR CARCINOMA                  4                162
  MEDULLARY CARCINOMA                             0                  5
  MIXED HISTOLOGY (PLEASE SPECIFY)                1                 28
  MUCINOUS CARCINOMA                              2                 12
  OTHER  SPECIFY                                  8                 36
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V9, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    28  58
  13Q GAIN WILD-TYPE 254 655
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     28   58
  13Q GAIN WILD-TYPE  254  655
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                28                254
  YES               58                655
[1] 2 2
[1] FALSE
D25V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q GAIN MUTATED                                  0     6
  13Q GAIN WILD-TYPE                                1    50
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED                           8    65
  13Q GAIN WILD-TYPE                       129   643
D25V11, multiclass
                                  clus
vv                                 13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           6                 50
  BLACK OR AFRICAN AMERICAN                       8                129
  WHITE                                          65                643
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V12, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     6  67
  13Q GAIN WILD-TYPE  30 729
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      6   67
  13Q GAIN WILD-TYPE   30  729
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                 30
  NOT HISPANIC OR LATINO               67                729
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED   118  14
  14Q GAIN WILD-TYPE 742 100
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               132                842 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                14                100 
$`14Q GAIN MUTATED`
TCGA-A2-A0D2 TCGA-A2-A0T3 TCGA-A2-A0YH TCGA-A2-A1FW TCGA-A2-A25C TCGA-A2-A3KD 
       33.76        18.71        21.67        17.36        17.19        39.65 
TCGA-A2-A4RX TCGA-A7-A0CJ TCGA-A7-A0DB TCGA-A7-A56D TCGA-A8-A075 TCGA-A8-A076 
        9.01        30.61        33.11        14.73        17.03        53.98 
TCGA-A8-A08B TCGA-A8-A08I TCGA-A8-A08S TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A095 
       23.08        12.00        19.07        19.07        16.01        41.98 
TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09M TCGA-A8-A09R TCGA-A8-A09X TCGA-A8-A0A2 
        9.99         1.02        15.02         8.98        14.01        19.04 
TCGA-A8-A0A9 TCGA-AC-A23E TCGA-AC-A2FM TCGA-AC-A62Y TCGA-AN-A04A TCGA-AN-A0FW 
       13.02         2.37        26.04         1.81         2.96         0.36 
TCGA-AN-A0FZ TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A0J7 
        0.33        80.28        66.77        81.63        84.69        20.32 
TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JM TCGA-AR-A24K TCGA-AR-A24M TCGA-AR-A24R 
       72.00        76.77        71.80        50.89        65.46        57.40 
TCGA-AR-A250 TCGA-AR-A2LK TCGA-AR-A5QM TCGA-B6-A0I5 TCGA-B6-A0IB TCGA-B6-A0RO 
       56.15        42.87        54.74       149.59       129.57       162.05 
TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WV TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A1KN 
      100.70       131.21        79.63       113.79       129.57       139.17 
TCGA-B6-A401 TCGA-B6-A408 TCGA-BH-A0BA TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0BT 
       85.35        49.94        37.22        44.05        48.69        45.57 
TCGA-BH-A0DG TCGA-BH-A0DL TCGA-BH-A0DS TCGA-BH-A0E9 TCGA-BH-A0EE TCGA-BH-A0HI 
       23.44        48.23         2.56        46.19        31.00        20.38 
TCGA-BH-A0HX TCGA-BH-A0W7 TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A1EN TCGA-BH-A1EV 
       27.25        44.81        90.84        26.66        69.93        12.00 
TCGA-BH-A1FM TCGA-BH-A1FU TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A130 TCGA-C8-A132 
       45.63        72.07        12.66        11.77         3.12         1.45 
TCGA-C8-A138 TCGA-C8-A1HI TCGA-C8-A27A TCGA-D8-A13Z TCGA-D8-A141 TCGA-D8-A143 
        3.75        11.34        12.20        20.88        20.58        14.17 
TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1JD TCGA-D8-A1JF TCGA-D8-A1JK TCGA-D8-A1X5 
       21.14        14.17        18.15        12.03        20.12        18.58 
TCGA-D8-A1XF TCGA-D8-A1XL TCGA-D8-A1XZ TCGA-D8-A27W TCGA-D8-A3Z6 TCGA-E2-A109 
       15.22        19.92        15.32        12.26        18.51        46.59 
TCGA-E2-A10C TCGA-E2-A14P TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A15E 
       40.11        40.96        27.12        23.24        19.43        20.71 
TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15K TCGA-E2-A1L9 TCGA-E2-A1LG TCGA-E2-A1LL 
       18.21        17.42         9.04        19.66        18.87        43.04 
TCGA-E2-A2P5 TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RF 
       16.93        20.05         9.86        40.24        34.65         6.58 
TCGA-E9-A1RH TCGA-E9-A22E TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A295 TCGA-E9-A5FL 
       34.59        12.89         0.69        27.22         0.72         0.26 
TCGA-EW-A1IY TCGA-EW-A1OZ TCGA-EW-A1P3 TCGA-EW-A1PG TCGA-EW-A2FS TCGA-GM-A2DB 
        8.48        40.41        52.96        34.55        52.73        53.13 
TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A6FQ TCGA-MS-A51U TCGA-OL-A5RW TCGA-S3-A6ZG 
        4.70         3.19         2.63         2.79        26.20         6.81 

$`14Q GAIN WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
       20.88        13.68        31.79         7.96        39.32        28.01 
TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R 
       19.20        18.21       104.81        18.02        41.95        82.16 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
       73.84        22.06        63.12        64.04        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
      125.59        64.57        24.79       112.08        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW 
      107.93        75.55        75.25         5.19        63.45        64.04 
TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM 
       56.81        21.14        34.55        28.77        25.22       101.72 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES 
       89.36        80.28       107.61        79.76        74.40        37.05 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY 
       35.05        34.29        31.82        29.75        24.72        24.16 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY 
       99.19        54.64        27.12        44.88        50.43        44.28 
TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.52        17.13         8.38        20.52        17.46        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG 
       20.75        32.55        25.28        18.21        15.42        21.90 
TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT 
       14.50        18.61        19.33        14.63        31.73        23.77 
TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 
       23.47        36.79        22.45        20.25        19.20        19.56 
TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25D TCGA-A2-A25E 
       16.47        52.47       107.70        16.31        18.15        91.92 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV 
       10.59        20.88        33.93        83.01        29.98        14.07 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW 
       49.48        38.40        34.98        31.99        38.37         7.30 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD 
        8.81         8.91        12.00         6.74         3.42        38.30 
TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A13D 
       35.31        34.29        35.47        37.45        35.67        31.73 
TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F 
       10.72        12.72        23.61        29.56        31.36        24.26 
TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY 
       23.74        23.80        21.73        20.61        22.32        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 
       10.59        10.29        11.28        13.41        14.70        11.97 
TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A5ZV 
       14.93        13.74        14.50        21.17        17.92        12.10 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY 
       10.72        11.05        10.29         9.37        10.42         8.75 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U 
       13.02        13.02         1.02        17.98        41.06        29.03 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E 
       31.00        26.01         1.02         9.01        33.01        19.99 
TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O 
       18.97        18.97        14.01        12.00        17.03         9.99 
TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z 
       10.98         8.98         7.99         9.96         9.99        28.04 
TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C 
       18.05        15.06        36.95        13.02         0.99        19.99 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P 
       18.05        19.96        37.05         9.99        31.00        31.00 
TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A093 TCGA-A8-A097 
        0.99        93.04        33.99        40.01        17.95        12.00 
TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K 
        9.99        12.00        13.02        31.00        33.07        29.98 
TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A1 
        1.02        25.02        19.04        15.02         0.99        12.00 
TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C 
       13.02        21.04         0.99        17.03        38.04         0.95 
TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB 
       10.85         2.66         1.48        38.53        38.20        40.57 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI 
       55.43        36.99        38.79        50.70         1.02         0.92 
TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN 
        2.27         0.99         0.69        14.83         9.40         1.12 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V 
        1.81         1.68         1.55         1.32         1.55         0.07 
TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AN-A03X 
        1.12         1.18         0.69         0.43         1.74         0.33 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D 
        0.33         0.23         0.33         0.62         1.78         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS 
        8.02         7.36         6.51         0.16         0.33         0.33 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL 
        0.33         6.44         4.64         7.96         7.00         7.59 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0FY 
        7.17         6.28         6.02         0.33         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS 
        0.33         0.33        12.33         0.30         0.33         0.33 
TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03R 
        0.33         0.33         5.33         5.59        47.84        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 
       47.87        59.05        29.13        32.78        21.40        17.65 
TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB 
       24.16        37.48        22.36        53.03        21.53        50.70 
TCGA-AO-A0JC TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL 
       50.86        21.37        26.24        38.53        62.04        55.33 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A 
      102.58        99.25        93.70        94.59        96.10        90.58 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
       77.56        64.04        57.30        48.36        41.62        28.37 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT 
       14.73        82.62        61.87        70.39         0.53        17.79 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       24.79        26.93       130.09         5.65        15.62        13.22 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
        2.56        21.86         9.99        82.88        49.32         5.26 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
       37.41        56.88        29.75        24.30        64.83        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 
       76.14        65.36        70.16        83.87        76.18        55.36 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM 
       75.55        61.84        52.77        51.25        48.82        62.56 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS 
       43.73        43.56        39.98        43.07        17.23        40.83 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H 
       46.32        42.58        35.24        36.26        20.22       109.58 
TCGA-AR-A24L TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24S 
       73.02        68.19        65.69         0.85        66.05        62.07 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
       53.26        53.36        54.18        50.96        48.16        51.75 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE 
       45.17        40.64        39.85        34.82        93.83       128.65 
TCGA-AR-A2LH TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       20.25         7.36        40.04        17.10        20.81        16.96 
TCGA-AR-A2LR TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 
       20.38        16.04        20.45        10.59        77.62       143.38 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH 
       12.13       220.90        50.70        65.72       146.50       112.37 
TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP 
      176.98        18.77       126.12        84.59       110.14       110.93 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL 
      140.88       211.56        68.45       189.01       234.28        81.17 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV 
       78.02       172.96       102.77       140.48        89.46       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0X0 TCGA-B6-A0X1 
       97.48       188.68        17.98        21.47       129.70       186.48 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI 
       28.27        68.94        58.88        43.59       101.52        73.51 
TCGA-B6-A2IU TCGA-B6-A402 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV 
      170.17        54.28        82.88        55.00        24.53        38.79 
TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 
       20.45        25.55        28.50        46.95        40.83        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC 
       39.16        48.36        56.94        56.98        51.68        32.02 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO 
       18.21        25.71        24.85        21.70        61.68        35.67 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ 
       27.19        53.69        53.95        49.94        11.67        49.05 
TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE 
       41.75        44.02        48.13        42.90        45.83        31.17 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ 
       38.01        22.13        13.91        17.26        15.65         3.22 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 
       38.47        45.17        47.41        16.27         4.41        15.68 
TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EI 
       14.30         9.63        44.81        32.65        24.49        24.43 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       30.35        10.78        15.16        37.78        35.51        24.56 
TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HK TCGA-BH-A0HO 
       23.08        41.00        52.96        26.50         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HY TCGA-BH-A0RX 
       13.61        36.85        12.89        51.32        50.79         5.59 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G 
       23.93        24.95        42.35        23.05         8.81         2.01 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q 
        7.23        20.12        72.56        37.74        30.28        55.63 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EO 
       37.55        66.05         7.36        51.39        51.16        91.99 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY 
      113.82        82.85        42.28        55.69        49.58        17.69 
TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB 
       25.81        31.53        89.16        97.48        24.66       120.62 
TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
      114.15        33.17        74.73       122.89        36.92        63.35 
TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 
       55.00        72.07       144.59         6.90         0.72        38.60 
TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
       83.31        57.83       130.16        10.65         6.44        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N 
        0.99       109.28         8.94        11.93        11.77        11.77 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A131 
        0.07        12.66        12.66        12.66        12.66         1.78 
TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG 
        0.69         0.62         3.85        12.33        10.92        11.34 
TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V 
        0.16        12.03        10.42         2.30         3.25         0.30 
TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 
        0.23         0.36         0.43         8.28         9.67         0.03 
TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y 
        0.03         0.03         0.99         0.03         0.23        11.90 
TCGA-D8-A140 TCGA-D8-A142 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA 
       13.25        13.97        13.48        19.20        17.49        16.50 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI 
       18.71        15.78        18.90        12.03        14.01        18.97 
TCGA-D8-A1JJ TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS 
       20.09        20.09        19.40        20.38        21.01        12.20 
TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 
       13.32        14.70        17.79        16.73        25.74        23.90 
TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ 
       27.58        18.15         2.66        17.16        14.73        21.83 
TCGA-D8-A1XK TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS 
       14.50        17.69         7.96        16.41        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1Y0 
        6.35        12.99        15.16        12.66        16.54        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G 
        3.81        14.24        14.14        17.42        16.04        13.45 
TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N 
       13.05        14.43         9.44        16.41        13.48         4.80 
TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A4Z1 
        0.76        10.09        13.08        12.53        14.50         7.33 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E 
       43.00        34.42        27.52        40.41        37.51        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S 
       28.87        47.15        44.68        38.24        38.60        33.17 
TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y 
       33.30        43.33        34.26        32.02        31.96        28.60 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 
       17.03        25.41        21.04        23.87        14.79        25.05 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15J 
       23.34        22.82        17.29        21.63        12.92        19.40 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
       20.58         7.73        13.02        19.56        17.06        14.07 
TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       14.99        60.53        53.62        53.03        29.95        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       28.50        16.47        17.10        38.30        37.41        32.78 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN 
       33.73        33.70        28.44        22.65         3.88        22.19 
TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LA 
       20.98        11.08        54.18        27.42        39.62        24.59 
TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P6 
       40.47        28.90       106.75       102.61         8.75         5.52 
TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N4 
       15.72         7.20        18.05        22.26        19.89        19.20 
TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC 
       36.82        13.48        12.00        13.12        36.56        39.55 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       12.59        35.77        21.57        11.90        14.30         0.62 
TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA 
        2.10         6.12         1.38         2.76        21.21        32.09 
TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
       20.81         0.66        21.27        35.64        34.13         0.79 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22G TCGA-E9-A22H 
       12.53        13.32        39.09        22.75        23.51        24.10 
TCGA-E9-A243 TCGA-E9-A245 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JS 
       17.06         0.85         1.94         0.95        12.56        17.75 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54Y 
        0.76        26.07        18.41         0.62        15.72         0.23 
TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ 
        0.39         0.23        15.39        12.20        39.72        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV 
       18.90        13.25        16.57        15.68        28.77        25.94 
TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 
       22.82        29.95        29.85        41.13        39.78        29.82 
TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB 
       23.11        18.48        30.08         7.86        18.90        19.99 
TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PH TCGA-EW-A2FR 
        6.15        13.94        10.52        14.43        19.96        55.00 
TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 
       25.91        22.09        21.27        17.49        10.16        10.59 
TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DC TCGA-GM-A2DD 
        7.40       109.87        59.57       194.27        53.52        43.04 
TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       42.71        42.28        61.91        62.33        90.84        76.64 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL 
       77.33        53.36       110.50        38.20        32.28        69.30 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX 
       53.95        57.63        13.55        18.12        11.84        11.57 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
        8.28         6.67         4.60         0.66         2.99         3.58 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y 
        6.90         5.56         3.65         3.25         3.88         4.14 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LQ-A4E4 
        4.50         4.50         5.59         3.22         6.21        15.91 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.10        12.66        46.55         7.53        44.61        27.65 
TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H 
       24.10        16.87        14.10        10.29         9.80        14.76 
TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O 
       23.70        54.51        33.90        31.07        18.21         7.23 
TCGA-OL-A66P TCGA-W8-A86G 
        4.44         5.29 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              0.26               0.03 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            162.05             234.28 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            20.795             21.550 
[1] "0.3 - 162.1 (20.8)" "0.0 - 234.3 (21.6)"
[1] "hr=" "1.3"
D26V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  14Q GAIN MUTATED         8        5        1        0        46        28
  14Q GAIN WILD-TYPE      72       72        8        9       289       196
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  14Q GAIN MUTATED           1         27          4          9        1
  14Q GAIN WILD-TYPE         1        111         23         50       16
                    vv
clus                 STAGE TIS STAGE X
  14Q GAIN MUTATED           0       4
  14Q GAIN WILD-TYPE         1      12
D26V3, multiclass
            clus
vv           14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                   8                 72
  STAGE IA                  5                 72
  STAGE IB                  1                  8
  STAGE II                  0                  9
  STAGE IIA                46                289
  STAGE IIB                28                196
  STAGE III                 1                  1
  STAGE IIIA               27                111
  STAGE IIIB                4                 23
  STAGE IIIC                9                 50
  STAGE IV                  1                 16
  STAGE TIS                 0                  1
  STAGE X                   4                 12
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  14Q GAIN MUTATED    25  89  15   5
  14Q GAIN WILD-TYPE 233 492 102  31
D26V4, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1               25                233
  T2               89                492
  T3               15                102
  T4                5                 31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  14Q GAIN MUTATED    54  43  24  10
  14Q GAIN WILD-TYPE 414 287  87  60
D26V5, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0               54                414
  N1               43                287
  N2               24                 87
  N3               10                 60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  14Q GAIN MUTATED          0 118   1  15
  14Q GAIN WILD-TYPE        2 727  16 116
D26V6, multiclass
          clus
vv         14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CM0 (I+)                0                  2
  M0                    118                727
  M1                      1                 16
  MX                     15                116
[1] 4 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   134   0
  14Q GAIN WILD-TYPE 850  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED    134    0
  14Q GAIN WILD-TYPE  850   11
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE              134                850
  MALE                  0                 11
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  14Q GAIN MUTATED                            0                           106
  14Q GAIN WILD-TYPE                          1                           629
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  14Q GAIN MUTATED                               13                   0
  14Q GAIN WILD-TYPE                            153                   5
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  14Q GAIN MUTATED                                  7                  2
  14Q GAIN WILD-TYPE                               22                 12
                    vv
clus                 OTHER  SPECIFY
  14Q GAIN MUTATED                6
  14Q GAIN WILD-TYPE             38
D26V8, multiclass
                                  clus
vv                                 14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 106                629
  INFILTRATING LOBULAR CARCINOMA                 13                153
  MEDULLARY CARCINOMA                             0                  5
  MIXED HISTOLOGY (PLEASE SPECIFY)                7                 22
  MUCINOUS CARCINOMA                              2                 12
  OTHER  SPECIFY                                  6                 38
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V9, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    41  93
  14Q GAIN WILD-TYPE 241 620
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     41   93
  14Q GAIN WILD-TYPE  241  620
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                41                241
  YES               93                620
[1] 2 2
[1] FALSE
D26V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q GAIN MUTATED                                  0     9
  14Q GAIN WILD-TYPE                                1    47
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED                          19    90
  14Q GAIN WILD-TYPE                       118   618
D26V11, multiclass
                                  clus
vv                                 14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           9                 47
  BLACK OR AFRICAN AMERICAN                      19                118
  WHITE                                          90                618
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V12, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     2 108
  14Q GAIN WILD-TYPE  34 688
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      2  108
  14Q GAIN WILD-TYPE   34  688
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 34
  NOT HISPANIC OR LATINO              108                688
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    74   7
  15Q GAIN WILD-TYPE 786 107
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                81                893 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 7                107 
$`15Q GAIN MUTATED`
TCGA-A1-A0SF TCGA-A1-A0SN TCGA-A2-A0CV TCGA-A2-A0D2 TCGA-A2-A0EV TCGA-A2-A0T2 
       48.10        39.32        63.45        33.76        31.82         8.38 
TCGA-A2-A1FW TCGA-A2-A1G4 TCGA-A2-A25C TCGA-A2-A3XT TCGA-A2-A3XY TCGA-A7-A0CE 
       17.36        19.56        17.19        83.01        34.98        35.31 
TCGA-A7-A0D9 TCGA-A7-A13F TCGA-A7-A26G TCGA-A7-A3IY TCGA-A7-A4SE TCGA-A8-A06O 
       37.45        12.72        23.74        11.34        21.17        13.02 
TCGA-A8-A06Q TCGA-A8-A07P TCGA-A8-A07U TCGA-A8-A08B TCGA-A8-A08P TCGA-A8-A097 
        1.02        10.98         9.96        23.08        31.00        12.00 
TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09M TCGA-AC-A2QH TCGA-AN-A0XU TCGA-AO-A0J2 
       31.00        29.98        15.02         1.02         0.33        32.78 
TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A12D TCGA-AQ-A04L TCGA-AR-A0TP TCGA-AR-A0U2 
       71.80       102.58        64.04       130.09        82.88        83.87 
TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A24K TCGA-AR-A254 TCGA-AR-A2LH TCGA-B6-A0I5 
       42.58        36.26        50.89        39.85        20.25       149.59 
TCGA-B6-A0IM TCGA-BH-A0BG TCGA-BH-A0BP TCGA-BH-A0DL TCGA-BH-A0DS TCGA-BH-A0EE 
      126.12        24.85        48.69        48.23         2.56        31.00 
TCGA-BH-A0WA TCGA-BH-A18N TCGA-BH-A18V TCGA-BH-A1FH TCGA-C8-A12O TCGA-C8-A132 
       23.05        37.74        51.16        36.92        12.66         1.45 
TCGA-C8-A1HI TCGA-C8-A1HM TCGA-C8-A26X TCGA-C8-A26Z TCGA-D8-A1JP TCGA-D8-A27R 
       11.34         2.30         0.36         8.28        21.01        10.09 
TCGA-E2-A10A TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A1IL TCGA-E2-A1LE TCGA-E2-A1LH 
       40.41        17.29        20.71         3.88        28.90       106.75 
TCGA-E2-A1LL TCGA-E2-A56Z TCGA-E9-A1N8 TCGA-E9-A1NF TCGA-E9-A1R3 TCGA-E9-A1RA 
       43.04         7.20        12.00        20.05         2.10        32.09 
TCGA-EW-A1IY TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1P5 TCGA-EW-A1PB TCGA-GM-A2DF 
        8.48        28.77        22.82        23.11        19.99        42.71 
TCGA-GM-A2DK TCGA-LL-A5YM TCGA-OL-A5RV 
       62.33         4.70        24.10 

$`15Q GAIN WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI 
        8.52        14.37        43.43        14.27        47.24        20.88 
TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ 
       13.68        31.79         7.96        28.01        19.20        18.21 
TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U 
      104.81        18.02        41.95        82.16        73.84        22.06 
TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL 
       63.12        64.04        55.43        36.13       125.59        64.57 
TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS 
       24.79       112.08        92.48        88.60       107.93        75.55 
TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 
       75.25         5.19        64.04        56.81        21.14        34.55 
TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP 
       28.77        25.22       101.72        89.36        80.28       107.61 
TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EW 
       79.76        74.40        37.05        35.05        34.29        29.75 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW 
       24.72        24.16        99.19        54.64        27.12        44.88 
TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T3 TCGA-A2-A0T4 
       50.43        44.28        17.52        17.13        18.71        20.52 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE 
       17.46        18.90        20.75        32.55        25.28        18.21 
TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK 
       15.42        21.90        21.67        14.50        18.61        19.33 
TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ 
       14.63        31.73        23.77        23.47        36.79        22.45 
TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B 
       20.25        19.20        16.47        52.47       107.70        16.31 
TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS 
       18.15        91.92        10.59        20.88        39.65        33.93 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XZ TCGA-A2-A3Y0 
       29.98        14.07        49.48        38.40        31.99        38.37 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 
        7.30         9.01         8.81         8.91        12.00         6.74 
TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0DA 
        3.42        38.30        34.29        35.47        30.61        35.67 
TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       33.11        31.73        10.72        23.61        29.56        31.36 
TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IZ 
       24.26        23.80        21.73        20.61        22.32        10.59 
TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA 
       10.29        11.28        13.41        14.70        11.97        14.93 
TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW 
       13.74        14.50        17.92        14.73        12.10        10.72 
TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P 
       11.05        10.29         9.37        10.42         8.75        13.02 
TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z 
       17.98        41.06        29.03        31.00        26.01         1.02 
TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F 
       17.03        53.98         9.01        33.01        19.99        18.97 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07R 
       18.97        14.01        12.00        17.03         9.99         8.98 
TCGA-A8-A07S TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 
        7.99         9.99        28.04        18.05        15.06        36.95 
TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I 
       13.02         0.99        19.99        18.05        19.96        12.00 
TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T 
       37.05         9.99        31.00         0.99        19.07        93.04 
TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 
       33.99        40.01        19.07        16.01        17.95        41.98 
TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09I 
        9.99         9.99        12.00         1.02        13.02        33.07 
TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
        1.02        25.02         8.98        19.04        15.02         0.99 
TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 
       14.01        12.00        19.04        13.02        21.04         0.99 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G 
       13.02        17.03        38.04         0.95         2.37        10.85 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF 
        2.66         1.48        38.53        38.20        40.57        55.43 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ 
       36.99        38.79        26.04        50.70         0.92         2.27 
TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 
        0.99         0.69        14.83         9.40         1.12         1.81 
TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X 
        1.68         1.55         1.32         1.55         0.07         1.12 
TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AN-A03X 
        1.81         1.18         0.69         0.43         1.74         0.33 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C 
        0.33         0.23         0.33         0.62         2.96         1.78 
TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR 
        1.71         8.02         7.36         6.51         0.16         0.33 
TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK 
        0.33         0.33         6.44         4.64         7.96         7.00 
TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW 
        7.59         7.17         6.28         6.02         0.33         0.36 
TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO 
        0.33         0.33         0.33         0.33         0.33        12.33 
TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AN-A0XW 
        0.30         0.33         0.33         0.33         5.33         5.59 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R 
       80.28        47.84        66.77        81.63        84.69        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 
       47.87        59.05        29.13        21.40        17.65        24.16 
TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB 
       37.48        20.32        22.36        53.03        21.53        50.70 
TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI 
       50.86        72.00        76.77        21.37        26.24        38.53 
TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 
       62.04        55.33        99.25        93.70        94.59        96.10 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
       90.58        77.56        57.30        48.36        41.62        28.37 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT 
       14.73        82.62        61.87        70.39         0.53        17.79 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N 
       24.79        26.93         5.65        15.62        13.22         2.56 
TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT 
       21.86         9.99        49.32         5.26        37.41        56.88 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 
       29.75        24.30        64.83        55.86        76.14        65.36 
TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ 
       70.16        76.18        55.36        75.55        61.84        52.77 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP 
       51.25        48.82        62.56        43.73        43.56        39.98 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AY 
       43.07        17.23        40.83        46.32        35.24        20.22 
TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
      109.58        73.02        65.46        68.19        65.69         0.85 
TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V 
       66.05        57.40        62.07        53.26        53.36        54.18 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 
       50.96        48.16        51.75        56.15        45.17        40.64 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM 
       34.82        93.83       128.65        42.87         7.36        40.04 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN 
       17.10        20.81        16.96        20.38        54.74        16.04 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I9 TCGA-B6-A0IA 
       20.45        10.59        77.62       143.38        12.13       220.90 
TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ 
      129.57        50.70        65.72       146.50       112.37       176.98 
TCGA-B6-A0IK TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE 
       18.77        84.59       110.14       110.93       140.88       211.56 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN 
       68.45       189.01       234.28        81.17        78.02       172.96 
TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU 
      162.05       102.77       140.48       100.70        89.46       131.21 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX 
      157.41        97.48       188.68        79.63        17.98        21.47 
TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
      113.79       129.57       129.70       186.48        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU 
       58.88        43.59       101.52        73.51       139.17       170.17 
TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
       85.35        54.28        49.94        82.88        55.00        24.53 
TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 
       38.79        20.45        25.55        28.50        46.95        40.83 
TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 
       39.55        39.16        48.36        56.94        56.98        51.68 
TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BL 
       37.22        32.02        18.21        25.71        21.70        44.05 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT 
       61.68        35.67        27.19        53.69        53.95        45.57 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 
       49.94        11.67        49.05        41.75        44.02        48.13 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI 
       42.90        45.83        31.17        23.44        38.01        22.13 
TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DT TCGA-BH-A0DV 
       13.91        17.26        15.65         3.22        38.47        45.17 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 
       47.41        16.27         4.41        15.68        14.30         9.63 
TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EI TCGA-BH-A0GY 
       44.81        46.19        32.65        24.49        24.43        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 
       10.78        15.16        37.78        35.51        24.56        23.08 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       41.00        52.96        26.50        20.38         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY 
       13.61        36.85        12.89        51.32        27.25        50.79 
TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18F 
        5.59        23.93        24.95        42.35        44.81         8.81 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M 
        2.01         7.23        20.12        90.84        26.66        72.56 
TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U 
       30.28        55.63        37.55        66.05         7.36        51.39 
TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV 
       69.93        91.99       113.82        82.85        42.28        12.00 
TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 
       55.69        49.58        17.69        25.81        31.53        89.16 
TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE 
       97.48        24.66       120.62       114.15        33.17        74.73 
TCGA-BH-A1FG TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR 
      122.89        63.35        55.00        45.63        72.07       144.59 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 
       72.07         6.90         0.72        38.60        83.31        57.83 
TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
      130.16        10.65         6.44        20.12         0.99       109.28 
TCGA-BH-A42V TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12P TCGA-C8-A12Q 
        8.94        11.93        11.77        11.77        11.77         0.07 
TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A131 
       12.66        12.66        12.66        12.66         3.12         1.78 
TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF 
        0.69         0.62         3.85         3.75        12.33        10.92 
TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26V 
       11.34         0.16        12.03        10.42         3.25         0.30 
TCGA-C8-A26W TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 
        0.23         0.43         9.67         0.03         0.03         0.03 
TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A13Z 
       12.20         0.99         0.03         0.23        11.90        20.88 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 
       13.25        20.58        13.97        14.17        13.48        21.14 
TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC 
       19.20        14.17        17.49        16.50        18.71        15.78 
TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI 
       18.15        18.90        12.03        12.03        14.01        18.97 
TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JS 
       20.09        20.12        20.09        19.40        20.38        12.20 
TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 
       13.32        14.70        18.58        17.79        16.73        25.74 
TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF 
       23.90        27.58        18.15         2.66        17.16        15.22 
TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO 
       14.73        21.83        14.50        19.92        17.69         7.96 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV 
       16.41        15.85        16.31         6.35        12.99        15.16 
TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 
       12.66        16.54        15.32        15.52         3.81        14.24 
TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I 
       14.14        17.42        16.04        13.45        13.05        14.43 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T 
        9.44        16.41        13.48         4.80         0.76        13.08 
TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 
       12.53        12.26        14.50        18.51         7.33        43.00 
TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E 
       34.42        27.52        46.59        37.51        40.11        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R 
       28.87        47.15        44.68        40.96        38.24        38.60 
TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X 
       33.17        33.30        43.33        34.26        32.02        31.96 
TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 
       28.60        17.03        25.41        27.12        23.24        19.43 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C 
       21.04        23.87        14.79        25.05        23.34        22.82 
TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       21.63        18.21        12.92        17.42        19.40         9.04 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
       20.58         7.73        13.02        19.56        17.06        14.07 
TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       14.99        60.53        53.62        53.03        29.95        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       28.50        16.47        17.10        38.30        37.41        32.78 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IN TCGA-E2-A1IO 
       33.73        33.70        28.44        22.65        22.19        20.98 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA 
       11.08        54.18        27.42        39.62        19.66        24.59 
TCGA-E2-A1LB TCGA-E2-A1LG TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A2P6 
       40.47        18.87       102.61         8.75        16.93         5.52 
TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N4 TCGA-E9-A1N5 
       15.72        18.05        22.26        19.89        19.20        36.82 
TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE 
       13.48        13.12        36.56        39.55        12.59        35.77 
TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R4 
       21.57         9.86        11.90        14.30         0.62         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD 
        1.38         2.76        21.21        20.81        40.24         0.66 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 
       34.65         6.58        21.27        34.59        35.64        34.13 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E 
        0.79        12.53        13.32        39.09        22.75        12.89 
TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A247 
       23.51        24.10        17.06         0.69         0.85        27.22 
TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT 
        1.94         0.95        12.56         0.72        17.75         0.76 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FK 
       26.07        18.41         0.62        15.72         0.23         0.39 
TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ 
        0.26         0.23        15.39        12.20        39.72        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OX 
       18.90        13.25        16.57        15.68        25.94        29.95 
TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 
       29.85        40.41        41.13        39.78        52.96        29.82 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PC TCGA-EW-A1PD 
       18.48        30.08         7.86        18.90         6.15        13.94 
TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS 
       10.52        14.43        34.55        19.96        55.00        52.73 
TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 
       25.91        22.09        21.27        17.49        10.16        10.59 
TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC 
        7.40       109.87        59.57       194.27        53.13        53.52 
TCGA-GM-A2DD TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       43.04        42.28        61.91        90.84        76.64        77.33 
TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN 
       53.36       110.50        38.20        32.28        69.30        53.95 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U 
       57.63        13.55        18.12        11.84        11.57         8.28 
TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y 
        6.67         4.60         0.66         2.99         3.58         6.90 
TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A6FR 
        5.56         3.65         3.19         3.25         2.63         3.88 
TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 
        4.14         4.50         4.50         5.59         3.22         6.21 
TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 
       15.91         2.79         2.10        12.66        46.55         7.53 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       44.61        27.65        26.20        16.87        14.10        10.29 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L 
        9.80        14.76        23.70        54.51        33.90        31.07 
TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-S3-A6ZG TCGA-W8-A86G 
       18.21         7.23         4.44         6.81         5.29 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.33               0.03 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            149.59             234.28 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             24.10              21.14 
[1] "0.3 - 149.6 (24.1)" "0.0 - 234.3 (21.1)"
[1] "hr=" "1.4"
D27V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  15Q GAIN MUTATED        10        5        0        0        29        17
  15Q GAIN WILD-TYPE      70       72        9        9       306       207
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  15Q GAIN MUTATED           1         12          2          5        2
  15Q GAIN WILD-TYPE         1        126         25         54       15
                    vv
clus                 STAGE TIS STAGE X
  15Q GAIN MUTATED           0       0
  15Q GAIN WILD-TYPE         1      16
D27V3, multiclass
            clus
vv           15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                  10                 70
  STAGE IA                  5                 72
  STAGE IB                  0                  9
  STAGE II                  0                  9
  STAGE IIA                29                306
  STAGE IIB                17                207
  STAGE III                 1                  1
  STAGE IIIA               12                126
  STAGE IIIB                2                 25
  STAGE IIIC                5                 54
  STAGE IV                  2                 15
  STAGE TIS                 0                  1
  STAGE X                   0                 16
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  15Q GAIN MUTATED    22  47  12   2
  15Q GAIN WILD-TYPE 236 534 105  34
D27V4, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1               22                236
  T2               47                534
  T3               12                105
  T4                2                 34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  15Q GAIN MUTATED    40  26   9   7
  15Q GAIN WILD-TYPE 428 304 102  63
D27V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0               40                428
  N1               26                304
  N2                9                102
  N3                7                 63
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  15Q GAIN MUTATED          0  73   2   8
  15Q GAIN WILD-TYPE        2 772  15 123
D27V6, multiclass
          clus
vv         15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CM0 (I+)                0                  2
  M0                     73                772
  M1                      2                 15
  MX                      8                123
[1] 4 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    82   1
  15Q GAIN WILD-TYPE 902  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     82    1
  15Q GAIN WILD-TYPE  902   10
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE               82                902
  MALE                  1                 10
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  15Q GAIN MUTATED                            0                            72
  15Q GAIN WILD-TYPE                          1                           663
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  15Q GAIN MUTATED                                2                   0
  15Q GAIN WILD-TYPE                            164                   5
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  15Q GAIN MUTATED                                  1                  2
  15Q GAIN WILD-TYPE                               28                 12
                    vv
clus                 OTHER  SPECIFY
  15Q GAIN MUTATED                5
  15Q GAIN WILD-TYPE             39
D27V8, multiclass
                                  clus
vv                                 15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                  72                663
  INFILTRATING LOBULAR CARCINOMA                  2                164
  MEDULLARY CARCINOMA                             0                  5
  MIXED HISTOLOGY (PLEASE SPECIFY)                1                 28
  MUCINOUS CARCINOMA                              2                 12
  OTHER  SPECIFY                                  5                 39
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V9, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    29  54
  15Q GAIN WILD-TYPE 253 659
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     29   54
  15Q GAIN WILD-TYPE  253  659
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                29                253
  YES               54                659
[1] 2 2
[1] FALSE
D27V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q GAIN MUTATED                                  0     8
  15Q GAIN WILD-TYPE                                1    48
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED                          12    51
  15Q GAIN WILD-TYPE                       125   657
D27V11, multiclass
                                  clus
vv                                 15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           8                 48
  BLACK OR AFRICAN AMERICAN                      12                125
  WHITE                                          51                657
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V12, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     3  65
  15Q GAIN WILD-TYPE  33 731
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      3   65
  15Q GAIN WILD-TYPE   33  731
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 33
  NOT HISPANIC OR LATINO               65                731
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED   382  53
  16P GAIN WILD-TYPE 478  61
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               435                539 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                53                 61 
$`16P GAIN MUTATED`
TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SO TCGA-A2-A04N 
       48.10        14.27        20.88        13.68        28.01       104.81 
TCGA-A2-A04P TCGA-A2-A04T TCGA-A2-A04V TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
       18.02        73.84        63.12        24.79       112.08        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CS TCGA-A2-A0CX TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM 
       88.60        75.55        56.81        33.76        28.77       101.72 
TCGA-A2-A0EO TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0SU TCGA-A2-A0SV 
       80.28        35.05        34.29        31.82        54.64        27.12 
TCGA-A2-A0SW TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T5 TCGA-A2-A0YD 
       44.88        17.13         8.38        18.71        17.46        25.28 
TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YJ TCGA-A2-A0YT 
       18.21        15.42        21.90        21.67        18.61        23.77 
TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1G0 TCGA-A2-A259 TCGA-A2-A3XX TCGA-A2-A3XY 
       17.36        36.79        20.25        52.47        38.40        34.98 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0DB TCGA-A7-A13H 
       12.00         6.74        38.30        35.31        33.11        29.56 
TCGA-A7-A26E TCGA-A7-A26H TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SB TCGA-A7-A4SE 
       31.36        23.80        14.70        11.97        13.74        21.17 
TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VX TCGA-A8-A06P TCGA-A8-A06R 
       17.92        12.10        10.72        10.42        13.02        17.98 
TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A07F TCGA-A8-A07J 
       29.03        31.00        26.01         1.02        18.97        12.00 
TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A084 
       10.98         8.98         7.99         9.99        28.04        15.06 
TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F 
       36.95        13.02         0.99        23.08        19.99        18.05 
TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z 
       19.96        12.00        31.00        19.07        93.04        40.01 
TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09A 
       19.07        16.01        17.95        41.98        12.00         9.99 
TCGA-A8-A09B TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09X 
       12.00        31.00        29.98        19.04        15.02        14.01 
TCGA-A8-A0A1 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23E 
       12.00         0.99        13.02        17.03        38.04         2.37 
TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2FG TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3BB 
       10.85         1.48        36.99        50.70         0.92         0.99 
TCGA-AC-A3QP TCGA-AC-A3W5 TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y 
        9.40         1.81         1.55         0.07         1.12         1.81 
TCGA-AC-A6IV TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A04A 
        1.18         0.33         0.33         0.23         0.62         2.96 
TCGA-AN-A04C TCGA-AN-A0AJ TCGA-AN-A0AM TCGA-AN-A0FK TCGA-AN-A0FV TCGA-AN-A0FW 
        1.78         8.02         0.16         7.00         0.33         0.36 
TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XO TCGA-AN-A0XS TCGA-AN-A0XT 
        0.33         0.33         0.33        12.33         0.33         0.33 
TCGA-AN-A0XU TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03V TCGA-AO-A0J7 
        0.33        80.28        66.77        81.63        29.13        20.32 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JE TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 
       22.36        53.03        76.77        55.33        71.80       102.58 
TCGA-AO-A125 TCGA-AO-A12A TCGA-AO-A12E TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS 
       99.25        90.58        57.30        82.62        61.87         0.53 
TCGA-AQ-A04H TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A54O TCGA-AR-A0TR TCGA-AR-A0TS 
       24.79         5.65        15.62        21.86         5.26        37.41 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0U2 TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AL 
       29.75        24.30        83.87        61.84        51.25        48.82 
TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A24L TCGA-AR-A24N 
       39.98        40.83        42.58        36.26        73.02        68.19 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A254 TCGA-AR-A255 
        0.85        66.05        48.16        56.15        39.85        34.82 
TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LO TCGA-AR-A5QM TCGA-AR-A5QP 
       42.87         7.36        40.04        20.81        54.74        20.45 
TCGA-B6-A0I2 TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH 
      143.38       129.57        50.70        65.72       146.50       112.37 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN 
      110.14       110.93       140.88       234.28        78.02       172.96 
TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0WS TCGA-B6-A0WT 
      162.05       102.77       140.48       100.70        97.48       188.68 
TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X1 TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A2IU 
      113.79       129.57       186.48       101.52        73.51       170.17 
TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV 
       85.35        49.94        82.88        55.00        24.53        38.79 
TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0BA TCGA-BH-A0BG 
       20.45        25.55        39.55        48.36        37.22        24.85 
TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BT TCGA-BH-A0C1 TCGA-BH-A0C3 
       44.05        48.69        27.19        45.57        44.02        48.13 
TCGA-BH-A0C7 TCGA-BH-A0DH TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DS 
       42.90        38.01        48.23        17.26        15.65         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E6 TCGA-BH-A0E7 
       38.47        45.17        47.41        16.27         9.63        44.81 
TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0GY TCGA-BH-A0H3 
       46.19        32.65        24.49        31.00        30.35        37.78 
TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HI TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0W3 
       24.56        41.00        20.38        36.85        12.89        23.93 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18I TCGA-BH-A18L 
       42.35        44.81        23.05         8.81         7.23        26.66 
TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EO 
       72.56        37.74        55.63         7.36        51.16        91.99 
TCGA-BH-A1EV TCGA-BH-A1EX TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1FB TCGA-BH-A1FG 
       12.00        49.58        31.53        89.16       120.62       122.89 
TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A202 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A42V 
       45.63        72.07         0.72        83.31        57.83         8.94 
TCGA-C8-A12L TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12U TCGA-C8-A12W TCGA-C8-A131 
       11.93        11.77        12.66        12.66        12.66         1.78 
TCGA-C8-A132 TCGA-C8-A138 TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HM 
        1.45         3.75        11.34        11.34        12.03         2.30 
TCGA-C8-A1HN TCGA-C8-A26W TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A274 TCGA-D8-A141 
        3.25         0.23         0.43         8.28         0.03        20.58 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 
       13.97        14.17        13.48        21.14        14.17        17.49 
TCGA-D8-A1JD TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1X5 
       18.15        12.03        12.03        20.09        20.12        18.58 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XF 
       17.79        16.73        27.58        18.15         2.66        15.22 
TCGA-D8-A1XJ TCGA-D8-A1XL TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XW 
       21.83        19.92        15.85        16.31        12.99        12.66 
TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27I TCGA-D8-A27K 
       16.54        15.32         3.81        14.24        14.43         9.44 
TCGA-D8-A27L TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-E2-A107 TCGA-E2-A10A TCGA-E2-A10B 
       16.41        12.26        14.50        34.42        40.41        37.51 
TCGA-E2-A10C TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14U TCGA-E2-A14V 
       40.11        28.87        44.68        38.24        43.33        34.26 
TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A156 
       31.96        17.03        27.12        23.24        19.43        23.87 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15K 
       22.82        17.29        20.71        18.21        17.42         9.04 
TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A1B0 TCGA-E2-A1B5 TCGA-E2-A1BC TCGA-E2-A1BD 
        7.73        13.02        53.62        32.35        16.47        17.10 
TCGA-E2-A1IF TCGA-E2-A1IJ TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L8 TCGA-E2-A1L9 
       37.41        28.44        20.98        11.08        39.62        19.66 
TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A56Z TCGA-E2-A570 TCGA-E9-A1N5 
       43.04        16.93         5.52         7.20        18.05        36.82 
TCGA-E9-A1N8 TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 
       12.00        20.05        21.57         9.86        11.90        14.30 
TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA 
        2.10         6.12         1.38         2.76        21.21        32.09 
TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A1RH 
       20.81        40.24         0.66        34.65        21.27        34.59 
TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A247 
       35.64        34.13        22.75        12.89        24.10        27.22 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A3Q9 TCGA-E9-A3X8 
        0.95        12.56         0.72        17.75        18.41        15.72 
TCGA-E9-A54Y TCGA-E9-A5FL TCGA-E9-A6HE TCGA-EW-A1IY TCGA-EW-A1J3 TCGA-EW-A1OV 
        0.23         0.26        15.39         8.48        16.57        25.94 
TCGA-EW-A1OW TCGA-EW-A1OZ TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 
       22.82        40.41        52.96        29.82        23.11        18.48 
TCGA-EW-A1PG TCGA-EW-A2FS TCGA-EW-A3E8 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2DA 
       34.55        52.73        21.27         7.40       109.87       194.27 
TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DI TCGA-GM-A2DN TCGA-GM-A3NY TCGA-GM-A3XN 
       53.13        43.04        61.91        77.33        38.20        53.95 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YX TCGA-LD-A66U TCGA-LL-A5YL TCGA-LL-A5YM 
       13.55        18.12        11.57         8.28         5.56         4.70 
TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A7SZ TCGA-LQ-A4E4 TCGA-MS-A51U 
        3.25         2.63         4.14         5.59        15.91         2.79 
TCGA-OK-A5Q2 TCGA-OL-A5D8 TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RZ TCGA-OL-A66K 
        2.10         7.53        24.10        16.87        10.29        33.90 
TCGA-OL-A66N TCGA-S3-A6ZG TCGA-W8-A86G 
       18.21         6.81         5.29 

$`16P GAIN WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SH TCGA-A1-A0SK TCGA-A1-A0SM 
        8.52        14.37        43.43        47.24        31.79         7.96 
TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04U 
       39.32        19.20        18.21        41.95        82.16        22.06 
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CR 
       64.04        55.43        36.13       125.59        64.57       107.93 
TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 
       75.25         5.19        63.45        64.04        21.14        34.55 
TCGA-A2-A0D4 TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES 
       25.22        89.36       107.61        79.76        74.40        37.05 
TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SX TCGA-A2-A0SY 
       29.75        24.72        24.16        99.19        50.43        44.28 
TCGA-A2-A0T0 TCGA-A2-A0T4 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YI 
       17.52        20.52        18.90        20.75        32.55        14.50 
TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FZ TCGA-A2-A1G1 
       19.33        14.63        31.73        23.47        22.45        19.20 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D 
       19.56        16.47       107.70        16.31        17.19        18.15 
TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT 
       91.92        10.59        20.88        39.65        33.93        83.01 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW 
       29.98        14.07        49.48        31.99        38.37         7.30 
TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S3 TCGA-A7-A0CG TCGA-A7-A0CH 
        9.01         8.81         8.91         3.42        34.29        35.47 
TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F 
       30.61        37.45        35.67        31.73        10.72        12.72 
TCGA-A7-A13G TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD 
       23.61        24.26        23.74        21.73        20.61        22.32 
TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A4SA 
       11.34        10.59        10.29        11.28        13.41        14.93 
TCGA-A7-A4SD TCGA-A7-A56D TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY 
       14.50        14.73        11.05        10.29         9.37         8.75 
TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A06T TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 
       13.02         1.02        41.06        17.03        53.98         9.01 
TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07L TCGA-A8-A07O 
       33.01        19.99        18.97        14.01        17.03         9.99 
TCGA-A8-A07U TCGA-A8-A082 TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R 
        9.96        18.05        37.05         9.99        31.00         0.99 
TCGA-A8-A08X TCGA-A8-A099 TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09I TCGA-A8-A09M 
       33.99         9.99         1.02        13.02        33.07        15.02 
TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09W TCGA-A8-A0A2 TCGA-A8-A0A4 
        1.02        25.02         8.98         0.99        19.04        13.02 
TCGA-A8-A0A6 TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB 
       21.04         0.95         2.66        38.53        38.20        40.57 
TCGA-AC-A2FF TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A3HN 
       55.43        38.79        26.04         1.02         2.27         0.69 
TCGA-AC-A3OD TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A6IW 
       14.83         1.12         1.68         1.55         1.32         0.69 
TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AN-A046 TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL 
        0.43         1.74         0.33         1.71         7.36         6.51 
TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ 
        0.33         0.33         0.33         6.44         4.64         7.96 
TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FX TCGA-AN-A0XN 
        7.59         7.17         6.28         6.02         0.33         0.33 
TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03P 
        0.30         0.33         5.33         5.59        47.84        84.69 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 
       68.75        47.87        59.05        32.78        21.40        17.65 
TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD 
       24.16        37.48        21.53        50.70        50.86        72.00 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A126 TCGA-AO-A128 
       21.37        26.24        38.53        62.04        93.70        94.59 
TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
       96.10        77.56        64.04        48.36        41.62        28.37 
TCGA-AO-A1KO TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H3 
       14.73        70.39        17.79        26.93       130.09        13.22 
TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TT TCGA-AR-A0TX 
        2.56         9.99        82.88        49.32        56.88        64.83 
TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 
       55.86        76.14        65.36        70.16        76.18        55.36 
TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AQ 
       75.55        52.77        62.56        43.73        43.56        43.07 
TCGA-AR-A1AR TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K 
       17.23        46.32        35.24        20.22       109.58        50.89 
TCGA-AR-A24M TCGA-AR-A24O TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U 
       65.46        65.69        57.40        62.07        53.26        53.36 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A256 
       54.18        50.96        51.75        45.17        40.64        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LN TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QN 
      128.65        20.25        17.10        16.96        20.38        16.04 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IJ 
       10.59        77.62       149.59        12.13       220.90       176.98 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH 
       18.77       126.12        84.59       211.56        68.45       189.01 
TCGA-B6-A0RL TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WV TCGA-B6-A0WW 
       81.17        89.46       131.21       157.41        79.63        17.98 
TCGA-B6-A0WX TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC 
       21.47       129.70        28.27        68.94        58.88        43.59 
TCGA-B6-A1KN TCGA-B6-A402 TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 
      139.17        54.28        28.50        46.95        40.83        39.16 
TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       56.94        56.98        51.68        32.02        18.21        25.71 
TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV 
       21.70        61.68        35.67        53.69        53.95        49.94 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG 
       11.67        49.05        41.75        45.83        31.17        23.44 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DQ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 
       22.13        13.91         3.22         4.41        15.68        14.30 
TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H5 TCGA-BH-A0H7 TCGA-BH-A0HA 
       24.43        10.78        15.16        35.51        23.08        52.96 
TCGA-BH-A0HB TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HW TCGA-BH-A0HX 
       26.50         5.85         2.50        13.61        51.32        27.25 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A18G TCGA-BH-A18J TCGA-BH-A18K 
       50.79         5.59        24.95         2.01        20.12        90.84 
TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1ES 
       30.28        37.55        66.05        51.39        69.93       113.82 
TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F6 
       82.85        42.28        55.69        17.69        25.81        97.48 
TCGA-BH-A1F8 TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FH TCGA-BH-A1FJ 
       24.66       114.15        33.17        74.73        36.92        63.35 
TCGA-BH-A1FL TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A209 
       55.00       144.59        72.07         6.90        38.60       130.16 
TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-C8-A12M 
       10.65         6.44        20.12         0.99       109.28        11.77 
TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A134 
       11.77         0.07        12.66        12.66         3.12         0.69 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HJ TCGA-C8-A1HL 
        0.62         3.85        12.33        10.92         0.16        10.42 
TCGA-C8-A26V TCGA-C8-A26X TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A 
        0.30         0.36         9.67         0.03         0.03        12.20 
TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 
        0.99         0.03         0.23        11.90        20.88        13.25 
TCGA-D8-A147 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JH 
       19.20        16.50        18.71        15.78        18.90        14.01 
TCGA-D8-A1JI TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS 
       18.97        20.09        19.40        20.38        21.01        12.20 
TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XD TCGA-D8-A1XG 
       13.32        14.70        25.74        23.90        17.16        14.73 
TCGA-D8-A1XK TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XT TCGA-D8-A1XV 
       14.50        17.69         7.96        16.41         6.35        15.16 
TCGA-D8-A1Y0 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H 
       15.52        14.14        17.42        16.04        13.45        13.05 
TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V 
       13.48         4.80         0.76        10.09        13.08        12.53 
TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10E 
       18.51         7.33        43.00        27.52        46.59        28.44 
TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14W 
       47.15        40.96        38.60        33.17        33.30        32.02 
TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A155 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A 
       28.60        25.41        21.04        14.79        25.05        23.34 
TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15J TCGA-E2-A15L TCGA-E2-A15P TCGA-E2-A15R 
       21.63        12.92        19.40        20.58        19.56        17.06 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B6 
       14.07        14.99        60.53        53.03        29.95        28.50 
TCGA-E2-A1IE TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IK TCGA-E2-A1IL 
       38.30        32.78        33.73        33.70        22.65         3.88 
TCGA-E2-A1IN TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       22.19        54.18        27.42        24.59        40.47        28.90 
TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A3DX TCGA-E2-A573 
       18.87       106.75       102.61         8.75        15.72        22.26 
TCGA-E2-A574 TCGA-E9-A1N4 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC 
       19.89        19.20        13.48        13.12        36.56        39.55 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1R2 TCGA-E9-A1RF TCGA-E9-A227 TCGA-E9-A228 
       12.59        35.77         0.62         6.58         0.79        12.53 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22G TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A245 
       13.32        39.09        23.51        17.06         0.69         0.85 
TCGA-E9-A248 TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3QA TCGA-E9-A5FK TCGA-E9-A5UO 
        1.94         0.76        26.07         0.62         0.39         0.23 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J5 
       12.20        39.72        18.21        18.90        13.25        15.68 
TCGA-EW-A1J6 TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P7 
       28.77        29.95        29.85        41.13        39.78        30.08 
TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE 
        7.86        18.90        19.99         6.15        13.94        10.52 
TCGA-EW-A1PF TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3U0 
       14.43        19.96        55.00        25.91        22.09        17.49 
TCGA-EW-A423 TCGA-EW-A424 TCGA-GM-A2D9 TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH 
       10.16        10.59        59.57        53.52        42.71        42.28 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3XG 
       62.33        90.84        76.64        53.36       110.50        32.28 
TCGA-GM-A3XL TCGA-GM-A4E0 TCGA-JL-A3YW TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 
       69.30        57.63        11.84         6.67         4.60         0.66 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FR 
        2.99         3.58         6.90         3.65         3.19         3.88 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-OL-A5D6 TCGA-OL-A5D7 
        4.50         4.50         3.22         6.21        12.66        46.55 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RW TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66H 
       44.61        27.65        26.20        14.10         9.80        14.76 
TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P 
       23.70        54.51        31.07         7.23         4.44 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.03               0.03 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            234.28             220.90 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             21.21              21.63 
[1] "0.0 - 234.3 (21.2)" "0.0 - 220.9 (21.6)"
[1] "hr=" "1"  
D28V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16P GAIN MUTATED        39       32        4        5       139       105
  16P GAIN WILD-TYPE      41       45        5        4       196       119
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16P GAIN MUTATED           1         65         16         21        9
  16P GAIN WILD-TYPE         1         73         11         38        8
                    vv
clus                 STAGE TIS STAGE X
  16P GAIN MUTATED           1       6
  16P GAIN WILD-TYPE         0      10
D28V3, multiclass
            clus
vv           16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                  39                 41
  STAGE IA                 32                 45
  STAGE IB                  4                  5
  STAGE II                  5                  4
  STAGE IIA               139                196
  STAGE IIB               105                119
  STAGE III                 1                  1
  STAGE IIIA               65                 73
  STAGE IIIB               16                 11
  STAGE IIIC               21                 38
  STAGE IV                  9                  8
  STAGE TIS                 1                  0
  STAGE X                   6                 10
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  16P GAIN MUTATED   110 258  56  17
  16P GAIN WILD-TYPE 148 323  61  19
D28V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1              110                148
  T2              258                323
  T3               56                 61
  T4               17                 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                  N0  N1  N2  N3
  16P GAIN MUTATED   207 148  54  25
  16P GAIN WILD-TYPE 261 182  57  45
D28V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0              207                261
  N1              148                182
  N2               54                 57
  N3               25                 45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  16P GAIN MUTATED          1 375   9  58
  16P GAIN WILD-TYPE        1 470   8  73
D28V6, multiclass
          clus
vv         16P GAIN MUTATED 16P GAIN WILD-TYPE
  CM0 (I+)                1                  1
  M0                    375                470
  M1                      9                  8
  MX                     58                 73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED   437   6
  16P GAIN WILD-TYPE 547   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED    437    6
  16P GAIN WILD-TYPE  547    5
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE              437                547
  MALE                  6                  5
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  16P GAIN MUTATED                            1                           329
  16P GAIN WILD-TYPE                          0                           406
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  16P GAIN MUTATED                               80                   2
  16P GAIN WILD-TYPE                             86                   3
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  16P GAIN MUTATED                                 15                  2
  16P GAIN WILD-TYPE                               14                 12
                    vv
clus                 OTHER  SPECIFY
  16P GAIN MUTATED               13
  16P GAIN WILD-TYPE             31
D28V8, multiclass
                                  clus
vv                                 16P GAIN MUTATED 16P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      1                  0
  INFILTRATING DUCTAL CARCINOMA                 329                406
  INFILTRATING LOBULAR CARCINOMA                 80                 86
  MEDULLARY CARCINOMA                             2                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)               15                 14
  MUCINOUS CARCINOMA                              2                 12
  OTHER  SPECIFY                                 13                 31
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V9, binary
                    cls
clus                   0   1
  16P GAIN MUTATED   120 323
  16P GAIN WILD-TYPE 162 390
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED    120  323
  16P GAIN WILD-TYPE  162  390
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO               120                162
  YES              323                390
[1] 2 2
[1] FALSE
D28V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P GAIN MUTATED                                  1    23
  16P GAIN WILD-TYPE                                0    33
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED                          50   317
  16P GAIN WILD-TYPE                        87   391
D28V11, multiclass
                                  clus
vv                                 16P GAIN MUTATED 16P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                          23                 33
  BLACK OR AFRICAN AMERICAN                      50                 87
  WHITE                                         317                391
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V12, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    11 348
  16P GAIN WILD-TYPE  25 448
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     11  348
  16P GAIN WILD-TYPE   25  448
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                   11                 25
  NOT HISPANIC OR LATINO              348                448
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED   104  23
  16Q GAIN WILD-TYPE 756  91
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               127                847 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                23                 91 
$`16Q GAIN MUTATED`
TCGA-A1-A0SG TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A2-A04P TCGA-A2-A04T TCGA-A2-A0CM 
       14.27        20.88        13.68        18.02        73.84        24.79 
TCGA-A2-A0CX TCGA-A2-A0D2 TCGA-A2-A0ET TCGA-A2-A0EV TCGA-A2-A0SV TCGA-A2-A0SW 
       56.81        33.76        35.05        31.82        27.12        44.88 
TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A3XX TCGA-A2-A3XY 
       18.21        21.90        23.77        17.36        38.40        34.98 
TCGA-A2-A4S1 TCGA-A7-A425 TCGA-A7-A5ZV TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A07W 
       12.00        14.70        12.10        26.01         1.02         9.99 
TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A0A7 TCGA-AC-A3BB TCGA-AC-A62V TCGA-AC-A62Y 
       18.05        12.00         0.99         0.99         0.07         1.81 
TCGA-AC-A6IV TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A0FY TCGA-AN-A0XO 
        1.18         0.23         0.62         2.96         0.33        12.33 
TCGA-AO-A03V TCGA-AO-A0JE TCGA-AO-A0JL TCGA-AO-A1KQ TCGA-AQ-A54O TCGA-AR-A0TR 
       29.13        76.77        55.33        61.87        21.86         5.26 
TCGA-AR-A0TS TCGA-AR-A0TW TCGA-AR-A1AV TCGA-AR-A24L TCGA-AR-A250 TCGA-AR-A255 
       37.41        24.30        42.58        73.02        56.15        34.82 
TCGA-B6-A0IE TCGA-B6-A0IO TCGA-B6-A0RM TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RS 
       65.72       110.14        78.02       162.05       140.48       100.70 
TCGA-B6-A0WT TCGA-B6-A0WY TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A401 TCGA-BH-A0BG 
      188.68       113.79       101.52        73.51        85.35        24.85 
TCGA-BH-A0BL TCGA-BH-A0BT TCGA-BH-A0DL TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 
       44.05        45.57        48.23        24.56        23.08        41.00 
TCGA-BH-A0W5 TCGA-BH-A18I TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18Q TCGA-BH-A18V 
       42.35         7.23        26.66        72.56        55.63        51.16 
TCGA-BH-A1EX TCGA-BH-A1FN TCGA-BH-A204 TCGA-BH-A208 TCGA-C8-A12L TCGA-C8-A12W 
       49.58        72.07        83.31        57.83        11.93        12.66 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A1HK TCGA-C8-A26Y TCGA-C8-A26Z TCGA-D8-A142 
        1.78         1.45        12.03         0.43         8.28        13.97 
TCGA-D8-A143 TCGA-D8-A1JF TCGA-D8-A1JK TCGA-D8-A1X7 TCGA-D8-A1XB TCGA-D8-A1XF 
       14.17        12.03        20.12        16.73        18.15        15.22 
TCGA-D8-A1XJ TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y2 TCGA-D8-A27I 
       21.83        12.99        12.66        15.32        14.24        14.43 
TCGA-D8-A27W TCGA-E2-A10F TCGA-E2-A14X TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A15M 
       12.26        28.87        31.96        27.12        19.43         7.73 
TCGA-E2-A1B0 TCGA-E2-A1B5 TCGA-E2-A1IJ TCGA-E2-A1LL TCGA-E9-A1RC TCGA-E9-A22B 
       53.62        32.35        28.44        43.04        40.24        22.75 
TCGA-E9-A247 TCGA-E9-A2JS TCGA-E9-A5FL TCGA-EW-A1OW TCGA-EW-A1P3 TCGA-EW-A1P4 
       27.22        17.75         0.26        22.82        52.96        29.82 
TCGA-EW-A1P5 TCGA-GI-A2C9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A3XN 
       23.11       109.87       194.27        53.13        43.04        53.95 
TCGA-LL-A5YM TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A7SZ TCGA-OK-A5Q2 
        4.70         3.25         2.63         4.14         5.59         2.10 
TCGA-OL-A5RZ 
       10.29 

$`16Q GAIN WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SH TCGA-A1-A0SK 
        8.52        14.37        43.43        48.10        47.24        31.79 
TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N 
        7.96        39.32        28.01        19.20        18.21       104.81 
TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X 
       41.95        82.16        22.06        63.12        64.04        55.43 
TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
       36.13       125.59        64.57       112.08        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW 
      107.93        75.55        75.25         5.19        63.45        64.04 
TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN 
       21.14        34.55        28.77        25.22       101.72        89.36 
TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EU 
       80.28       107.61        79.76        74.40        37.05        34.29 
TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SX 
       29.75        24.72        24.16        99.19        54.64        50.43 
TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 
       44.28        17.52        17.13         8.38        18.71        20.52 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF 
       17.46        18.90        20.75        32.55        25.28        15.42 
TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       21.67        14.50        18.61        19.33        14.63        31.73 
TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 
       23.47        36.79        22.45        20.25        19.20        19.56 
TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D 
       16.47        52.47       107.70        16.31        17.19        18.15 
TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT 
       91.92        10.59        20.88        39.65        33.93        83.01 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW 
       29.98        14.07        49.48        31.99        38.37         7.30 
TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD 
        9.01         8.81         8.91         6.74         3.42        38.30 
TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA 
       35.31        34.29        35.47        30.61        37.45        35.67 
TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H 
       33.11        31.73        10.72        12.72        23.61        29.56 
TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J 
       31.36        24.26        23.74        23.80        21.73        20.61 
TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF 
       22.32        11.34        10.59        10.29        11.28        13.41 
TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF 
       11.97        14.93        13.74        14.50        21.17        17.92 
TCGA-A7-A56D TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX 
       14.73        10.72        11.05        10.29         9.37        10.42 
TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T 
        8.75        13.02        13.02         1.02        17.98        41.06 
TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B 
       29.03        31.00        17.03        53.98         9.01        33.01 
TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
       19.99        18.97        18.97        14.01        12.00        17.03 
TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07Z 
        9.99        10.98         8.98         7.99         9.96        28.04 
TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B 
       18.05        15.06        36.95        13.02         0.99        23.08 
TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P 
       19.99        19.96        37.05         9.99        31.00        31.00 
TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 
        0.99        19.07        93.04        33.99        40.01        19.07 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A 
       16.01        17.95        41.98        12.00         9.99         9.99 
TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K 
       12.00         1.02        13.02        31.00        33.07        29.98 
TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       15.02         1.02        25.02         8.98        19.04        15.02 
TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 
        0.99        14.01        12.00        19.04        13.02        21.04 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G 
       13.02        17.03        38.04         0.95         2.37        10.85 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF 
        2.66         1.48        38.53        38.20        40.57        55.43 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI 
       36.99        38.79        26.04        50.70         1.02         0.92 
TCGA-AC-A2QJ TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 
        2.27         0.69        14.83         9.40         1.12         1.81 
TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62X TCGA-AC-A6IW 
        1.68         1.55         1.32         1.55         1.12         0.69 
TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A046 TCGA-AN-A04C 
        0.43         1.74         0.33         0.33         0.33         1.78 
TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR 
        1.71         8.02         7.36         6.51         0.16         0.33 
TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK 
        0.33         0.33         6.44         4.64         7.96         7.00 
TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW 
        7.59         7.17         6.28         6.02         0.33         0.36 
TCGA-AN-A0FX TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XP TCGA-AN-A0XR 
        0.33         0.33         0.33         0.33         0.30         0.33 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L 
        0.33         0.33         0.33         5.33         5.59        80.28 
TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T 
       47.84        66.77        81.63        84.69        68.75        47.87 
TCGA-AO-A03U TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       59.05        32.78        21.40        17.65        24.16        37.48 
TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC 
       20.32        22.36        53.03        21.53        50.70        50.86 
TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JM 
       72.00        21.37        26.24        38.53        62.04        71.80 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A 
      102.58        99.25        93.70        94.59        96.10        90.58 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
       77.56        64.04        57.30        48.36        41.62        28.37 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H 
       14.73        82.62        70.39         0.53        17.79        24.79 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N 
       26.93       130.09         5.65        15.62        13.22         2.56 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TX 
        9.99        82.88        49.32        56.88        29.75        64.83 
TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 
       55.86        76.14        65.36        70.16        83.87        76.18 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL 
       55.36        75.55        61.84        52.77        51.25        48.82 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR 
       62.56        43.73        43.56        39.98        43.07        17.23 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H 
       40.83        46.32        35.24        36.26        20.22       109.58 
TCGA-AR-A24K TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q 
       50.89        65.46        68.19        65.69         0.85        66.05 
TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W 
       57.40        62.07        53.26        53.36        54.18        50.96 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A256 
       48.16        51.75        45.17        40.64        39.85        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN 
      128.65        20.25        42.87         7.36        40.04        17.10 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP 
       20.81        16.96        20.38        54.74        16.04        20.45 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA 
       10.59        77.62       143.38       149.59        12.13       220.90 
TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK 
      129.57        50.70       146.50       112.37       176.98        18.77 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG 
      126.12        84.59       110.93       140.88       211.56        68.45 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RT 
      189.01       234.28        81.17       172.96       102.77        89.46 
TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX 
      131.21       157.41        97.48        79.63        17.98        21.47 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      129.57       129.70       186.48        28.27        68.94        58.88 
TCGA-B6-A1KC TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B 
       43.59       139.17       170.17        54.28        49.94        82.88 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ 
       55.00        24.53        38.79        20.45        25.55        28.50 
TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 
       46.95        40.83        39.55        39.16        48.36        56.94 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       56.98        51.68        37.22        32.02        18.21        25.71 
TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR 
       21.70        61.68        35.67        48.69        27.19        53.69 
TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 
       53.95        49.94        11.67        49.05        41.75        44.02 
TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH 
       48.13        42.90        45.83        31.17        23.44        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS 
       22.13        13.91        17.26        15.65         3.22         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 
       38.47        45.17        47.41        16.27         4.41        15.68 
TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB 
       14.30         9.63        44.81        46.19        32.65        24.49 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       31.00        24.43        30.35        10.78        15.16        37.78 
TCGA-BH-A0H5 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       35.51        52.96        26.50        20.38         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY 
       13.61        36.85        12.89        51.32        27.25        50.79 
TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F 
        5.59        23.93        24.95        44.81        23.05         8.81 
TCGA-BH-A18G TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18R 
        2.01        20.12        90.84        37.74        30.28        37.55 
TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES 
       66.05         7.36        51.39        69.93        91.99       113.82 
TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EY TCGA-BH-A1F0 
       82.85        42.28        12.00        55.69        17.69        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC 
       31.53        89.16        97.48        24.66       120.62       114.15 
TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
       33.17        74.73       122.89        36.92        63.35        55.00 
TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 
       45.63       144.59        72.07         6.90         0.72        38.60 
TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
      130.16        10.65         6.44        20.12         0.99       109.28 
TCGA-BH-A42V TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q 
        8.94        11.77        11.77        12.66        11.77         0.07 
TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A134 TCGA-C8-A135 
       12.66        12.66        12.66         3.12         0.69         0.62 
TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI 
        3.85         3.75        12.33        10.92        11.34        11.34 
TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W 
        0.16        10.42         2.30         3.25         0.30         0.23 
TCGA-C8-A26X TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A 
        0.36         9.67         0.03         0.03         0.03        12.20 
TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 
        0.99         0.03         0.23        11.90        20.88        13.25 
TCGA-D8-A141 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 
       20.58        13.48        21.14        19.20        14.17        17.49 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG 
       16.50        18.71        15.78        18.15        18.90        12.03 
TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN 
       14.01        18.97        20.09        20.09        19.40        20.38 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 
       21.01        12.20        13.32        14.70        18.58        17.79 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG 
       25.74        23.90        27.58         2.66        17.16        14.73 
TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR 
       14.50        19.92        17.69         7.96        16.41        15.85 
TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       16.31         6.35        15.16        16.54        15.52         3.81 
TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27K 
       14.14        17.42        16.04        13.45        13.05         9.44 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T 
       16.41        13.48         4.80         0.76        10.09        13.08 
TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A107 
       12.53        14.50        18.51         7.33        43.00        34.42 
TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E 
       27.52        46.59        40.41        37.51        40.11        28.44 
TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S 
       47.15        44.68        40.96        38.24        38.60        33.17 
TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A14Z 
       33.30        43.33        34.26        32.02        28.60        17.03 
TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 
       25.41        23.24        21.04        23.87        14.79        25.05 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G 
       23.34        22.82        17.29        20.71        21.63        18.21 
TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15O 
       12.92        17.42        19.40         9.04        20.58        13.02 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B1 
       19.56        17.06        14.07        14.99        60.53        53.03 
TCGA-E2-A1B4 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF 
       29.95        28.50        16.47        17.10        38.30        37.41 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN 
       32.78        33.73        33.70        22.65         3.88        22.19 
TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 
       20.98        11.08        54.18        27.42        39.62        19.66 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI 
       24.59        40.47        28.90        18.87       106.75       102.61 
TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
        8.75        16.93         5.52        15.72         7.20        18.05 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 
       22.26        19.89        19.20        36.82        13.48        12.00 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF 
       13.12        36.56        39.55        12.59        35.77        20.05 
TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 
       21.57         9.86        11.90        14.30         0.62         2.10 
TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB 
        6.12         1.38         2.76        21.21        32.09        20.81 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI 
        0.66        34.65         6.58        21.27        34.59        35.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22E 
       34.13         0.79        12.53        13.32        39.09        12.89 
TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A248 
       23.51        24.10        17.06         0.69         0.85         1.94 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 
        0.95        12.56         0.72         0.76        26.07        18.41 
TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A6HE 
        0.62        15.72         0.23         0.39         0.23        15.39 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 
       12.20        39.72         8.48        18.21        18.90        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY 
       16.57        15.68        28.77        25.94        29.95        29.85 
TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 
       40.41        41.13        39.78        18.48        30.08         7.86 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
       18.90        19.99         6.15        13.94        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW 
       34.55        19.96        55.00        52.73        25.91        22.09 
TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GM-A2D9 
       21.27        17.49        10.16        10.59         7.40        59.57 
TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       53.52        42.71        42.28        61.91        62.33        90.84 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
       76.64        77.33        53.36       110.50        38.20        32.28 
TCGA-GM-A3XL TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX 
       69.30        57.63        13.55        18.12        11.84        11.57 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
        8.28         6.67         4.60         0.66         2.99         3.58 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FR TCGA-LL-A73Z 
        6.90         5.56         3.65         3.19         3.88         4.50 
TCGA-LL-A740 TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OL-A5D6 
        4.50         3.22         6.21        15.91         2.79        12.66 
TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW 
       46.55         7.53        44.61        27.65        24.10        26.20 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J 
       16.87        14.10         9.80        14.76        23.70        54.51 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-S3-A6ZG 
       33.90        31.07        18.21         7.23         4.44         6.81 
TCGA-W8-A86G 
        5.29 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.07               0.03 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            194.27             234.28 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             23.77              21.14 
[1] "0.1 - 194.3 (23.8)" "0.0 - 234.3 (21.1)"
[1] "hr=" "1.5"
D29V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16Q GAIN MUTATED        10        6        1        1        38        33
  16Q GAIN WILD-TYPE      70       71        8        8       297       191
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16Q GAIN MUTATED           0         23          6          5        4
  16Q GAIN WILD-TYPE         2        115         21         54       13
                    vv
clus                 STAGE TIS STAGE X
  16Q GAIN MUTATED           1       1
  16Q GAIN WILD-TYPE         0      15
D29V3, multiclass
            clus
vv           16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                  10                 70
  STAGE IA                  6                 71
  STAGE IB                  1                  8
  STAGE II                  1                  8
  STAGE IIA                38                297
  STAGE IIB                33                191
  STAGE III                 0                  2
  STAGE IIIA               23                115
  STAGE IIIB                6                 21
  STAGE IIIC                5                 54
  STAGE IV                  4                 13
  STAGE TIS                 1                  0
  STAGE X                   1                 15
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  16Q GAIN MUTATED    26  78  16   7
  16Q GAIN WILD-TYPE 232 503 101  29
D29V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1               26                232
  T2               78                503
  T3               16                101
  T4                7                 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                  N0  N1  N2  N3
  16Q GAIN MUTATED    57  43  20   5
  16Q GAIN WILD-TYPE 411 287  91  65
D29V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               57                411
  N1               43                287
  N2               20                 91
  N3                5                 65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  16Q GAIN MUTATED          1 106   4  18
  16Q GAIN WILD-TYPE        1 739  13 113
D29V6, multiclass
          clus
vv         16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CM0 (I+)                1                  1
  M0                    106                739
  M1                      4                 13
  MX                     18                113
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED   125   4
  16Q GAIN WILD-TYPE 859   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED    125    4
  16Q GAIN WILD-TYPE  859    7
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE              125                859
  MALE                  4                  7
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  16Q GAIN MUTATED                            1                           103
  16Q GAIN WILD-TYPE                          0                           632
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  16Q GAIN MUTATED                               14                   1
  16Q GAIN WILD-TYPE                            152                   4
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  16Q GAIN MUTATED                                  3                  1
  16Q GAIN WILD-TYPE                               26                 13
                    vv
clus                 OTHER  SPECIFY
  16Q GAIN MUTATED                6
  16Q GAIN WILD-TYPE             38
D29V8, multiclass
                                  clus
vv                                 16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      1                  0
  INFILTRATING DUCTAL CARCINOMA                 103                632
  INFILTRATING LOBULAR CARCINOMA                 14                152
  MEDULLARY CARCINOMA                             1                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                3                 26
  MUCINOUS CARCINOMA                              1                 13
  OTHER  SPECIFY                                  6                 38
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V9, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    36  93
  16Q GAIN WILD-TYPE 246 620
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     36   93
  16Q GAIN WILD-TYPE  246  620
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                36                246
  YES               93                620
[1] 2 2
[1] FALSE
D29V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q GAIN MUTATED                                  0     7
  16Q GAIN WILD-TYPE                                1    49
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED                          23    90
  16Q GAIN WILD-TYPE                       114   618
D29V11, multiclass
                                  clus
vv                                 16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           7                 49
  BLACK OR AFRICAN AMERICAN                      23                114
  WHITE                                          90                618
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V12, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     2 112
  16Q GAIN WILD-TYPE  34 684
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      2  112
  16Q GAIN WILD-TYPE   34  684
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 34
  NOT HISPANIC OR LATINO              112                684
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    87  14
  17P GAIN WILD-TYPE 773 100
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               101                873 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                14                100 
$`17P GAIN MUTATED`
TCGA-A1-A0SJ TCGA-A2-A0CX TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0YJ 
       13.68        56.81        35.05        34.29        31.82        18.61 
TCGA-A2-A0YT TCGA-A2-A1FX TCGA-A2-A259 TCGA-A2-A3XU TCGA-A2-A3XX TCGA-A2-A3XZ 
       23.77        36.79        52.47        29.98        38.40        31.99 
TCGA-A7-A0CD TCGA-A7-A26J TCGA-A7-A3J0 TCGA-A8-A07P TCGA-A8-A08G TCGA-A8-A08J 
       38.30        20.61        10.29        10.98        19.96        37.05 
TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A097 TCGA-A8-A09B TCGA-A8-A09E TCGA-AC-A23G 
       31.00        19.07        12.00        12.00        31.00        10.85 
TCGA-AC-A23H TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A8OP TCGA-AN-A04A TCGA-AO-A03L 
        2.66        26.04         1.02         1.74         2.96        80.28 
TCGA-AO-A0J5 TCGA-AO-A0J7 TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A12B TCGA-AO-A12E 
       24.16        20.32        55.33       102.58        77.56        57.30 
TCGA-AO-A1KQ TCGA-AR-A0TQ TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A24K TCGA-AR-A24Q 
       61.87        49.32        42.58        35.24        50.89        66.05 
TCGA-AR-A24R TCGA-AR-A252 TCGA-AR-A2LK TCGA-AR-A2LL TCGA-B6-A0WX TCGA-B6-A1KC 
       57.40        40.64        42.87         7.36        21.47        43.59 
TCGA-B6-A1KI TCGA-B6-A401 TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0B4 TCGA-BH-A0BG 
       73.51        85.35        24.53        20.45        39.16        24.85 
TCGA-BH-A0BT TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0HQ TCGA-BH-A0HW 
       45.57        41.75        48.13        42.90        36.85        51.32 
TCGA-BH-A18N TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1FC TCGA-BH-A204 TCGA-C8-A12W 
       37.74        49.58        25.81       114.15        83.31        12.66 
TCGA-C8-A130 TCGA-C8-A132 TCGA-C8-A1HI TCGA-C8-A1HN TCGA-D8-A143 TCGA-D8-A1JB 
        3.12         1.45        11.34         3.25        14.17        18.71 
TCGA-D8-A1JF TCGA-D8-A1JJ TCGA-D8-A1XB TCGA-D8-A1XS TCGA-D8-A27W TCGA-E2-A107 
       12.03        20.09        18.15        16.31        12.26        34.42 
TCGA-E2-A109 TCGA-E2-A14O TCGA-E2-A14T TCGA-E2-A14W TCGA-E2-A1B1 TCGA-E2-A1B5 
       46.59        44.68        33.30        32.02        53.03        32.35 
TCGA-E2-A1LK TCGA-E2-A574 TCGA-E9-A1QZ TCGA-E9-A1R6 TCGA-E9-A1RH TCGA-E9-A22E 
        8.75        19.89        11.90         2.76        34.59        12.89 
TCGA-E9-A54Y TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1PC TCGA-EW-A2FS TCGA-GM-A2DK 
        0.23        29.95        29.85         6.15        52.73        62.33 
TCGA-LL-A5YP TCGA-LL-A7SZ TCGA-MS-A51U TCGA-OL-A66K TCGA-S3-A6ZG 
        3.25         5.59         2.79        33.90         6.81 

$`17P GAIN WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP 
       20.88        31.79         7.96        39.32        28.01        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T 
       18.21       104.81        18.02        41.95        82.16        73.84 
TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK 
       22.06        63.12        64.04        55.43        36.13       125.59 
TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
       64.57        24.79       112.08        92.48        88.60       107.93 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 
       75.55        75.25         5.19        63.45        64.04        21.14 
TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN 
       34.55        33.76        28.77        25.22       101.72        89.36 
TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EW 
       80.28       107.61        79.76        74.40        37.05        29.75 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW 
       24.72        24.16        99.19        54.64        27.12        44.88 
TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 
       50.43        44.28        17.52        17.13         8.38        18.71 
TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD 
       20.52        17.46        18.90        20.75        32.55        25.28 
TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK 
       18.21        15.42        21.90        21.67        14.50        19.33 
TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FZ TCGA-A2-A1G0 
       14.63        31.73        23.47        17.36        22.45        20.25 
TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C 
       19.20        19.56        16.47       107.70        16.31        17.19 
TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS 
       18.15        91.92        10.59        20.88        39.65        33.93 
TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RW 
       83.01        14.07        49.48        34.98        38.37         7.30 
TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 
        9.01         8.81         8.91        12.00         6.74         3.42 
TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA 
       35.31        34.29        35.47        30.61        37.45        35.67 
TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H 
       33.11        31.73        10.72        12.72        23.61        29.56 
TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A2KD 
       31.36        24.26        23.74        23.80        21.73        22.32 
TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 
       11.34        10.59        11.28        13.41        14.70        11.97 
TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D 
       14.93        13.74        14.50        21.17        17.92        14.73 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX 
       12.10        10.72        11.05        10.29         9.37        10.42 
TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T 
        8.75        13.02        13.02         1.02        17.98        41.06 
TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 
       29.03        31.00        26.01         1.02        17.03        53.98 
TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I 
        9.01        33.01        19.99        18.97        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U 
       12.00        17.03         9.99         8.98         7.99         9.96 
TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 
        9.99        28.04        18.05        15.06        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08L 
        0.99        23.08        19.99        18.05        12.00         9.99 
TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 
       31.00         0.99        93.04        33.99        40.01        19.07 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09C 
       16.01        17.95        41.98         9.99         9.99         1.02 
TCGA-A8-A09D TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q 
       13.02        33.07        29.98        15.02         1.02        25.02 
TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 
        8.98        19.04        15.02         0.99        14.01        12.00 
TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB 
       19.04        13.02        21.04         0.99        13.02        17.03 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM 
       38.04         0.95         2.37         1.48        38.53        38.20 
TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QI 
       40.57        55.43        36.99        38.79        50.70         0.92 
TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN 
        2.27         0.99         0.69        14.83         9.40         1.12 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V 
        1.81         1.68         1.55         1.32         1.55         0.07 
TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AN-A03X 
        1.12         1.81         1.18         0.69         0.43         0.33 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D 
        0.33         0.23         0.33         0.62         1.78         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS 
        8.02         7.36         6.51         0.16         0.33         0.33 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL 
        0.33         6.44         4.64         7.96         7.00         7.59 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX 
        7.17         6.28         6.02         0.33         0.36         0.33 
TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP 
        0.33         0.33         0.33         0.33        12.33         0.30 
TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW 
        0.33         0.33         0.33         0.33         5.33         5.59 
TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T 
       47.84        66.77        81.63        84.69        68.75        47.87 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J6 
       59.05        29.13        32.78        21.40        17.65        37.48 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD 
       22.36        53.03        21.53        50.70        50.86        72.00 
TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JM 
       76.77        21.37        26.24        38.53        62.04        71.80 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12D 
       99.25        93.70        94.59        96.10        90.58        64.04 
TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR 
       48.36        41.62        28.37        14.73        82.62        70.39 
TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 
        0.53        17.79        24.79        26.93       130.09         5.65 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP 
       15.62        13.22         2.56        21.86         9.99        82.88 
TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX 
        5.26        37.41        56.88        29.75        24.30        64.83 
TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 
       55.86        76.14        65.36        70.16        83.87        76.18 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL 
       55.36        75.55        61.84        52.77        51.25        48.82 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR 
       62.56        43.73        43.56        39.98        43.07        17.23 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L 
       40.83        46.32        36.26        20.22       109.58        73.02 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24S TCGA-AR-A24T 
       65.46        68.19        65.69         0.85        62.07        53.26 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 
       53.36        54.18        50.96        48.16        51.75        56.15 
TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH 
       45.17        39.85        34.82        93.83       128.65        20.25 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM 
       40.04        17.10        20.81        16.96        20.38        54.74 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 
       16.04        20.45        10.59        77.62       143.38       149.59 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG 
       12.13       220.90       129.57        50.70        65.72       146.50 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO 
      112.37       176.98        18.77       126.12        84.59       110.14 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
      110.93       140.88       211.56        68.45       189.01       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ 
       81.17        78.02       172.96       162.05       102.77       140.48 
TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT 
      100.70        89.46       131.21       157.41        97.48       188.68 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 
       79.63        17.98       113.79       129.57       129.70       186.48 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU 
       28.27        68.94        58.88       101.52       139.17       170.17 
TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AY 
       54.28        49.94        82.88        55.00        38.79        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0B6 
       28.50        46.95        40.83        39.55        48.36        56.94 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       56.98        51.68        37.22        32.02        18.21        25.71 
TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ 
       21.70        44.05        61.68        35.67        48.69        27.19 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 
       53.69        53.95        49.94        11.67        49.05        44.02 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       45.83        31.17        23.44        38.01        22.13        13.91 
TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT 
       48.23        17.26        15.65         3.22         2.56        38.47 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 
       45.17        47.41        16.27         4.41        15.68        14.30 
TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE 
        9.63        44.81        46.19        32.65        24.49        31.00 
TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       24.43        30.35        10.78        15.16        37.78        35.51 
TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI 
       24.56        23.08        41.00        52.96        26.50        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0HY 
        5.85         2.50        13.61        12.89        27.25        50.79 
TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA 
        5.59        23.93        24.95        42.35        44.81        23.05 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L 
        8.81         2.01         7.23        20.12        90.84        26.66 
TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T 
       72.56        30.28        55.63        37.55        66.05         7.36 
TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET 
       51.39        51.16        69.93        91.99       113.82        82.85 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EY TCGA-BH-A1F2 TCGA-BH-A1F5 
       42.28        12.00        55.69        17.69        31.53        89.16 
TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG 
       97.48        24.66       120.62        33.17        74.73       122.89 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR 
       36.92        63.35        55.00        45.63        72.07       144.59 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A209 
       72.07         6.90         0.72        38.60        57.83       130.16 
TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V 
       10.65         6.44        20.12         0.99       109.28         8.94 
TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q 
       11.93        11.77        11.77        12.66        11.77         0.07 
TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A135 
       12.66        12.66        12.66         1.78         0.69         0.62 
TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ 
        3.85         3.75        12.33        10.92        11.34         0.16 
TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X 
       12.03        10.42         2.30         0.30         0.23         0.36 
TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 
        0.43         8.28         9.67         0.03         0.03         0.03 
TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A13Z 
       12.20         0.99         0.03         0.23        11.90        20.88 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 
       13.25        20.58        13.97        13.48        21.14        19.20 
TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE 
       14.17        17.49        16.50        15.78        18.15        18.90 
TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM 
       12.03        14.01        18.97        20.12        20.09        19.40 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 
       20.38        21.01        12.20        13.32        14.70        18.58 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XC 
       17.79        16.73        25.74        23.90        27.58         2.66 
TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL 
       17.16        15.22        14.73        21.83        14.50        19.92 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XT TCGA-D8-A1XU 
       17.69         7.96        16.41        15.85         6.35        12.99 
TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       15.16        12.66        16.54        15.32        15.52         3.81 
TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H 
       14.24        14.14        17.42        16.04        13.45        13.05 
TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P 
       14.43         9.44        16.41        13.48         4.80         0.76 
TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 
       10.09        13.08        12.53        14.50        18.51         7.33 
TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E 
       43.00        27.52        40.41        37.51        40.11        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S 
       28.87        47.15        40.96        38.24        38.60        33.17 
TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 
       43.33        34.26        31.96        28.60        17.03        25.41 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 
       27.12        23.24        19.43        21.04        23.87        14.79 
TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F 
       25.05        23.34        22.82        17.29        20.71        21.63 
TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       18.21        12.92        17.42        19.40         9.04        20.58 
TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
        7.73        13.02        19.56        17.06        14.07        14.99 
TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B4 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD 
       60.53        53.62        29.95        28.50        16.47        17.10 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ 
       38.30        37.41        32.78        33.73        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       22.65         3.88        22.19        20.98        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       27.42        39.62        19.66        24.59        40.47        28.90 
TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 
       18.87       106.75       102.61        43.04        16.93         5.52 
TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E9-A1N4 TCGA-E9-A1N5 
       15.72         7.20        18.05        22.26        19.20        36.82 
TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND 
       13.48        12.00        13.12        36.56        39.55        12.59 
TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1R0 TCGA-E9-A1R2 
       35.77        20.05        21.57         9.86        14.30         0.62 
TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB 
        2.10         6.12         1.38        21.21        32.09        20.81 
TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI 
       40.24         0.66        34.65         6.58        21.27        35.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       34.13         0.79        12.53        13.32        39.09        22.75 
TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A247 
       23.51        24.10        17.06         0.69         0.85        27.22 
TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT 
        1.94         0.95        12.56         0.72        17.75         0.76 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A5FK TCGA-E9-A5FL 
       26.07        18.41         0.62        15.72         0.39         0.26 
TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
        0.23        15.39        12.20        39.72         8.48        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV 
       18.90        13.25        16.57        15.68        28.77        25.94 
TCGA-EW-A1OW TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 
       22.82        40.41        41.13        39.78        52.96        29.82 
TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB 
       23.11        18.48        30.08         7.86        18.90        19.99 
TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR 
       13.94        10.52        14.43        34.55        19.96        55.00 
TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 
       25.91        22.09        21.27        17.49        10.16        10.59 
TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC 
        7.40       109.87        59.57       194.27        53.13        53.52 
TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DL TCGA-GM-A2DM 
       43.04        42.71        42.28        61.91        90.84        76.64 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL 
       77.33        53.36       110.50        38.20        32.28        69.30 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX 
       53.95        57.63        13.55        18.12        11.84        11.57 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
        8.28         6.67         4.60         0.66         2.99         3.58 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FQ 
        6.90         5.56         4.70         3.65         3.19         2.63 
TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7T0 TCGA-LL-A8F5 
        3.88         4.14         4.50         4.50         3.22         6.21 
TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA 
       15.91         2.10        12.66        46.55         7.53        44.61 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       27.65        24.10        26.20        16.87        14.10        10.29 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66N 
        9.80        14.76        23.70        54.51        31.07        18.21 
TCGA-OL-A66O TCGA-OL-A66P TCGA-W8-A86G 
        7.23         4.44         5.29 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.23               0.03 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            114.15             234.28 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             31.00              21.01 
[1] "0.2 - 114.2 (31.0)" "0.0 - 234.3 (21.0)"
[1] "hr=" "1.5"
D30V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17P GAIN MUTATED         6        6        0        1        36        22
  17P GAIN WILD-TYPE      74       71        9        8       299       202
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17P GAIN MUTATED           1         19          6          2        2
  17P GAIN WILD-TYPE         1        119         21         57       15
                    vv
clus                 STAGE TIS STAGE X
  17P GAIN MUTATED           0       0
  17P GAIN WILD-TYPE         1      16
D30V3, multiclass
            clus
vv           17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                   6                 74
  STAGE IA                  6                 71
  STAGE IB                  0                  9
  STAGE II                  1                  8
  STAGE IIA                36                299
  STAGE IIB                22                202
  STAGE III                 1                  1
  STAGE IIIA               19                119
  STAGE IIIB                6                 21
  STAGE IIIC                2                 57
  STAGE IV                  2                 15
  STAGE TIS                 0                  1
  STAGE X                   0                 16
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  17P GAIN MUTATED    22  55  15   9
  17P GAIN WILD-TYPE 236 526 102  27
D30V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1               22                236
  T2               55                526
  T3               15                102
  T4                9                 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                  N0  N1  N2  N3
  17P GAIN MUTATED    43  37  17   3
  17P GAIN WILD-TYPE 425 293  94  67
D30V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0               43                425
  N1               37                293
  N2               17                 94
  N3                3                 67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  17P GAIN MUTATED          0  90   2   9
  17P GAIN WILD-TYPE        2 755  15 122
D30V6, multiclass
          clus
vv         17P GAIN MUTATED 17P GAIN WILD-TYPE
  CM0 (I+)                0                  2
  M0                     90                755
  M1                      2                 15
  MX                      9                122
[1] 4 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    96   5
  17P GAIN WILD-TYPE 888   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     96    5
  17P GAIN WILD-TYPE  888    6
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               96                888
  MALE                  5                  6
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  17P GAIN MUTATED                            0                            80
  17P GAIN WILD-TYPE                          1                           655
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  17P GAIN MUTATED                               10                   1
  17P GAIN WILD-TYPE                            156                   4
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  17P GAIN MUTATED                                  1                  3
  17P GAIN WILD-TYPE                               28                 11
                    vv
clus                 OTHER  SPECIFY
  17P GAIN MUTATED                6
  17P GAIN WILD-TYPE             38
D30V8, multiclass
                                  clus
vv                                 17P GAIN MUTATED 17P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                  80                655
  INFILTRATING LOBULAR CARCINOMA                 10                156
  MEDULLARY CARCINOMA                             1                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                1                 28
  MUCINOUS CARCINOMA                              3                 11
  OTHER  SPECIFY                                  6                 38
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V9, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    37  64
  17P GAIN WILD-TYPE 245 649
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     37   64
  17P GAIN WILD-TYPE  245  649
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                37                245
  YES               64                649
[1] 2 2
[1] FALSE
D30V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P GAIN MUTATED                                  0     7
  17P GAIN WILD-TYPE                                1    49
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED                          16    70
  17P GAIN WILD-TYPE                       121   638
D30V11, multiclass
                                  clus
vv                                 17P GAIN MUTATED 17P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           7                 49
  BLACK OR AFRICAN AMERICAN                      16                121
  WHITE                                          70                638
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V12, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     4  80
  17P GAIN WILD-TYPE  32 716
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      4   80
  17P GAIN WILD-TYPE   32  716
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 32
  NOT HISPANIC OR LATINO               80                716
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED   176  28
  17Q GAIN WILD-TYPE 684  86
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               204                770 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                28                 86 
$`17Q GAIN MUTATED`
TCGA-A1-A0SH TCGA-A1-A0SJ TCGA-A2-A04R TCGA-A2-A0CU TCGA-A2-A0CX TCGA-A2-A0D2 
       47.24        13.68        82.16         5.19        56.81        33.76 
TCGA-A2-A0D4 TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0T3 TCGA-A2-A0T7 
       25.22        35.05        34.29        31.82        18.71        20.75 
TCGA-A2-A0YT TCGA-A2-A1FX TCGA-A2-A1G0 TCGA-A2-A259 TCGA-A2-A25D TCGA-A2-A25E 
       23.77        36.79        20.25        52.47        18.15        91.92 
TCGA-A2-A3XU TCGA-A2-A3XX TCGA-A2-A3XZ TCGA-A7-A0CD TCGA-A7-A0DA TCGA-A7-A13F 
       29.98        38.40        31.99        38.30        35.67        12.72 
TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3J0 TCGA-A7-A4SA TCGA-A7-A4SF 
       23.80        20.61        22.32        10.29        14.93        17.92 
TCGA-A8-A06O TCGA-A8-A06U TCGA-A8-A06Z TCGA-A8-A07G TCGA-A8-A07P TCGA-A8-A07W 
       13.02        29.03         1.02        18.97        10.98         9.99 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A092 
       18.05        19.96        37.05        31.00        19.07        16.01 
TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09E TCGA-A8-A09M TCGA-A8-A09R 
       12.00         9.99        12.00        31.00        15.02         8.98 
TCGA-A8-A09X TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A8OP 
       14.01        10.85         2.66        26.04         1.02         1.74 
TCGA-AN-A041 TCGA-AN-A04A TCGA-AN-A0FD TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AO-A03L 
        0.23         2.96         6.44         0.33         0.33        80.28 
TCGA-AO-A03P TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J7 TCGA-AO-A124 TCGA-AO-A12B 
       84.69        17.65        24.16        20.32       102.58        77.56 
TCGA-AO-A12E TCGA-AO-A1KQ TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AR-A0TQ TCGA-AR-A0U2 
       57.30        61.87        13.22        21.86        49.32        83.87 
TCGA-AR-A1AK TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L 
       51.25        42.58        35.24       109.58        50.89        73.02 
TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24V TCGA-AR-A24Z TCGA-AR-A252 TCGA-AR-A255 
        0.85        57.40        54.18        51.75        40.64        34.82 
TCGA-AR-A2LK TCGA-AR-A2LL TCGA-B6-A0WV TCGA-B6-A0X1 TCGA-B6-A1KC TCGA-B6-A1KI 
       42.87         7.36        79.63       186.48        43.59        73.51 
TCGA-B6-A401 TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B4 TCGA-BH-A0BT 
       85.35        24.53        20.45        28.50        39.16        45.57 
TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DP 
       49.05        41.75        48.13        42.90        31.17        15.65 
TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18S 
       36.85        12.89        51.32        26.66        37.74        66.05 
TCGA-BH-A18U TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1FC TCGA-BH-A1FG 
       51.39        55.69        49.58        25.81       114.15       122.89 
TCGA-BH-A1FJ TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A209 TCGA-C8-A12O 
       63.35         0.72        38.60        83.31       130.16        12.66 
TCGA-C8-A12W TCGA-C8-A130 TCGA-C8-A132 TCGA-C8-A138 TCGA-C8-A1HG TCGA-C8-A1HI 
       12.66         3.12         1.45         3.75        11.34        11.34 
TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A27A TCGA-C8-A3M8 TCGA-D8-A142 TCGA-D8-A143 
        2.30         3.25        12.20         0.23        13.97        14.17 
TCGA-D8-A1JB TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JJ TCGA-D8-A1JT TCGA-D8-A1X7 
       18.71        12.03        12.03        20.09        13.32        16.73 
TCGA-D8-A1XB TCGA-D8-A1XF TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XS TCGA-D8-A1XY 
       18.15        15.22        19.92        17.69        16.31        16.54 
TCGA-D8-A1Y2 TCGA-D8-A27R TCGA-D8-A27W TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A109 
       14.24        10.09        12.26        43.00        34.42        46.59 
TCGA-E2-A10C TCGA-E2-A14O TCGA-E2-A14T TCGA-E2-A14W TCGA-E2-A15A TCGA-E2-A15T 
       40.11        44.68        33.30        32.02        23.34        14.99 
TCGA-E2-A1B1 TCGA-E2-A1B5 TCGA-E2-A1IE TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ 
       53.03        32.35        38.30        32.78        33.73        28.44 
TCGA-E2-A1LA TCGA-E2-A1LK TCGA-E2-A56Z TCGA-E2-A574 TCGA-E9-A1N8 TCGA-E9-A1NF 
       24.59         8.75         7.20        19.89        12.00        20.05 
TCGA-E9-A1QZ TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 
       11.90         0.62         6.12         1.38         2.76        21.21 
TCGA-E9-A1RE TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A22B TCGA-E9-A22E 
       34.65        34.59        35.64        34.13        22.75        12.89 
TCGA-E9-A247 TCGA-E9-A2JS TCGA-E9-A54Y TCGA-E9-A5UO TCGA-EW-A1J2 TCGA-EW-A1J5 
       27.22        17.75         0.23         0.23        13.25        15.68 
TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1PC TCGA-EW-A1PD 
       29.95        29.85        52.96        23.11         6.15        13.94 
TCGA-EW-A2FS TCGA-EW-A423 TCGA-GM-A2DC TCGA-GM-A2DK TCGA-GM-A3XL TCGA-LL-A5YM 
       52.73        10.16        53.52        62.33        69.30         4.70 
TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-MS-A51U TCGA-OL-A5RZ TCGA-OL-A66K TCGA-S3-A6ZG 
        5.59         3.22         2.79        10.29        33.90         6.81 

$`17Q GAIN WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SI 
        8.52        14.37        43.43        48.10        14.27        20.88 
TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ 
       31.79         7.96        39.32        28.01        19.20        18.21 
TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V 
      104.81        18.02        41.95        73.84        22.06        63.12 
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM 
       64.04        55.43        36.13       125.59        64.57        24.79 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT 
      112.08        92.48        88.60       107.93        75.55        75.25 
TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0EM 
       63.45        64.04        21.14        34.55        28.77       101.72 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES 
       89.36        80.28       107.61        79.76        74.40        37.05 
TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV 
       29.75        24.72        24.16        99.19        54.64        27.12 
TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 
       44.88        50.43        44.28        17.52        17.13         8.38 
TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE 
       20.52        17.46        18.90        32.55        25.28        18.21 
TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK 
       15.42        21.90        21.67        14.50        18.61        19.33 
TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FZ TCGA-A2-A1G1 
       14.63        31.73        23.47        17.36        22.45        19.20 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25F 
       19.56        16.47       107.70        16.31        17.19        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XW 
       20.88        39.65        33.93        83.01        14.07        49.48 
TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       34.98        38.37         7.30         9.01         8.81         8.91 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH 
       12.00         6.74         3.42        35.31        34.29        35.47 
TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13G 
       30.61        37.45        33.11        31.73        10.72        23.61 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26I TCGA-A7-A3IY 
       29.56        31.36        24.26        23.74        21.73        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SB 
       10.59        11.28        13.41        14.70        11.97        13.74 
TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX 
       14.50        21.17        14.73        12.10        10.72        11.05 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q 
       10.29         9.37        10.42         8.75        13.02         1.02 
TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A076 
       17.98        41.06        31.00        26.01        17.03        53.98 
TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07J 
        9.01        33.01        19.99        18.97        14.01        12.00 
TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07Z 
       17.03         9.99         8.98         7.99         9.96        28.04 
TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B 
       18.05        15.06        36.95        13.02         0.99        23.08 
TCGA-A8-A08C TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08T 
       19.99        12.00         9.99        31.00         0.99        93.04 
TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 
       33.99        40.01        19.07        17.95        41.98         9.99 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09N TCGA-A8-A09Q 
        1.02        13.02        33.07        29.98         1.02        25.02 
TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 
       19.04        15.02         0.99        12.00        19.04        13.02 
TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C 
       21.04         0.99        13.02        17.03        38.04         0.95 
TCGA-AC-A23E TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF 
        2.37         1.48        38.53        38.20        40.57        55.43 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB 
       36.99        38.79        50.70         0.92         2.27         0.99 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 
        0.69        14.83         9.40         1.12         1.81         1.68 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y 
        1.55         1.32         1.55         0.07         1.12         1.81 
TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A046 
        1.18         0.69         0.43         0.33         0.33         0.33 
TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL 
        0.62         1.78         1.71         8.02         7.36         6.51 
TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FF TCGA-AN-A0FJ 
        0.16         0.33         0.33         0.33         4.64         7.96 
TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV 
        7.00         7.59         7.17         6.28         6.02         0.33 
TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP 
        0.36         0.33         0.33         0.33        12.33         0.30 
TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW 
        0.33         0.33         0.33         0.33         5.33         5.59 
TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U 
       47.84        66.77        81.63        68.75        47.87        59.05 
TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 
       29.13        32.78        21.40        37.48        22.36        53.03 
TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF 
       21.53        50.70        50.86        72.00        76.77        21.37 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A125 
       26.24        38.53        62.04        55.33        71.80        99.25 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12D TCGA-AO-A12F 
       93.70        94.59        96.10        90.58        64.04        48.36 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AO-A1KS 
       41.62        28.37        14.73        82.62        70.39         0.53 
TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 
       17.79        24.79        26.93       130.09         5.65        15.62 
TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT 
        2.56         9.99        82.88         5.26        37.41        56.88 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 
       29.75        24.30        64.83        55.86        76.14        65.36 
TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ 
       70.16        76.18        55.36        75.55        61.84        52.77 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ 
       48.82        62.56        43.73        43.56        39.98        43.07 
TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24M 
       17.23        40.83        46.32        36.26        20.22        65.46 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U 
       68.19        65.69        66.05        62.07        53.26        53.36 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A256 
       50.96        48.16        56.15        45.17        39.85        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
      128.65        20.25        40.04        17.10        20.81        16.96 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       20.38        54.74        16.04        20.45        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC 
      143.38       149.59        12.13       220.90       129.57        50.70 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM 
       65.72       146.50       112.37       176.98        18.77       126.12 
TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG 
       84.59       110.14       110.93       140.88       211.56        68.45 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
      189.01       234.28        81.17        78.02       172.96       162.05 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV 
      102.77       140.48       100.70        89.46       131.21       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ 
       97.48       188.68        17.98        21.47       113.79       129.57 
TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KN 
      129.70        28.27        68.94        58.88       101.52       139.17 
TCGA-B6-A2IU TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV 
      170.17        54.28        49.94        82.88        55.00        38.79 
TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0B6 
       25.55        46.95        40.83        39.55        48.36        56.94 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       56.98        51.68        37.22        32.02        18.21        25.71 
TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP 
       24.85        21.70        44.05        61.68        35.67        48.69 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0C1 
       27.19        53.69        53.95        49.94        11.67        44.02 
TCGA-BH-A0DD TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL 
       45.83        23.44        38.01        22.13        13.91        48.23 
TCGA-BH-A0DO TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       17.26         3.22         2.56        38.47        45.17        47.41 
TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 
       16.27         4.41        15.68        14.30         9.63        44.81 
TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY 
       46.19        32.65        24.49        31.00        24.43        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 
       10.78        15.16        37.78        35.51        24.56        23.08 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       41.00        52.96        26.50        20.38         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 
       13.61        27.25        50.79         5.59        23.93        24.95 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I 
       42.35        44.81        23.05         8.81         2.01         7.23 
TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R 
       20.12        90.84        72.56        30.28        55.63        37.55 
TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET 
        7.36        51.16        69.93        91.99       113.82        82.85 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EY TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 
       42.28        12.00        17.69        31.53        89.16        97.48 
TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FH TCGA-BH-A1FL 
       24.66       120.62        33.17        74.73        36.92        55.00 
TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A208 
       45.63        72.07       144.59        72.07         6.90        57.83 
TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V 
       10.65         6.44        20.12         0.99       109.28         8.94 
TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U 
       11.93        11.77        11.77        11.77         0.07        12.66 
TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 
       12.66        12.66         1.78         0.69         0.62         3.85 
TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A26V 
       12.33        10.92         0.16        12.03        10.42         0.30 
TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 
        0.23         0.36         0.43         8.28         9.67         0.03 
TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-D8-A13Y TCGA-D8-A13Z 
        0.03         0.03         0.99         0.03        11.90        20.88 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 
       13.25        20.58        13.48        21.14        19.20        14.17 
TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JH 
       17.49        16.50        15.78        18.15        18.90        14.01 
TCGA-D8-A1JI TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP 
       18.97        20.12        20.09        19.40        20.38        21.01 
TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X8 TCGA-D8-A1X9 
       12.20        14.70        18.58        17.79        25.74        23.90 
TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK 
       27.58         2.66        17.16        14.73        21.83        14.50 
TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV 
        7.96        16.41        15.85         6.35        12.99        15.16 
TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27E 
       12.66        15.32        15.52         3.81        14.14        17.42 
TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       16.04        13.45        13.05        14.43         9.44        16.41 
TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 
       13.48         4.80         0.76        13.08        12.53        14.50 
TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E 
       18.51         7.33        27.52        40.41        37.51        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S 
       28.87        47.15        40.96        38.24        38.60        33.17 
TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 
       43.33        34.26        31.96        28.60        17.03        25.41 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 
       27.12        23.24        19.43        21.04        23.87        14.79 
TCGA-E2-A159 TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G 
       25.05        22.82        17.29        20.71        21.63        18.21 
TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M 
       12.92        17.42        19.40         9.04        20.58         7.73 
TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A1AZ TCGA-E2-A1B0 
       13.02        19.56        17.06        14.07        60.53        53.62 
TCGA-E2-A1B4 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IF TCGA-E2-A1II 
       29.95        28.50        16.47        17.10        37.41        33.70 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       22.65         3.88        22.19        20.98        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG 
       27.42        39.62        19.66        40.47        28.90        18.87 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX 
      106.75       102.61        43.04        16.93         5.52        15.72 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 
       18.05        22.26        19.20        36.82        13.48        13.12 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NI 
       36.56        39.55        12.59        35.77        21.57         9.86 
TCGA-E9-A1R0 TCGA-E9-A1R3 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD 
       14.30         2.10        32.09        20.81        40.24         0.66 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
        6.58        21.27         0.79        12.53        13.32        39.09 
TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A248 
       23.51        24.10        17.06         0.69         0.85         1.94 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 
        0.95        12.56         0.72         0.76        26.07        18.41 
TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A6HE TCGA-EW-A1IW 
        0.62        15.72         0.39         0.26        15.39        12.20 
TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J3 TCGA-EW-A1J6 
       39.72         8.48        18.21        18.90        16.57        28.77 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 
       25.94        22.82        40.41        41.13        39.78        29.82 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PE 
       18.48        30.08         7.86        18.90        19.99        10.52 
TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A2FW 
       14.43        34.55        19.96        55.00        25.91        22.09 
TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 
       21.27        17.49        10.59         7.40       109.87        59.57 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI 
      194.27        53.13        43.04        42.71        42.28        61.91 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY 
       90.84        76.64        77.33        53.36       110.50        38.20 
TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW 
       32.28        53.95        57.63        13.55        18.12        11.84 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 
       11.57         8.28         6.67         4.60         0.66         2.99 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP 
        3.58         6.90         5.56         3.65         3.19         3.25 
TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A8F5 
        2.63         3.88         4.14         4.50         4.50         6.21 
TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA 
       15.91         2.10        12.66        46.55         7.53        44.61 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5S0 
       27.65        24.10        26.20        16.87        14.10         9.80 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O 
       14.76        23.70        54.51        31.07        18.21         7.23 
TCGA-OL-A66P TCGA-W8-A86G 
        4.44         5.29 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.23               0.03 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            186.48             234.28 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             22.93              21.27 
[1] "0.2 - 186.5 (22.9)" "0.0 - 234.3 (21.3)"
[1] "hr=" "1.5"
D31V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17Q GAIN MUTATED        14       16        1        2        76        44
  17Q GAIN WILD-TYPE      66       61        8        7       259       180
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17Q GAIN MUTATED           1         31          8         10        4
  17Q GAIN WILD-TYPE         1        107         19         49       13
                    vv
clus                 STAGE TIS STAGE X
  17Q GAIN MUTATED           0       1
  17Q GAIN WILD-TYPE         1      15
D31V3, multiclass
            clus
vv           17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                  14                 66
  STAGE IA                 16                 61
  STAGE IB                  1                  8
  STAGE II                  2                  7
  STAGE IIA                76                259
  STAGE IIB                44                180
  STAGE III                 1                  1
  STAGE IIIA               31                107
  STAGE IIIB                8                 19
  STAGE IIIC               10                 49
  STAGE IV                  4                 13
  STAGE TIS                 0                  1
  STAGE X                   1                 15
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  17Q GAIN MUTATED    48 128  21  11
  17Q GAIN WILD-TYPE 210 453  96  25
D31V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1               48                210
  T2              128                453
  T3               21                 96
  T4               11                 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                  N0  N1  N2  N3
  17Q GAIN MUTATED    98  68  26  11
  17Q GAIN WILD-TYPE 370 262  85  59
D31V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               98                370
  N1               68                262
  N2               26                 85
  N3               11                 59
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  17Q GAIN MUTATED          1 183   4  20
  17Q GAIN WILD-TYPE        1 662  13 111
D31V6, multiclass
          clus
vv         17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CM0 (I+)                1                  1
  M0                    183                662
  M1                      4                 13
  MX                     20                111
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED   201   7
  17Q GAIN WILD-TYPE 783   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED    201    7
  17Q GAIN WILD-TYPE  783    4
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE              201                783
  MALE                  7                  4
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  17Q GAIN MUTATED                            0                           166
  17Q GAIN WILD-TYPE                          1                           569
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  17Q GAIN MUTATED                               23                   2
  17Q GAIN WILD-TYPE                            143                   3
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  17Q GAIN MUTATED                                  4                  5
  17Q GAIN WILD-TYPE                               25                  9
                    vv
clus                 OTHER  SPECIFY
  17Q GAIN MUTATED                8
  17Q GAIN WILD-TYPE             36
D31V8, multiclass
                                  clus
vv                                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 166                569
  INFILTRATING LOBULAR CARCINOMA                 23                143
  MEDULLARY CARCINOMA                             2                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)                4                 25
  MUCINOUS CARCINOMA                              5                  9
  OTHER  SPECIFY                                  8                 36
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V9, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    71 137
  17Q GAIN WILD-TYPE 211 576
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     71  137
  17Q GAIN WILD-TYPE  211  576
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                71                211
  YES              137                576
[1] 2 2
[1] FALSE
D31V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q GAIN MUTATED                                  0    13
  17Q GAIN WILD-TYPE                                1    43
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED                          29   143
  17Q GAIN WILD-TYPE                       108   565
D31V11, multiclass
                                  clus
vv                                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          13                 43
  BLACK OR AFRICAN AMERICAN                      29                108
  WHITE                                         143                565
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V12, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     6 168
  17Q GAIN WILD-TYPE  30 628
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      6  168
  17Q GAIN WILD-TYPE   30  628
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                 30
  NOT HISPANIC OR LATINO              168                628
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED   143  17
  18P GAIN WILD-TYPE 717  97
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               160                814 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                17                 97 
$`18P GAIN MUTATED`
TCGA-A1-A0SK TCGA-A1-A0SP TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A0CM TCGA-A2-A0D2 
       31.79        19.20        73.84        22.06        24.79        33.76 
TCGA-A2-A0EM TCGA-A2-A0EQ TCGA-A2-A0T2 TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A1FV 
      101.72        79.76         8.38        18.61        31.73        23.47 
TCGA-A2-A3XS TCGA-A2-A3XX TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A13D 
       33.93        38.40        38.30        30.61        35.67        31.73 
TCGA-A7-A13E TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A8-A06Z 
       10.72        14.50        21.17        10.29         9.37         1.02 
TCGA-A8-A075 TCGA-A8-A079 TCGA-A8-A07R TCGA-A8-A086 TCGA-A8-A08C TCGA-A8-A08I 
       17.03         9.01         8.98        13.02        19.99        12.00 
TCGA-A8-A08P TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A091 TCGA-A8-A097 TCGA-A8-A09K 
       31.00        93.04        33.99        19.07        12.00        29.98 
TCGA-A8-A09R TCGA-A8-A09W TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-AC-A2BK TCGA-AC-A2QH 
        8.98         0.99        13.02        17.03        38.53         1.02 
TCGA-AC-A62Y TCGA-AC-A6IW TCGA-AN-A03Y TCGA-AN-A04C TCGA-AN-A0AT TCGA-AN-A0FJ 
        1.81         0.69         0.33         1.78         0.33         7.96 
TCGA-AN-A0FY TCGA-AO-A03P TCGA-AO-A0J2 TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A12A 
        0.33        84.69        32.78        55.33       102.58        90.58 
TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A54N TCGA-AR-A0TS 
       48.36        61.87         0.53        17.79         2.56        37.41 
TCGA-AR-A0U0 TCGA-AR-A1AJ TCGA-AR-A1AQ TCGA-AR-A24K TCGA-AR-A24Q TCGA-AR-A24U 
       65.36        52.77        43.07        50.89        66.05        53.36 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A2LH TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0IB 
       51.75        56.15        20.25        77.62       143.38       129.57 
TCGA-B6-A0IH TCGA-B6-A0IM TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RO TCGA-B6-A0RU 
      112.37       126.12       140.88       211.56       162.05       131.21 
TCGA-B6-A0WS TCGA-B6-A1KC TCGA-B6-A401 TCGA-B6-A408 TCGA-BH-A0BG TCGA-BH-A0BL 
       97.48        43.59        85.35        49.94        24.85        44.05 
TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0E0 
       44.02        45.83        15.65         2.56        38.47         4.41 
TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0WA TCGA-BH-A18N TCGA-BH-A18T 
       46.19        24.49        31.00        23.05        37.74         7.36 
TCGA-BH-A1FC TCGA-BH-A1FU TCGA-BH-A208 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12U 
      114.15        72.07        57.83        11.93        11.77        12.66 
TCGA-C8-A1HG TCGA-C8-A27A TCGA-D8-A13Z TCGA-D8-A1JC TCGA-D8-A1JF TCGA-D8-A1JL 
       11.34        12.20        20.88        15.78        12.03        20.09 
TCGA-D8-A1JP TCGA-D8-A1JT TCGA-D8-A1XW TCGA-D8-A1Y2 TCGA-D8-A27H TCGA-D8-A27N 
       21.01        13.32        12.66        14.24        13.05         4.80 
TCGA-E2-A10B TCGA-E2-A14P TCGA-E2-A14T TCGA-E2-A14X TCGA-E2-A150 TCGA-E2-A15C 
       37.51        40.96        33.30        31.96        25.41        22.82 
TCGA-E2-A15D TCGA-E2-A15G TCGA-E2-A15O TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L7 
       17.29        18.21        13.02        22.19        11.08        27.42 
TCGA-E2-A1L8 TCGA-E2-A1LH TCGA-E2-A2P5 TCGA-E2-A56Z TCGA-E9-A1N6 TCGA-E9-A1N8 
       39.62       106.75        16.93         7.20        13.48        12.00 
TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1RA TCGA-E9-A1RD 
       20.05         9.86         2.10         6.12        32.09         0.66 
TCGA-E9-A1RH TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A249 TCGA-E9-A6HE TCGA-EW-A1OW 
       34.59        23.51         0.69         0.95        15.39        22.82 
TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1PB TCGA-EW-A3U0 TCGA-GI-A2C9 TCGA-GM-A2DC 
       29.82        23.11        19.99        17.49       109.87        53.52 
TCGA-GM-A3XL TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A7SZ 
       69.30         3.19         3.25         3.88         4.14         5.59 
TCGA-LL-A8F5 TCGA-OL-A5D7 TCGA-OL-A66I TCGA-S3-A6ZG 
        6.21        46.55        23.70         6.81 

$`18P GAIN WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ 
       20.88        13.68         7.96        39.32        28.01        18.21 
TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04W 
      104.81        18.02        41.95        82.16        63.12        64.04 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP 
       55.43        36.13       125.59        64.57       112.08        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV 
       88.60       107.93        75.55        75.25         5.19        63.45 
TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0D4 
       64.04        56.81        21.14        34.55        28.77        25.22 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET 
       89.36        80.28       107.61        74.40        37.05        35.05 
TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST 
       34.29        31.82        29.75        24.72        24.16        99.19 
TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 
       54.64        27.12        44.88        50.43        44.28        17.52 
TCGA-A2-A0T1 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 
       17.13        18.71        20.52        17.46        18.90        20.75 
TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH 
       32.55        25.28        18.21        15.42        21.90        21.67 
TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX 
       14.50        19.33        14.63        23.77        17.36        36.79 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       22.45        20.25        19.20        19.56        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
      107.70        16.31        17.19        18.15        91.92        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW 
       20.88        39.65        83.01        29.98        14.07        49.48 
TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY 
       34.98        31.99        38.37         7.30         9.01         8.81 
TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG 
        8.91        12.00         6.74         3.42        35.31        34.29 
TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H 
       35.47        37.45        33.11        12.72        23.61        29.56 
TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J 
       31.36        24.26        23.74        23.80        21.73        20.61 
TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF 
       22.32        11.34        10.59        10.29        11.28        13.41 
TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SF TCGA-A7-A56D 
       14.70        11.97        14.93        13.74        17.92        14.73 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O 
       12.10        10.72        11.05        10.42         8.75        13.02 
TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X 
       13.02         1.02        17.98        41.06        29.03        31.00 
TCGA-A8-A06Y TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G 
       26.01        53.98        33.01        19.99        18.97        18.97 
TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S 
       14.01        12.00        17.03         9.99        10.98         7.99 
TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 
        9.96         9.99        28.04        18.05        15.06        36.95 
TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08L 
        0.99        23.08        18.05        19.96        37.05         9.99 
TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A093 
       31.00         0.99        19.07        40.01        16.01        17.95 
TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D 
       41.98         9.99         9.99        12.00         1.02        13.02 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09T 
       31.00        33.07        15.02         1.02        25.02        19.04 
TCGA-A8-A09V TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 
       15.02        14.01        12.00        19.04        13.02        21.04 
TCGA-A8-A0A7 TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H 
        0.99        38.04         0.95         2.37        10.85         2.66 
TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
        1.48        38.20        40.57        55.43        36.99        38.79 
TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN 
       26.04        50.70         0.92         2.27         0.99         0.69 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI 
       14.83         9.40         1.12         1.81         1.68         1.55 
TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IX 
        1.32         1.55         0.07         1.12         1.18         0.43 
TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A 
        1.74         0.33         0.23         0.33         0.62         2.96 
TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR 
        1.71         8.02         7.36         6.51         0.16         0.33 
TCGA-AN-A0AS TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN 
        0.33         6.44         4.64         7.00         7.59         7.17 
TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FZ 
        6.28         6.02         0.33         0.36         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS 
        0.33         0.33        12.33         0.30         0.33         0.33 
TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M 
        0.33         0.33         5.33         5.59        80.28        47.84 
TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V 
       66.77        81.63        68.75        47.87        59.05        29.13 
TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 
       21.40        17.65        24.16        37.48        20.32        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE 
       53.03        21.53        50.70        50.86        72.00        76.77 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A125 
       21.37        26.24        38.53        62.04        71.80        99.25 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
       93.70        94.59        96.10        77.56        64.04        57.30 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AQ-A04H 
       41.62        28.37        14.73        82.62        70.39        24.79 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54O 
       26.93       130.09         5.65        15.62        13.22        21.86 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TV 
        9.99        82.88        49.32         5.26        56.88        29.75 
TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 
       24.30        64.83        55.86        76.14        70.16        83.87 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AL 
       76.18        55.36        75.55        61.84        51.25        48.82 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AR TCGA-AR-A1AS 
       62.56        43.73        43.56        39.98        17.23        40.83 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H 
       46.32        42.58        35.24        36.26        20.22       109.58 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R 
       73.02        65.46        68.19        65.69         0.85        57.40 
TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A251 
       62.07        53.26        54.18        50.96        48.16        45.17 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LK 
       40.64        39.85        34.82        93.83       128.65        42.87 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
        7.36        40.04        17.10        20.81        16.96        20.38 
TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I5 TCGA-B6-A0I9 
       54.74        16.04        20.45        10.59       149.59        12.13 
TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IJ TCGA-B6-A0IK 
      220.90        50.70        65.72       146.50       176.98        18.77 
TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
       84.59       110.14       110.93        68.45       189.01       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS 
       81.17        78.02       172.96       102.77       140.48       100.70 
TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX 
       89.46       157.41       188.68        79.63        17.98        21.47 
TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
      113.79       129.57       129.70       186.48        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A402 
       58.88       101.52        73.51       139.17       170.17        54.28 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY 
       82.88        55.00        24.53        38.79        20.45        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 
       28.50        46.95        40.83        39.55        39.16        48.36 
TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
       56.94        56.98        51.68        37.22        32.02        18.21 
TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ 
       25.71        21.70        61.68        35.67        48.69        27.19 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ 
       53.69        53.95        45.57        49.94        11.67        49.05 
TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH 
       41.75        48.13        42.90        31.17        23.44        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DQ TCGA-BH-A0DV 
       22.13        13.91        48.23        17.26         3.22        45.17 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 
       47.41        16.27        15.68        14.30         9.63        44.81 
TCGA-BH-A0EA TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       32.65        24.43        30.35        10.78        15.16        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB 
       35.51        24.56        23.08        41.00        52.96        26.50 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU 
       20.38         5.85         2.50        13.61        36.85        12.89 
TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 
       51.32        27.25        50.79         5.59        23.93        24.95 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J 
       42.35        44.81         8.81         2.01         7.23        20.12 
TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R 
       90.84        26.66        72.56        30.28        55.63        37.55 
TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES 
       66.05        51.39        51.16        69.93        91.99       113.82 
TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY 
       82.85        42.28        12.00        55.69        49.58        17.69 
TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB 
       25.81        31.53        89.16        97.48        24.66       120.62 
TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
       33.17        74.73       122.89        36.92        63.35        55.00 
TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 
       45.63        72.07       144.59         6.90         0.72        38.60 
TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T 
       83.31       130.16        10.65         6.44        20.12         0.99 
TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q 
      109.28         8.94        11.77        12.66        11.77         0.07 
TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 
       12.66        12.66        12.66         3.12         1.78         1.45 
TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF 
        0.69         0.62         3.85         3.75        12.33        10.92 
TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN 
       11.34         0.16        12.03        10.42         2.30         3.25 
TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 
        0.30         0.23         0.36         0.43         8.28         9.67 
TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 
        0.03         0.03         0.03         0.99         0.03         0.23 
TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 
       11.90        13.25        20.58        13.97        14.17        13.48 
TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
       21.14        19.20        14.17        17.49        16.50        18.71 
TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ 
       18.15        18.90        12.03        14.01        18.97        20.09 
TCGA-D8-A1JK TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X5 
       20.12        19.40        20.38        12.20        14.70        18.58 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB 
       17.79        16.73        25.74        23.90        27.58        18.15 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK 
        2.66        17.16        15.22        14.73        21.83        14.50 
TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS 
       19.92        17.69         7.96        16.41        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 
        6.35        12.99        15.16        16.54        15.32        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27I 
        3.81        14.14        17.42        16.04        13.45        14.43 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T 
        9.44        16.41        13.48         0.76        10.09        13.08 
TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 
       12.53        12.26        14.50        18.51         7.33        43.00 
TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A10E 
       34.42        27.52        46.59        40.41        40.11        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S 
       28.87        47.15        44.68        38.24        38.60        33.17 
TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A152 
       43.33        34.26        32.02        28.60        17.03        27.12 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 
       23.24        19.43        21.04        23.87        14.79        25.05 
TCGA-E2-A15A TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J 
       23.34        20.71        21.63        12.92        17.42        19.40 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
        9.04        20.58         7.73        19.56        17.06        14.07 
TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       14.99        60.53        53.62        53.03        29.95        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       28.50        16.47        17.10        38.30        37.41        32.78 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IO 
       33.73        33.70        28.44        22.65         3.88        20.98 
TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG 
       54.18        19.66        24.59        40.47        28.90        18.87 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 
      102.61         8.75        43.04         5.52        15.72        18.05 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N9 TCGA-E9-A1NA 
       22.26        19.89        19.20        36.82        13.12        36.56 
TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1QZ TCGA-E9-A1R0 
       39.55        12.59        35.77        21.57        11.90        14.30 
TCGA-E9-A1R2 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RB TCGA-E9-A1RC 
        0.62         1.38         2.76        21.21        20.81        40.24 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
       34.65         6.58        21.27        35.64        34.13         0.79 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22H 
       12.53        13.32        39.09        22.75        12.89        24.10 
TCGA-E9-A243 TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A295 
       17.06         0.85        27.22         1.94        12.56         0.72 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
       17.75         0.76        26.07        18.41         0.62        15.72 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-EW-A1IW TCGA-EW-A1IX 
        0.23         0.39         0.26         0.23        12.20        39.72 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
        8.48        18.21        18.90        13.25        16.57        15.68 
TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 
       28.77        25.94        29.95        29.85        40.41        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA 
       39.78        52.96        18.48        30.08         7.86        18.90 
TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH 
        6.15        13.94        10.52        14.43        34.55        19.96 
TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A423 
       55.00        52.73        25.91        22.09        21.27        10.16 
TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DD 
       10.59         7.40        59.57       194.27        53.13        43.04 
TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       42.71        42.28        61.91        62.33        90.84        76.64 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN 
       77.33        53.36       110.50        38.20        32.28        53.95 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U 
       57.63        13.55        18.12        11.84        11.57         8.28 
TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y 
        6.67         4.60         0.66         2.99         3.58         6.90 
TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A6FQ TCGA-LL-A73Z TCGA-LL-A740 
        5.56         4.70         3.65         2.63         4.50         4.50 
TCGA-LL-A7T0 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 
        3.22        15.91         2.79         2.10        12.66         7.53 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY 
       44.61        27.65        24.10        26.20        16.87        14.10 
TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L 
       10.29         9.80        14.76        54.51        33.90        31.07 
TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-W8-A86G 
       18.21         7.23         4.44         5.29 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.33               0.03 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            211.56             234.28 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             22.82              21.27 
[1] "0.3 - 211.6 (22.8)" "0.0 - 234.3 (21.3)"
[1] "hr=" "1.3"
D32V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18P GAIN MUTATED         9       12        1        0        75        29
  18P GAIN WILD-TYPE      71       65        8        9       260       195
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18P GAIN MUTATED           1         16          5          8        4
  18P GAIN WILD-TYPE         1        122         22         51       13
                    vv
clus                 STAGE TIS STAGE X
  18P GAIN MUTATED           0       3
  18P GAIN WILD-TYPE         1      13
D32V3, multiclass
            clus
vv           18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                   9                 71
  STAGE IA                 12                 65
  STAGE IB                  1                  8
  STAGE II                  0                  9
  STAGE IIA                75                260
  STAGE IIB                29                195
  STAGE III                 1                  1
  STAGE IIIA               16                122
  STAGE IIIB                5                 22
  STAGE IIIC                8                 51
  STAGE IV                  4                 13
  STAGE TIS                 0                  1
  STAGE X                   3                 13
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  18P GAIN MUTATED    34 104  19   5
  18P GAIN WILD-TYPE 224 477  98  31
D32V4, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1               34                224
  T2              104                477
  T3               19                 98
  T4                5                 31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  18P GAIN MUTATED    93  41  14  13
  18P GAIN WILD-TYPE 375 289  97  57
D32V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0               93                375
  N1               41                289
  N2               14                 97
  N3               13                 57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  18P GAIN MUTATED          0 141   4  18
  18P GAIN WILD-TYPE        2 704  13 113
D32V6, multiclass
          clus
vv         18P GAIN MUTATED 18P GAIN WILD-TYPE
  CM0 (I+)                0                  2
  M0                    141                704
  M1                      4                 13
  MX                     18                113
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED   161   2
  18P GAIN WILD-TYPE 823   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED    161    2
  18P GAIN WILD-TYPE  823    9
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE              161                823
  MALE                  2                  9
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  18P GAIN MUTATED                            0                           136
  18P GAIN WILD-TYPE                          1                           599
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  18P GAIN MUTATED                               13                   2
  18P GAIN WILD-TYPE                            153                   3
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  18P GAIN MUTATED                                  4                  0
  18P GAIN WILD-TYPE                               25                 14
                    vv
clus                 OTHER  SPECIFY
  18P GAIN MUTATED                7
  18P GAIN WILD-TYPE             37
D32V8, multiclass
                                  clus
vv                                 18P GAIN MUTATED 18P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 136                599
  INFILTRATING LOBULAR CARCINOMA                 13                153
  MEDULLARY CARCINOMA                             2                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)                4                 25
  MUCINOUS CARCINOMA                              0                 14
  OTHER  SPECIFY                                  7                 37
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V9, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    50 113
  18P GAIN WILD-TYPE 232 600
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     50  113
  18P GAIN WILD-TYPE  232  600
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                50                232
  YES              113                600
[1] 2 2
[1] FALSE
D32V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P GAIN MUTATED                                  0     7
  18P GAIN WILD-TYPE                                1    49
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED                          39    98
  18P GAIN WILD-TYPE                        98   610
D32V11, multiclass
                                  clus
vv                                 18P GAIN MUTATED 18P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           7                 49
  BLACK OR AFRICAN AMERICAN                      39                 98
  WHITE                                          98                610
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V12, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     2 129
  18P GAIN WILD-TYPE  34 667
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2  129
  18P GAIN WILD-TYPE   34  667
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 34
  NOT HISPANIC OR LATINO              129                667
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED   119  16
  18Q GAIN WILD-TYPE 741  98
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
               135                839 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                16                 98 
$`18Q GAIN MUTATED`
TCGA-A1-A0SK TCGA-A1-A0SP TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A0CM TCGA-A2-A0D2 
       31.79        19.20        73.84        22.06        24.79        33.76 
TCGA-A2-A0EM TCGA-A2-A0EQ TCGA-A2-A0T2 TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A1FV 
      101.72        79.76         8.38        18.61        31.73        23.47 
TCGA-A2-A25E TCGA-A2-A3XS TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A7-A0CD TCGA-A7-A0CJ 
       91.92        33.93        38.40        34.98        38.30        30.61 
TCGA-A7-A13E TCGA-A7-A4SD TCGA-A7-A6VW TCGA-A8-A079 TCGA-A8-A07P TCGA-A8-A07R 
       10.72        14.50         9.37         9.01        10.98         8.98 
TCGA-A8-A086 TCGA-A8-A08C TCGA-A8-A08I TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A091 
       13.02        19.99        12.00        93.04        33.99        19.07 
TCGA-A8-A097 TCGA-A8-A09K TCGA-A8-A09R TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-AC-A6IW 
       12.00        29.98         8.98        13.02        17.03         0.69 
TCGA-AN-A03Y TCGA-AN-A04C TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FJ 
        0.33         1.78         0.33         0.33         0.33         7.96 
TCGA-AN-A0FY TCGA-AN-A0XO TCGA-AO-A03P TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A12A 
        0.33        12.33        84.69        55.33       102.58        90.58 
TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AQ-A54N TCGA-AR-A0U0 TCGA-AR-A1AJ 
       48.36        61.87         0.53         2.56        65.36        52.77 
TCGA-AR-A24K TCGA-AR-A24Q TCGA-AR-A24Z TCGA-AR-A2LH TCGA-B6-A0I2 TCGA-B6-A0IB 
       50.89        66.05        51.75        20.25       143.38       129.57 
TCGA-B6-A0IH TCGA-B6-A0IM TCGA-B6-A0IQ TCGA-B6-A0RO TCGA-B6-A0WS TCGA-B6-A1KC 
      112.37       126.12       140.88       162.05        97.48        43.59 
TCGA-B6-A401 TCGA-B6-A408 TCGA-BH-A0BL TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0DD 
       85.35        49.94        44.05        41.75        44.02        45.83 
TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0E9 
       15.65         2.56        38.47         4.41         9.63        46.19 
TCGA-BH-A0EB TCGA-BH-A0HB TCGA-BH-A0HY TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18Q 
       24.49        26.50        50.79        26.66        37.74        55.63 
TCGA-BH-A18T TCGA-BH-A208 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12U TCGA-C8-A1HG 
        7.36        57.83        11.93        11.77        12.66        11.34 
TCGA-C8-A1HN TCGA-C8-A27A TCGA-D8-A1JF TCGA-D8-A1JL TCGA-D8-A1JP TCGA-D8-A1JT 
        3.25        12.20        12.03        20.09        21.01        13.32 
TCGA-D8-A1Y2 TCGA-D8-A27H TCGA-E2-A10B TCGA-E2-A14T TCGA-E2-A14X TCGA-E2-A15C 
       14.24        13.05        37.51        33.30        31.96        22.82 
TCGA-E2-A15D TCGA-E2-A15G TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L7 TCGA-E2-A1L8 
       17.29        18.21        22.19        11.08        27.42        39.62 
TCGA-E2-A1LH TCGA-E2-A2P5 TCGA-E2-A56Z TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1NF 
      106.75        16.93         7.20        13.48        12.00        20.05 
TCGA-E9-A1NI TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1RA TCGA-E9-A1RD 
        9.86         0.62         2.10         6.12        32.09         0.66 
TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A249 TCGA-E9-A3HO TCGA-E9-A6HE TCGA-EW-A1OW 
       23.51         0.69         0.95        26.07        15.39        22.82 
TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1PB TCGA-GM-A2DC TCGA-GM-A3XL TCGA-LL-A5YP 
       29.82        23.11        19.99        53.52        69.30         3.25 
TCGA-LL-A7SZ TCGA-OL-A66I TCGA-S3-A6ZG 
        5.59        23.70         6.81 

$`18Q GAIN WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ 
       20.88        13.68         7.96        39.32        28.01        18.21 
TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04W 
      104.81        18.02        41.95        82.16        63.12        64.04 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP 
       55.43        36.13       125.59        64.57       112.08        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV 
       88.60       107.93        75.55        75.25         5.19        63.45 
TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0D4 
       64.04        56.81        21.14        34.55        28.77        25.22 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET 
       89.36        80.28       107.61        74.40        37.05        35.05 
TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST 
       34.29        31.82        29.75        24.72        24.16        99.19 
TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 
       54.64        27.12        44.88        50.43        44.28        17.52 
TCGA-A2-A0T1 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 
       17.13        18.71        20.52        17.46        18.90        20.75 
TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH 
       32.55        25.28        18.21        15.42        21.90        21.67 
TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX 
       14.50        19.33        14.63        23.77        17.36        36.79 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       22.45        20.25        19.20        19.56        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25F TCGA-A2-A3KC 
      107.70        16.31        17.19        18.15        10.59        20.88 
TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XZ 
       39.65        83.01        29.98        14.07        49.48        31.99 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 
       38.37         7.30         9.01         8.81         8.91        12.00 
TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 
        6.74         3.42        35.31        34.29        35.47        37.45 
TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H 
       35.67        33.11        31.73        12.72        23.61        29.56 
TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J 
       31.36        24.26        23.74        23.80        21.73        20.61 
TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF 
       22.32        11.34        10.59        10.29        11.28        13.41 
TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A4SF 
       14.70        11.97        14.93        13.74        21.17        17.92 
TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VX 
       14.73        12.10        10.72        11.05        10.29        10.42 
TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T 
        8.75        13.02        13.02         1.02        17.98        41.06 
TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 
       29.03        31.00        26.01         1.02        17.03        53.98 
TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J 
       33.01        19.99        18.97        18.97        14.01        12.00 
TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z 
       17.03         9.99         7.99         9.96         9.99        28.04 
TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08F 
       18.05        15.06        36.95         0.99        23.08        18.05 
TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R 
       19.96        37.05         9.99        31.00        31.00         0.99 
TCGA-A8-A08S TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 
       19.07        40.01        16.01        17.95        41.98         9.99 
TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I 
        9.99        12.00         1.02        13.02        31.00        33.07 
TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
       15.02         1.02        25.02        19.04        15.02         0.99 
TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 
       14.01        12.00        19.04        13.02        21.04         0.99 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 
       38.04         0.95         2.37        10.85         2.66         1.48 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
       38.53        38.20        40.57        55.43        36.99        38.79 
TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB 
       26.04        50.70         1.02         0.92         2.27         0.99 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 
        0.69        14.83         9.40         1.12         1.81         1.68 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y 
        1.55         1.32         1.55         0.07         1.12         1.81 
TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 
        1.18         0.43         1.74         0.33         0.23         0.33 
TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL 
        0.62         2.96         1.71         8.02         7.36         6.51 
TCGA-AN-A0AM TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN 
        0.16         6.44         4.64         7.00         7.59         7.17 
TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FZ 
        6.28         6.02         0.33         0.36         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT 
        0.33         0.33         0.30         0.33         0.33         0.33 
TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N 
        0.33         5.33         5.59        80.28        47.84        66.77 
TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 
       81.63        68.75        47.87        59.05        29.13        32.78 
TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 
       21.40        17.65        24.16        37.48        20.32        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE 
       53.03        21.53        50.70        50.86        72.00        76.77 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A125 
       21.37        26.24        38.53        62.04        71.80        99.25 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
       93.70        94.59        96.10        77.56        64.04        57.30 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AO-A1KT 
       41.62        28.37        14.73        82.62        70.39        17.79 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       24.79        26.93       130.09         5.65        15.62        13.22 
TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS 
       21.86         9.99        82.88        49.32         5.26        37.41 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
       56.88        29.75        24.30        64.83        55.86        76.14 
TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
       70.16        83.87        76.18        55.36        75.55        61.84 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP 
       51.25        48.82        62.56        43.73        43.56        39.98 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       43.07        17.23        40.83        46.32        42.58        35.24 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       36.26        20.22       109.58        73.02        65.46        68.19 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U 
       65.69         0.85        57.40        62.07        53.26        53.36 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 
       54.18        50.96        48.16        56.15        45.17        40.64 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LK TCGA-AR-A2LL 
       39.85        34.82        93.83       128.65        42.87         7.36 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM 
       40.04        17.10        20.81        16.96        20.38        54.74 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I5 TCGA-B6-A0I9 
       16.04        20.45        10.59        77.62       149.59        12.13 
TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IJ TCGA-B6-A0IK 
      220.90        50.70        65.72       146.50       176.98        18.77 
TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH 
       84.59       110.14       110.93       211.56        68.45       189.01 
TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RQ 
      234.28        81.17        78.02       172.96       102.77       140.48 
TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WT TCGA-B6-A0WV 
      100.70        89.46       131.21       157.41       188.68        79.63 
TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 
       17.98        21.47       113.79       129.57       129.70       186.48 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN 
       28.27        68.94        58.88       101.52        73.51       139.17 
TCGA-B6-A2IU TCGA-B6-A402 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV 
      170.17        54.28        82.88        55.00        24.53        38.79 
TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 
       20.45        25.55        28.50        46.95        40.83        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA 
       39.16        48.36        56.94        56.98        51.68        37.22 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BM 
       32.02        18.21        25.71        24.85        21.70        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT 
       35.67        48.69        27.19        53.69        53.95        45.57 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DE 
       49.94        11.67        49.05        48.13        42.90        31.17 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO 
       23.44        38.01        22.13        13.91        48.23        17.26 
TCGA-BH-A0DQ TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 
        3.22        45.17        47.41        16.27        15.68        14.30 
TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ 
       44.81        32.65        31.00        24.43        30.35        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 
       15.16        37.78        35.51        24.56        23.08        41.00 
TCGA-BH-A0HA TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ 
       52.96        20.38         5.85         2.50        13.61        36.85 
TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 
       12.89        51.32        27.25         5.59        23.93        24.95 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I 
       42.35        44.81        23.05         8.81         2.01         7.23 
TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S 
       20.12        90.84        72.56        30.28        37.55        66.05 
TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET 
       51.39        51.16        69.93        91.99       113.82        82.85 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 
       42.28        12.00        55.69        49.58        17.69        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC 
       31.53        89.16        97.48        24.66       120.62       114.15 
TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
       33.17        74.73       122.89        36.92        63.35        55.00 
TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 
       45.63        72.07       144.59        72.07         6.90         0.72 
TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
       38.60        83.31       130.16        10.65         6.44        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P 
        0.99       109.28         8.94        11.77        12.66        11.77 
TCGA-C8-A12Q TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A131 
        0.07        12.66        12.66        12.66         3.12         1.78 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE 
        1.45         0.69         0.62         3.85         3.75        12.33 
TCGA-C8-A1HF TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM 
       10.92        11.34         0.16        12.03        10.42         2.30 
TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 
        0.30         0.23         0.36         0.43         8.28         9.67 
TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 
        0.03         0.03         0.03         0.99         0.03         0.23 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 
       11.90        20.88        13.25        20.58        13.97        14.17 
TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA 
       13.48        21.14        19.20        14.17        17.49        16.50 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH 
       18.71        15.78        18.15        18.90        12.03        14.01 
TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JS 
       18.97        20.09        20.12        19.40        20.38        12.20 
TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 
       14.70        18.58        17.79        16.73        25.74        23.90 
TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG 
       27.58        18.15         2.66        17.16        15.22        14.73 
TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ 
       21.83        14.50        19.92        17.69         7.96        16.41 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW 
       15.85        16.31         6.35        12.99        15.16        12.66 
TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27E 
       16.54        15.32        15.52         3.81        14.14        17.42 
TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M 
       16.04        13.45        14.43         9.44        16.41        13.48 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W 
        4.80         0.76        10.09        13.08        12.53        12.26 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 
       14.50        18.51         7.33        43.00        34.42        27.52 
TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N 
       46.59        40.41        40.11        28.44        28.87        47.15 
TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14U 
       44.68        40.96        38.24        38.60        33.17        43.33 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 
       34.26        32.02        28.60        17.03        25.41        27.12 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 
       23.24        19.43        21.04        23.87        14.79        25.05 
TCGA-E2-A15A TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J 
       23.34        20.71        21.63        12.92        17.42        19.40 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R 
        9.04        20.58         7.73        13.02        19.56        17.06 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 
       14.07        14.99        60.53        53.62        53.03        29.95 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF 
       32.35        28.50        16.47        17.10        38.30        37.41 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       32.78        33.73        33.70        28.44        22.65         3.88 
TCGA-E2-A1IO TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       20.98        54.18        19.66        24.59        40.47        28.90 
TCGA-E2-A1LG TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX 
       18.87       102.61         8.75        43.04         5.52        15.72 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N9 
       18.05        22.26        19.89        19.20        36.82        13.12 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1QZ 
       36.56        39.55        12.59        35.77        21.57        11.90 
TCGA-E9-A1R0 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RB TCGA-E9-A1RC 
       14.30         1.38         2.76        21.21        20.81        40.24 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 
       34.65         6.58        21.27        34.59        35.64        34.13 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E 
        0.79        12.53        13.32        39.09        22.75        12.89 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A24A 
       24.10        17.06         0.85        27.22         1.94        12.56 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
        0.72        17.75         0.76        18.41         0.62        15.72 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-EW-A1IW TCGA-EW-A1IX 
        0.23         0.39         0.26         0.23        12.20        39.72 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
        8.48        18.21        18.90        13.25        16.57        15.68 
TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 
       28.77        25.94        29.95        29.85        40.41        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA 
       39.78        52.96        18.48        30.08         7.86        18.90 
TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH 
        6.15        13.94        10.52        14.43        34.55        19.96 
TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 
       55.00        52.73        25.91        22.09        21.27        17.49 
TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       10.16        10.59         7.40       109.87        59.57       194.27 
TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK 
       53.13        43.04        42.71        42.28        61.91        62.33 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY 
       90.84        76.64        77.33        53.36       110.50        38.20 
TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW 
       32.28        53.95        57.63        13.55        18.12        11.84 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 
       11.57         8.28         6.67         4.60         0.66         2.99 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO 
        3.58         6.90         5.56         4.70         3.65         3.19 
TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7T0 
        2.63         3.88         4.14         4.50         4.50         3.22 
TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 
        6.21        15.91         2.79         2.10        12.66        46.55 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX 
        7.53        44.61        27.65        24.10        26.20        16.87 
TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K 
       14.10        10.29         9.80        14.76        54.51        33.90 
TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-W8-A86G 
       31.07        18.21         7.23         4.44         5.29 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.33               0.03 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            162.05             234.28 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             22.19              21.37 
[1] "0.3 - 162.1 (22.2)" "0.0 - 234.3 (21.4)"
[1] "hr=" "1.1"
D33V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18Q GAIN MUTATED         7        9        1        0        63        25
  18Q GAIN WILD-TYPE      73       68        8        9       272       199
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18Q GAIN MUTATED           1         15          4          8        4
  18Q GAIN WILD-TYPE         1        123         23         51       13
                    vv
clus                 STAGE TIS STAGE X
  18Q GAIN MUTATED           0       1
  18Q GAIN WILD-TYPE         1      15
D33V3, multiclass
            clus
vv           18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                   7                 73
  STAGE IA                  9                 68
  STAGE IB                  1                  8
  STAGE II                  0                  9
  STAGE IIA                63                272
  STAGE IIB                25                199
  STAGE III                 1                  1
  STAGE IIIA               15                123
  STAGE IIIB                4                 23
  STAGE IIIC                8                 51
  STAGE IV                  4                 13
  STAGE TIS                 0                  1
  STAGE X                   1                 15
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  18Q GAIN MUTATED    27  91  15   5
  18Q GAIN WILD-TYPE 231 490 102  31
D33V4, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1               27                231
  T2               91                490
  T3               15                102
  T4                5                 31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  18Q GAIN MUTATED    74  39  12  12
  18Q GAIN WILD-TYPE 394 291  99  58
D33V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0               74                394
  N1               39                291
  N2               12                 99
  N3               12                 58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  18Q GAIN MUTATED          0 124   4  10
  18Q GAIN WILD-TYPE        2 721  13 121
D33V6, multiclass
          clus
vv         18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CM0 (I+)                0                  2
  M0                    124                721
  M1                      4                 13
  MX                     10                121
[1] 4 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   136   2
  18Q GAIN WILD-TYPE 848   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED    136    2
  18Q GAIN WILD-TYPE  848    9
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE              136                848
  MALE                  2                  9
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  18Q GAIN MUTATED                            0                           116
  18Q GAIN WILD-TYPE                          1                           619
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  18Q GAIN MUTATED                               12                   1
  18Q GAIN WILD-TYPE                            154                   4
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  18Q GAIN MUTATED                                  4                  0
  18Q GAIN WILD-TYPE                               25                 14
                    vv
clus                 OTHER  SPECIFY
  18Q GAIN MUTATED                5
  18Q GAIN WILD-TYPE             39
D33V8, multiclass
                                  clus
vv                                 18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 116                619
  INFILTRATING LOBULAR CARCINOMA                 12                154
  MEDULLARY CARCINOMA                             1                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                4                 25
  MUCINOUS CARCINOMA                              0                 14
  OTHER  SPECIFY                                  5                 39
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V9, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    43  95
  18Q GAIN WILD-TYPE 239 618
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     43   95
  18Q GAIN WILD-TYPE  239  618
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                43                239
  YES               95                618
[1] 2 2
[1] FALSE
D33V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q GAIN MUTATED                                  0     8
  18Q GAIN WILD-TYPE                                1    48
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED                          26    88
  18Q GAIN WILD-TYPE                       111   620
D33V11, multiclass
                                  clus
vv                                 18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           8                 48
  BLACK OR AFRICAN AMERICAN                      26                111
  WHITE                                          88                620
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V12, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     2 106
  18Q GAIN WILD-TYPE  34 690
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      2  106
  18Q GAIN WILD-TYPE   34  690
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 34
  NOT HISPANIC OR LATINO              106                690
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED   150  18
  19P GAIN WILD-TYPE 710  96
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               168                806 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                18                 96 
$`19P GAIN MUTATED`
TCGA-A1-A0SF TCGA-A1-A0SK TCGA-A2-A04Q TCGA-A2-A0CT TCGA-A2-A0D0 TCGA-A2-A0D1 
       48.10        31.79        41.95        75.25        21.14        34.55 
TCGA-A2-A0D2 TCGA-A2-A0EQ TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EY TCGA-A2-A0SX 
       33.76        79.76        35.05        34.29        24.16        50.43 
TCGA-A2-A0T6 TCGA-A2-A0YJ TCGA-A2-A1G1 TCGA-A2-A3XU TCGA-A2-A3Y0 TCGA-A2-A4S2 
       18.90        18.61        19.20        29.98        38.37         6.74 
TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CJ TCGA-A7-A0DB TCGA-A7-A26E TCGA-A7-A3J0 
       38.30        35.31        30.61        33.11        31.36        10.29 
TCGA-A7-A4SE TCGA-A7-A5ZV TCGA-A8-A06X TCGA-A8-A07R TCGA-A8-A08B TCGA-A8-A08X 
       21.17        12.10        31.00         8.98        23.08        33.99 
TCGA-A8-A093 TCGA-A8-A09B TCGA-A8-A09E TCGA-A8-A09M TCGA-A8-A0A7 TCGA-A8-A0A9 
       17.95        12.00        31.00        15.02         0.99        13.02 
TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2FO TCGA-AC-A3OD TCGA-AC-A62Y TCGA-AC-A6IW 
        2.37        10.85        50.70        14.83         1.81         0.69 
TCGA-AC-A8OP TCGA-AN-A03Y TCGA-AN-A04C TCGA-AN-A0AK TCGA-AN-A0FK TCGA-AN-A0FW 
        1.74         0.33         1.78         7.36         7.00         0.36 
TCGA-AN-A0FX TCGA-AN-A0XN TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A0J2 TCGA-AO-A0J7 
        0.33         0.33         5.59        80.28        32.78        20.32 
TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D 
       55.33       102.58        94.59        90.58        77.56        64.04 
TCGA-AO-A1KS TCGA-AQ-A54O TCGA-AR-A0U0 TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX 
        0.53        21.86        65.36        42.58        35.24        36.26 
TCGA-AR-A24K TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LQ 
       50.89        54.18        50.96        34.82        93.83        16.96 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0RU TCGA-B6-A0WX 
       20.38        54.74       112.37       176.98       131.21        21.47 
TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A401 TCGA-BH-A0AU 
      113.79       129.57        43.59        73.51        85.35        24.53 
TCGA-BH-A0B6 TCGA-BH-A0BA TCGA-BH-A0BJ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C7 
       56.94        37.22        21.70        41.75        44.02        42.90 
TCGA-BH-A0DD TCGA-BH-A0DO TCGA-BH-A0E9 TCGA-BH-A0GY TCGA-BH-A0HQ TCGA-BH-A18K 
       45.83        17.26        46.19        30.35        36.85        90.84 
TCGA-BH-A18N TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A208 
       37.74        55.63         7.36        51.16        91.99        57.83 
TCGA-C8-A12L TCGA-C8-A12V TCGA-C8-A130 TCGA-C8-A1HM TCGA-C8-A275 TCGA-D8-A13Z 
       11.93        12.66         3.12         2.30         0.03        20.88 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1JF TCGA-D8-A1JH 
       14.17        13.48        19.20        14.17        12.03        14.01 
TCGA-D8-A1JL TCGA-D8-A1JN TCGA-D8-A1X6 TCGA-D8-A1XJ TCGA-D8-A1XU TCGA-D8-A27N 
       20.09        20.38        17.79        21.83        12.99         4.80 
TCGA-D8-A27R TCGA-D8-A27V TCGA-D8-A27W TCGA-E2-A10B TCGA-E2-A14N TCGA-E2-A14R 
       10.09        12.53        12.26        37.51        47.15        38.60 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A15M 
       31.96        28.60        17.03        25.41        23.24         7.73 
TCGA-E2-A1II TCGA-E2-A1IN TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E9-A1N8 TCGA-E9-A1N9 
       33.70        22.19        28.90        18.87        12.00        13.12 
TCGA-E9-A1NA TCGA-E9-A1NF TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RD TCGA-E9-A22E 
       36.56        20.05         2.76        32.09         0.66        12.89 
TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A249 TCGA-E9-A295 TCGA-E9-A3QA TCGA-E9-A5FK 
       17.06         0.69         0.95         0.72         0.62         0.39 
TCGA-E9-A5FL TCGA-EW-A1J6 TCGA-EW-A1P4 TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A1PD 
        0.26        28.77        29.82         7.86        19.99        13.94 
TCGA-EW-A423 TCGA-GI-A2C9 TCGA-GM-A2DD TCGA-LD-A7W6 TCGA-LL-A5YN TCGA-LL-A5YP 
       10.16       109.87        43.04         4.60         3.65         3.25 
TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A8F5 TCGA-OL-A5RW TCGA-S3-A6ZG TCGA-W8-A86G 
        2.63         4.14         6.21        26.20         6.81         5.29 

$`19P GAIN WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI 
        8.52        14.37        43.43        14.27        47.24        20.88 
TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ 
       13.68         7.96        39.32        28.01        19.20        18.21 
TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V 
      104.81        18.02        82.16        73.84        22.06        63.12 
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM 
       64.04        55.43        36.13       125.59        64.57        24.79 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CU 
      112.08        92.48        88.60       107.93        75.55         5.19 
TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM 
       63.45        64.04        56.81        28.77        25.22       101.72 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EV 
       89.36        80.28       107.61        74.40        37.05        31.82 
TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW 
       29.75        24.72        99.19        54.64        27.12        44.88 
TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 
       44.28        17.52        17.13         8.38        18.71        20.52 
TCGA-A2-A0T5 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF 
       17.46        20.75        32.55        25.28        18.21        15.42 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       21.90        21.67        14.50        19.33        14.63        31.73 
TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 
       23.77        23.47        17.36        36.79        22.45        20.25 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C 
       19.56        16.47        52.47       107.70        16.31        17.19 
TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS 
       18.15        91.92        10.59        20.88        39.65        33.93 
TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ 
       83.01        14.07        49.48        38.40        34.98        31.99 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S3 
        7.30         9.01         8.81         8.91        12.00         3.42 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E 
       34.29        35.47        37.45        35.67        31.73        10.72 
TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H 
       12.72        23.61        29.56        24.26        23.74        23.80 
TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J1 
       21.73        20.61        22.32        11.34        10.59        11.28 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD 
       13.41        14.70        11.97        14.93        13.74        14.50 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW 
       17.92        14.73        10.72        11.05        10.29         9.37 
TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R 
       10.42         8.75        13.02        13.02         1.02        17.98 
TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 
       41.06        29.03        26.01         1.02        17.03        53.98 
TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I 
        9.01        33.01        19.99        18.97        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U 
       12.00        17.03         9.99        10.98         7.99         9.96 
TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 
        9.99        28.04        18.05        15.06        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J 
        0.99        19.99        18.05        19.96        12.00        37.05 
TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T 
        9.99        31.00        31.00         0.99        19.07        93.04 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 
       40.01        19.07        16.01        41.98        12.00         9.99 
TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09N 
        9.99         1.02        13.02        33.07        29.98         1.02 
TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X 
       25.02         8.98        19.04        15.02         0.99        14.01 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0AB TCGA-A8-A0AD 
       12.00        19.04        13.02        21.04        17.03        38.04 
TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB 
        0.95         2.66         1.48        38.53        38.20        40.57 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A2QI 
       55.43        36.99        38.79        26.04         1.02         0.92 
TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 
        2.27         0.99         0.69         9.40         1.12         1.81 
TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X 
        1.68         1.55         1.32         1.55         0.07         1.12 
TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 
        1.18         0.43         0.33         0.23         0.33         0.62 
TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR 
        2.96         1.71         8.02         6.51         0.16         0.33 
TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FL 
        0.33         0.33         6.44         4.64         7.96         7.59 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FY TCGA-AN-A0FZ 
        7.17         6.28         6.02         0.33         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT 
        0.33        12.33         0.30         0.33         0.33         0.33 
TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P 
        0.33         5.33        47.84        66.77        81.63        84.69 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J4 
       68.75        47.87        59.05        29.13        21.40        17.65 
TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB 
       24.16        37.48        22.36        53.03        21.53        50.70 
TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI 
       50.86        72.00        76.77        21.37        26.24        38.53 
TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12E 
       62.04        71.80        99.25        93.70        96.10        57.30 
TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ 
       48.36        41.62        28.37        14.73        82.62        61.87 
TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 
       70.39        17.79        24.79        26.93       130.09         5.65 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ 
       15.62        13.22         2.56         9.99        82.88        49.32 
TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX 
        5.26        37.41        56.88        29.75        24.30        64.83 
TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 
       55.86        76.14        70.16        83.87        76.18        55.36 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM 
       75.55        61.84        52.77        51.25        48.82        62.56 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS 
       43.73        43.56        39.98        43.07        17.23        40.83 
TCGA-AR-A1AU TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       46.32        20.22       109.58        73.02        65.46        68.19 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T 
       65.69         0.85        66.05        57.40        62.07        53.26 
TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 
       53.36        48.16        51.75        56.15        45.17        40.64 
TCGA-AR-A254 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM 
       39.85       128.65        20.25        42.87         7.36        40.04 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       17.10        20.81        16.04        20.45        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC 
      143.38       149.59        12.13       220.90       129.57        50.70 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO 
       65.72       146.50        18.77       126.12        84.59       110.14 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
      110.93       140.88       211.56        68.45       189.01       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ 
       81.17        78.02       172.96       162.05       102.77       140.48 
TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV 
      100.70        89.46       157.41        97.48       188.68        79.63 
TCGA-B6-A0WW TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
       17.98       129.70       186.48        28.27        68.94        58.88 
TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B 
      101.52       139.17       170.17        54.28        49.94        82.88 
TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 
       55.00        38.79        20.45        25.55        28.50        46.95 
TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 
       40.83        39.55        39.16        48.36        56.98        51.68 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BM 
       32.02        18.21        25.71        24.85        44.05        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT 
       35.67        48.69        27.19        53.69        53.95        45.57 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C3 TCGA-BH-A0DE TCGA-BH-A0DG 
       49.94        11.67        49.05        48.13        31.17        23.44 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DQ 
       38.01        22.13        13.91        48.23        15.65         3.22 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
        2.56        38.47        45.17        47.41        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EB 
       15.68        14.30         9.63        44.81        32.65        24.49 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       31.00        24.43        10.78        15.16        37.78        35.51 
TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI 
       24.56        23.08        41.00        52.96        26.50        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX 
        5.85         2.50        13.61        12.89        51.32        27.25 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       50.79         5.59        23.93        24.95        42.35        44.81 
TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18L 
       23.05         8.81         2.01         7.23        20.12        26.66 
TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A1EN 
       72.56        30.28        37.55        66.05        51.39        69.93 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX 
      113.82        82.85        42.28        12.00        55.69        49.58 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 
       17.69        25.81        31.53        89.16        97.48        24.66 
TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH 
      120.62       114.15        33.17        74.73       122.89        36.92 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU 
       63.35        55.00        45.63        72.07       144.59        72.07 
TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A28O 
        6.90         0.72        38.60        83.31       130.16        10.65 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12M 
        6.44        20.12         0.99       109.28         8.94        11.77 
TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12W 
       11.77        12.66        11.77         0.07        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 
       12.66         1.78         1.45         0.69         0.62         3.85 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ 
        3.75        12.33        10.92        11.34        11.34         0.16 
TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X 
       12.03        10.42         3.25         0.30         0.23         0.36 
TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A278 TCGA-C8-A27A 
        0.43         8.28         9.67         0.03         0.03        12.20 
TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 
        0.99         0.03         0.23        11.90        13.25        20.58 
TCGA-D8-A142 TCGA-D8-A146 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC 
       13.97        21.14        17.49        16.50        18.71        15.78 
TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK 
       18.15        18.90        12.03        18.97        20.09        20.12 
TCGA-D8-A1JM TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 
       19.40        21.01        12.20        13.32        14.70        18.58 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC 
       16.73        25.74        23.90        27.58        18.15         2.66 
TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM 
       17.16        15.22        14.73        14.50        19.92        17.69 
TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV 
        7.96        16.41        15.85        16.31         6.35        15.16 
TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 
       12.66        16.54        15.32        15.52         3.81        14.24 
TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I 
       14.14        17.42        16.04        13.45        13.05        14.43 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A3Z5 
        9.44        16.41        13.48         0.76        13.08        14.50 
TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 
       18.51         7.33        43.00        34.42        27.52        46.59 
TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14P 
       40.41        40.11        28.44        28.87        44.68        40.96 
TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W 
       38.24        33.17        33.30        43.33        34.26        32.02 
TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 
       27.12        19.43        21.04        23.87        14.79        25.05 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G 
       23.34        22.82        17.29        20.71        21.63        18.21 
TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15O 
       12.92        17.42        19.40         9.04        20.58        13.02 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 
       19.56        17.06        14.07        14.99        60.53        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD 
       53.03        29.95        32.35        28.50        16.47        17.10 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK 
       38.30        37.41        32.78        33.73        28.44        22.65 
TCGA-E2-A1IL TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 
        3.88        20.98        11.08        54.18        27.42        39.62 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK 
       19.66        24.59        40.47       106.75       102.61         8.75 
TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
       43.04        16.93         5.52        15.72         7.20        18.05 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1NC 
       22.26        19.89        19.20        36.82        13.48        39.55 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 
       12.59        35.77        21.57         9.86        11.90        14.30 
TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RB 
        0.62         2.10         6.12         1.38        21.21        20.81 
TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI 
       40.24        34.65         6.58        21.27        34.59        35.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       34.13         0.79        12.53        13.32        39.09        22.75 
TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A24A 
       23.51        24.10         0.85        27.22         1.94        12.56 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A54Y 
       17.75         0.76        26.07        18.41        15.72         0.23 
TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
        0.23        15.39        12.20        39.72         8.48        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OW 
       18.90        13.25        16.57        15.68        25.94        22.82 
TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 
       29.95        29.85        40.41        41.13        39.78        52.96 
TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PC TCGA-EW-A1PE 
       23.11        18.48        30.08        18.90         6.15        10.52 
TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV 
       14.43        34.55        19.96        55.00        52.73        25.91 
TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GM-A2D9 
       22.09        21.27        17.49        10.59         7.40        59.57 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI 
      194.27        53.13        53.52        42.71        42.28        61.91 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
       62.33        90.84        76.64        77.33        53.36       110.50 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV 
       38.20        32.28        69.30        53.95        57.63        13.55 
TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LL-A440 
       18.12        11.84        11.57         8.28         6.67         0.66 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YO 
        2.99         3.58         6.90         5.56         4.70         3.19 
TCGA-LL-A6FR TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LQ-A4E4 
        3.88         4.50         4.50         5.59         3.22        15.91 
TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA 
        2.79         2.10        12.66        46.55         7.53        44.61 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 
       27.65        24.10        16.87        14.10        10.29         9.80 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       14.76        23.70        54.51        33.90        31.07        18.21 
TCGA-OL-A66O TCGA-OL-A66P 
        7.23         4.44 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.03               0.03 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            176.98             234.28 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            21.765             21.320 
[1] "0.0 - 177.0 (21.8)" "0.0 - 234.3 (21.3)"
[1] "hr=" "1"  
D34V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19P GAIN MUTATED        13       10        0        2        74        34
  19P GAIN WILD-TYPE      67       67        9        7       261       190
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19P GAIN MUTATED           0         22          4          9        0
  19P GAIN WILD-TYPE         2        116         23         50       17
                    vv
clus                 STAGE TIS STAGE X
  19P GAIN MUTATED           0       2
  19P GAIN WILD-TYPE         1      14
D34V3, multiclass
            clus
vv           19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                  13                 67
  STAGE IA                 10                 67
  STAGE IB                  0                  9
  STAGE II                  2                  7
  STAGE IIA                74                261
  STAGE IIB                34                190
  STAGE III                 0                  2
  STAGE IIIA               22                116
  STAGE IIIB                4                 23
  STAGE IIIC                9                 50
  STAGE IV                  0                 17
  STAGE TIS                 0                  1
  STAGE X                   2                 14
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  19P GAIN MUTATED    34 111  20   5
  19P GAIN WILD-TYPE 224 470  97  31
D34V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1               34                224
  T2              111                470
  T3               20                 97
  T4                5                 31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  19P GAIN MUTATED    94  50  17   9
  19P GAIN WILD-TYPE 374 280  94  61
D34V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0               94                374
  N1               50                280
  N2               17                 94
  N3                9                 61
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  19P GAIN MUTATED          0 151   0  19
  19P GAIN WILD-TYPE        2 694  17 112
D34V6, multiclass
          clus
vv         19P GAIN MUTATED 19P GAIN WILD-TYPE
  CM0 (I+)                0                  2
  M0                    151                694
  M1                      0                 17
  MX                     19                112
[1] 4 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   166   4
  19P GAIN WILD-TYPE 818   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED    166    4
  19P GAIN WILD-TYPE  818    7
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE              166                818
  MALE                  4                  7
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  19P GAIN MUTATED                            1                           128
  19P GAIN WILD-TYPE                          0                           607
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  19P GAIN MUTATED                               23                   2
  19P GAIN WILD-TYPE                            143                   3
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  19P GAIN MUTATED                                  4                  2
  19P GAIN WILD-TYPE                               25                 12
                    vv
clus                 OTHER  SPECIFY
  19P GAIN MUTATED               10
  19P GAIN WILD-TYPE             34
D34V8, multiclass
                                  clus
vv                                 19P GAIN MUTATED 19P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      1                  0
  INFILTRATING DUCTAL CARCINOMA                 128                607
  INFILTRATING LOBULAR CARCINOMA                 23                143
  MEDULLARY CARCINOMA                             2                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)                4                 25
  MUCINOUS CARCINOMA                              2                 12
  OTHER  SPECIFY                                 10                 34
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V9, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    55 115
  19P GAIN WILD-TYPE 227 598
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     55  115
  19P GAIN WILD-TYPE  227  598
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                55                227
  YES              115                598
[1] 2 2
[1] FALSE
D34V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P GAIN MUTATED                                  0     8
  19P GAIN WILD-TYPE                                1    48
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED                          24   128
  19P GAIN WILD-TYPE                       113   580
D34V11, multiclass
                                  clus
vv                                 19P GAIN MUTATED 19P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           8                 48
  BLACK OR AFRICAN AMERICAN                      24                113
  WHITE                                         128                580
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V12, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     6 139
  19P GAIN WILD-TYPE  30 657
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      6  139
  19P GAIN WILD-TYPE   30  657
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                 30
  NOT HISPANIC OR LATINO              139                657
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED   176  23
  19Q GAIN WILD-TYPE 684  91
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               199                775 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                23                 91 
$`19Q GAIN MUTATED`
TCGA-A1-A0SF TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A0CT 
       48.10        13.68        31.79        18.02        41.95        75.25 
TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0D4 TCGA-A2-A0EQ TCGA-A2-A0ET TCGA-A2-A0EU 
       21.14        33.76        25.22        79.76        35.05        34.29 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0SX TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T6 
       24.72        24.16        50.43         8.38        18.71        18.90 
TCGA-A2-A0YH TCGA-A2-A1G0 TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3Y0 TCGA-A2-A4S2 
       21.67        20.25        33.93        29.98        38.37         6.74 
TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A26E TCGA-A7-A26I 
       38.30        30.61        33.11        31.73        31.36        21.73 
TCGA-A7-A3J0 TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A07B 
       10.29        14.50        21.17        10.42        13.02        33.01 
TCGA-A8-A07R TCGA-A8-A08B TCGA-A8-A08X TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A09B 
        8.98        23.08        33.99        16.01        17.95        12.00 
TCGA-A8-A09E TCGA-A8-A09Q TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-AC-A23E TCGA-AC-A23G 
       31.00        25.02         0.99        13.02         2.37        10.85 
TCGA-AC-A2FO TCGA-AC-A3OD TCGA-AC-A62Y TCGA-AC-A6IW TCGA-AN-A03Y TCGA-AN-A04C 
       50.70        14.83         1.81         0.69         0.33         1.78 
TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0FK TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY 
        7.36         0.16         7.00         0.36         0.33         0.33 
TCGA-AN-A0XW TCGA-AO-A0J2 TCGA-AO-A0J7 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B 
        5.59        32.78        20.32        94.59        90.58        77.56 
TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A54N TCGA-AQ-A54O 
       64.04        48.36        70.39         0.53         2.56        21.86 
TCGA-AR-A0TQ TCGA-AR-A0TW TCGA-AR-A0U0 TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX 
       49.32        24.30        65.36        42.58        35.24        36.26 
TCGA-AR-A24K TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A255 
       50.89        54.18        50.96        51.75        56.15        34.82 
TCGA-AR-A256 TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-B6-A0IH TCGA-B6-A0IJ 
       93.83        16.96        20.38        54.74       112.37       176.98 
TCGA-B6-A0IO TCGA-B6-A0IQ TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WY TCGA-B6-A0WZ 
      110.14       140.88       100.70       131.21       113.79       129.57 
TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A401 TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0B3 
       43.59        73.51        85.35        24.53        20.45        39.55 
TCGA-BH-A0B6 TCGA-BH-A0BA TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0C1 
       56.94        37.22        24.85        21.70        44.05        44.02 
TCGA-BH-A0DD TCGA-BH-A0DO TCGA-BH-A0E9 TCGA-BH-A0GY TCGA-BH-A0HQ TCGA-BH-A18K 
       45.83        17.26        46.19        30.35        36.85        90.84 
TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EN 
       26.66        37.74        55.63         7.36        51.16        69.93 
TCGA-BH-A1EO TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A208 TCGA-C8-A12V TCGA-C8-A12W 
       91.99        12.00        55.69        57.83        12.66        12.66 
TCGA-C8-A130 TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26Z TCGA-C8-A274 
        3.12        12.03         2.30         3.25         8.28         0.03 
TCGA-C8-A275 TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 
        0.03        20.88        13.97        14.17        13.48        19.20 
TCGA-D8-A1J8 TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JL TCGA-D8-A1JN 
       14.17        12.03        12.03        14.01        20.09        20.38 
TCGA-D8-A1JU TCGA-D8-A1X6 TCGA-D8-A1XJ TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A27N 
       14.70        17.79        21.83        12.99        12.66         4.80 
TCGA-D8-A27R TCGA-D8-A27V TCGA-D8-A27W TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A14N 
       10.09        12.53        12.26        37.51        40.11        47.15 
TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 
       38.60        31.96        28.60        17.03        25.41        27.12 
TCGA-E2-A153 TCGA-E2-A15F TCGA-E2-A15M TCGA-E2-A1II TCGA-E2-A1IN TCGA-E2-A1LG 
       23.24        21.63         7.73        33.70        22.19        18.87 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RD TCGA-E9-A1RI 
       12.00        13.12         2.76        32.09         0.66        35.64 
TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A249 TCGA-E9-A295 TCGA-E9-A3QA TCGA-E9-A3X8 
       22.75        12.89         0.95         0.72         0.62        15.72 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-EW-A1J6 TCGA-EW-A1P4 TCGA-EW-A1P8 TCGA-EW-A1PD 
        0.39         0.26        28.77        29.82         7.86        13.94 
TCGA-EW-A1PH TCGA-EW-A423 TCGA-GM-A2DD TCGA-LD-A7W6 TCGA-LL-A5YP TCGA-LL-A6FQ 
       19.96        10.16        43.04         4.60         3.25         2.63 
TCGA-LL-A73Y TCGA-LL-A8F5 TCGA-MS-A51U TCGA-OL-A5RW TCGA-OL-A66I TCGA-S3-A6ZG 
        4.14         6.21         2.79        26.20        23.70         6.81 
TCGA-W8-A86G 
        5.29 

$`19Q GAIN WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI 
        8.52        14.37        43.43        14.27        47.24        20.88 
TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N 
        7.96        39.32        28.01        19.20        18.21       104.81 
TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X 
       82.16        73.84        22.06        63.12        64.04        55.43 
TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
       36.13       125.59        64.57        24.79       112.08        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW 
       88.60       107.93        75.55         5.19        63.45        64.04 
TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO 
       56.81        34.55        28.77       101.72        89.36        80.28 
TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0ST 
      107.61        74.40        37.05        31.82        29.75        99.19 
TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 
       54.64        27.12        44.88        44.28        17.52        17.13 
TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE 
       20.52        17.46        20.75        32.55        25.28        18.21 
TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL 
       15.42        21.90        14.50        18.61        19.33        14.63 
TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ 
       31.73        23.77        23.47        17.36        36.79        22.45 
TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B 
       19.20        19.56        16.47        52.47       107.70        16.31 
TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD 
       17.19        18.15        91.92        10.59        20.88        39.65 
TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ 
       83.01        14.07        49.48        38.40        34.98        31.99 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S3 
        7.30         9.01         8.81         8.91        12.00         3.42 
TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A13E 
       35.31        34.29        35.47        37.45        35.67        10.72 
TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H 
       12.72        23.61        29.56        24.26        23.74        23.80 
TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J1 TCGA-A7-A3RF 
       20.61        22.32        11.34        10.59        11.28        13.41 
TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SF TCGA-A7-A56D 
       14.70        11.97        14.93        13.74        17.92        14.73 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY 
       12.10        10.72        11.05        10.29         9.37         8.75 
TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X 
       13.02         1.02        17.98        41.06        29.03        31.00 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07E 
       26.01         1.02        17.03        53.98         9.01        19.99 
TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O 
       18.97        18.97        14.01        12.00        17.03         9.99 
TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 
       10.98         7.99         9.96         9.99        28.04        18.05 
TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08F 
       15.06        36.95        13.02         0.99        19.99        18.05 
TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P 
       19.96        12.00        37.05         9.99        31.00        31.00 
TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A095 
        0.99        19.07        93.04        40.01        19.07        41.98 
TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09I 
       12.00         9.99         9.99         1.02        13.02        33.07 
TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       29.98        15.02         1.02         8.98        19.04        15.02 
TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 
        0.99        14.01        12.00        19.04        13.02        21.04 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK 
       17.03        38.04         0.95         2.66         1.48        38.53 
TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM 
       38.20        40.57        55.43        36.99        38.79        26.04 
TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3QP 
        1.02         0.92         2.27         0.99         0.69         9.40 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS 
        1.12         1.81         1.68         1.55         1.32         1.55 
TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AN-A03X 
        0.07         1.12         1.18         0.43         1.74         0.33 
TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ 
        0.23         0.33         0.62         2.96         1.71         8.02 
TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF 
        6.51         0.33         0.33         0.33         6.44         4.64 
TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV 
        7.96         7.59         7.17         6.28         6.02         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR 
        0.33         0.33         0.33        12.33         0.30         0.33 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AO-A03L TCGA-AO-A03M 
        0.33         0.33         0.33         5.33        80.28        47.84 
TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U 
       66.77        81.63        84.69        68.75        47.87        59.05 
TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 
       29.13        21.40        17.65        24.16        37.48        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE 
       53.03        21.53        50.70        50.86        72.00        76.77 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM 
       21.37        26.24        38.53        62.04        55.33        71.80 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12E TCGA-AO-A12G 
      102.58        99.25        93.70        96.10        57.30        41.62 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KT TCGA-AQ-A04H 
       28.37        14.73        82.62        61.87        17.79        24.79 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A7U7 
       26.93       130.09         5.65        15.62        13.22         9.99 
TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TX 
       82.88         5.26        37.41        56.88        29.75        64.83 
TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 
       55.86        76.14        70.16        83.87        76.18        55.36 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM 
       75.55        61.84        52.77        51.25        48.82        62.56 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS 
       43.73        43.56        39.98        43.07        17.23        40.83 
TCGA-AR-A1AU TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       46.32        20.22       109.58        73.02        65.46        68.19 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T 
       65.69         0.85        66.05        57.40        62.07        53.26 
TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A2LE 
       53.36        48.16        45.17        40.64        39.85       128.65 
TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       20.25        42.87         7.36        40.04        17.10        20.81 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 
       16.04        20.45        10.59        77.62       143.38       149.59 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG 
       12.13       220.90       129.57        50.70        65.72       146.50 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0RE TCGA-B6-A0RG 
       18.77       126.12        84.59       110.93       211.56        68.45 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
      189.01       234.28        81.17        78.02       172.96       162.05 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT 
      102.77       140.48        89.46       157.41        97.48       188.68 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
       79.63        17.98        21.47       129.70       186.48        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A402 
       68.94        58.88       101.52       139.17       170.17        54.28 
TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0AZ 
       49.94        82.88        55.00        38.79        25.55        28.50 
TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 
       46.95        40.83        39.16        48.36        56.98        51.68 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP 
       32.02        18.21        25.71        61.68        35.67        48.69 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW 
       27.19        53.69        53.95        45.57        49.94        11.67 
TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DG 
       49.05        41.75        48.13        42.90        31.17        23.44 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DQ 
       38.01        22.13        13.91        48.23        15.65         3.22 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
        2.56        38.47        45.17        47.41        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EB 
       15.68        14.30         9.63        44.81        32.65        24.49 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       31.00        24.43        10.78        15.16        37.78        35.51 
TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI 
       24.56        23.08        41.00        52.96        26.50        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX 
        5.85         2.50        13.61        12.89        51.32        27.25 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       50.79         5.59        23.93        24.95        42.35        44.81 
TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18M 
       23.05         8.81         2.01         7.23        20.12        72.56 
TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A1ES TCGA-BH-A1ET 
       30.28        37.55        66.05        51.39       113.82        82.85 
TCGA-BH-A1EU TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 
       42.28        49.58        17.69        25.81        31.53        89.16 
TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE 
       97.48        24.66       120.62       114.15        33.17        74.73 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN 
      122.89        36.92        63.35        55.00        45.63        72.07 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 
      144.59        72.07         6.90         0.72        38.60        83.31 
TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
      130.16        10.65         6.44        20.12         0.99       109.28 
TCGA-BH-A42V TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P 
        8.94        11.93        11.77        11.77        12.66        11.77 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12X TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 
        0.07        12.66        12.66         1.78         1.45         0.69 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG 
        0.62         3.85         3.75        12.33        10.92        11.34 
TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X 
       11.34         0.16        10.42         0.30         0.23         0.36 
TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 
        0.43         9.67         0.03        12.20         0.99         0.03 
TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A146 TCGA-D8-A1J9 
        0.23        11.90        13.25        20.58        21.14        17.49 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JI 
       16.50        18.71        15.78        18.15        18.90        18.97 
TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JM TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT 
       20.09        20.12        19.40        21.01        12.20        13.32 
TCGA-D8-A1X5 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB 
       18.58        16.73        25.74        23.90        27.58        18.15 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XL 
        2.66        17.16        15.22        14.73        14.50        19.92 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT 
       17.69         7.96        16.41        15.85        16.31         6.35 
TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 
       15.16        16.54        15.32        15.52         3.81        14.24 
TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I 
       14.14        17.42        16.04        13.45        13.05        14.43 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A3Z5 
        9.44        16.41        13.48         0.76        13.08        14.50 
TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 
       18.51         7.33        43.00        34.42        27.52        46.59 
TCGA-E2-A10A TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q 
       40.41        28.44        28.87        44.68        40.96        38.24 
TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A154 
       33.17        33.30        43.33        34.26        32.02        19.43 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C 
       21.04        23.87        14.79        25.05        23.34        22.82 
TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J 
       17.29        20.71        18.21        12.92        17.42        19.40 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
        9.04        20.58        13.02        19.56        17.06        14.07 
TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       14.99        60.53        53.62        53.03        29.95        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       28.50        16.47        17.10        38.30        37.41        32.78 
TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IO TCGA-E2-A1IU 
       33.73        28.44        22.65         3.88        20.98        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB 
       54.18        27.42        39.62        19.66        24.59        40.47 
TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 
       28.90       106.75       102.61         8.75        43.04        16.93 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 
        5.52        15.72         7.20        18.05        22.26        19.89 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND 
       19.20        36.82        13.48        36.56        39.55        12.59 
TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 
       35.77        20.05        21.57         9.86        11.90        14.30 
TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RB 
        0.62         2.10         6.12         1.38        21.21        20.81 
TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A226 
       40.24        34.65         6.58        21.27        34.59        34.13 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22G TCGA-E9-A22H 
        0.79        12.53        13.32        39.09        23.51        24.10 
TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A24A 
       17.06         0.69         0.85        27.22         1.94        12.56 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A54Y TCGA-E9-A5UO 
       17.75         0.76        26.07        18.41         0.23         0.23 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 
       15.39        12.20        39.72         8.48        18.21        18.90 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX 
       13.25        16.57        15.68        25.94        22.82        29.95 
TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P5 
       29.85        40.41        41.13        39.78        52.96        23.11 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PE 
       18.48        30.08        18.90        19.99         6.15        10.52 
TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW 
       14.43        34.55        55.00        52.73        25.91        22.09 
TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 
       21.27        17.49        10.59         7.40       109.87        59.57 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI 
      194.27        53.13        53.52        42.71        42.28        61.91 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
       62.33        90.84        76.64        77.33        53.36       110.50 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV 
       38.20        32.28        69.30        53.95        57.63        13.55 
TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LL-A440 
       18.12        11.84        11.57         8.28         6.67         0.66 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN 
        2.99         3.58         6.90         5.56         4.70         3.65 
TCGA-LL-A5YO TCGA-LL-A6FR TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 
        3.19         3.88         4.50         4.50         5.59         3.22 
TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA 
       15.91         2.10        12.66        46.55         7.53        44.61 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 
       27.65        24.10        16.87        14.10        10.29         9.80 
TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O 
       14.76        54.51        33.90        31.07        18.21         7.23 
TCGA-OL-A66P 
        4.44 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.03               0.03 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            176.98             234.28 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             21.73              21.27 
[1] "0.0 - 177.0 (21.7)" "0.0 - 234.3 (21.3)"
[1] "hr=" "1.2"
D35V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19Q GAIN MUTATED        18       11        2        2        86        39
  19Q GAIN WILD-TYPE      62       66        7        7       249       185
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19Q GAIN MUTATED           0         26          6          8        1
  19Q GAIN WILD-TYPE         2        112         21         51       16
                    vv
clus                 STAGE TIS STAGE X
  19Q GAIN MUTATED           0       2
  19Q GAIN WILD-TYPE         1      14
D35V3, multiclass
            clus
vv           19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                  18                 62
  STAGE IA                 11                 66
  STAGE IB                  2                  7
  STAGE II                  2                  7
  STAGE IIA                86                249
  STAGE IIB                39                185
  STAGE III                 0                  2
  STAGE IIIA               26                112
  STAGE IIIB                6                 21
  STAGE IIIC                8                 51
  STAGE IV                  1                 16
  STAGE TIS                 0                  1
  STAGE X                   2                 14
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  19Q GAIN MUTATED    46 125  23   7
  19Q GAIN WILD-TYPE 212 456  94  29
D35V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1               46                212
  T2              125                456
  T3               23                 94
  T4                7                 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                  N0  N1  N2  N3
  19Q GAIN MUTATED   109  64  18   9
  19Q GAIN WILD-TYPE 359 266  93  61
D35V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0              109                359
  N1               64                266
  N2               18                 93
  N3                9                 61
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  19Q GAIN MUTATED          0 183   1  17
  19Q GAIN WILD-TYPE        2 662  16 114
D35V6, multiclass
          clus
vv         19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CM0 (I+)                0                  2
  M0                    183                662
  M1                      1                 16
  MX                     17                114
[1] 4 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   197   4
  19Q GAIN WILD-TYPE 787   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED    197    4
  19Q GAIN WILD-TYPE  787    7
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE              197                787
  MALE                  4                  7
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  19Q GAIN MUTATED                            0                           159
  19Q GAIN WILD-TYPE                          1                           576
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  19Q GAIN MUTATED                               26                   2
  19Q GAIN WILD-TYPE                            140                   3
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  19Q GAIN MUTATED                                  4                  2
  19Q GAIN WILD-TYPE                               25                 12
                    vv
clus                 OTHER  SPECIFY
  19Q GAIN MUTATED                8
  19Q GAIN WILD-TYPE             36
D35V8, multiclass
                                  clus
vv                                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 159                576
  INFILTRATING LOBULAR CARCINOMA                 26                140
  MEDULLARY CARCINOMA                             2                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)                4                 25
  MUCINOUS CARCINOMA                              2                 12
  OTHER  SPECIFY                                  8                 36
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V9, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    62 139
  19Q GAIN WILD-TYPE 220 574
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     62  139
  19Q GAIN WILD-TYPE  220  574
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                62                220
  YES              139                574
[1] 2 2
[1] FALSE
D35V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q GAIN MUTATED                                  0    11
  19Q GAIN WILD-TYPE                                1    45
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED                          27   151
  19Q GAIN WILD-TYPE                       110   557
D35V11, multiclass
                                  clus
vv                                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          11                 45
  BLACK OR AFRICAN AMERICAN                      27                110
  WHITE                                         151                557
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V12, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     8 163
  19Q GAIN WILD-TYPE  28 633
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      8  163
  19Q GAIN WILD-TYPE   28  633
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    8                 28
  NOT HISPANIC OR LATINO              163                633
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED   330  47
  20P GAIN WILD-TYPE 530  67
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               377                597 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                47                 67 
$`20P GAIN MUTATED`
TCGA-A1-A0SD TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM 
       14.37        48.10        14.27        20.88        13.68         7.96 
TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A2-A04P TCGA-A2-A04X TCGA-A2-A0CL TCGA-A2-A0CM 
       39.32        19.20        18.02        55.43        64.57        24.79 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D0 
       75.55        75.25         5.19        63.45        56.81        21.14 
TCGA-A2-A0D2 TCGA-A2-A0D4 TCGA-A2-A0EQ TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV 
       33.76        25.22        79.76        35.05        34.29        31.82 
TCGA-A2-A0EY TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0T2 TCGA-A2-A0T7 
       24.16        27.12        44.88        50.43         8.38        20.75 
TCGA-A2-A0YD TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YJ TCGA-A2-A0YT TCGA-A2-A1FW 
       25.28        21.90        21.67        18.61        23.77        17.36 
TCGA-A2-A1FX TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A3KC TCGA-A2-A3XS TCGA-A2-A3XT 
       36.79        20.25        19.20        20.88        33.93        83.01 
TCGA-A2-A4RX TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA 
        9.01         6.74        38.30        30.61        37.45        35.67 
TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A26G TCGA-A7-A26J 
       33.11        31.73        10.72        12.72        23.74        20.61 
TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SD TCGA-A7-A56D TCGA-A7-A6VV TCGA-A7-A6VW 
       14.70        14.93        14.50        14.73        10.29         9.37 
TCGA-A8-A06O TCGA-A8-A06R TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A076 
       13.02        17.98        29.03        26.01        17.03        53.98 
TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A086 
       10.98         8.98         9.96         9.99        28.04        13.02 
TCGA-A8-A08B TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S 
       23.08        12.00        37.05        31.00         0.99        19.07 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E 
       16.01        17.95        41.98         1.02        13.02        31.00 
TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A0A1 TCGA-A8-A0A7 
       33.07        29.98         1.02         8.98        12.00         0.99 
TCGA-A8-A0A9 TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2BM TCGA-AC-A2FM TCGA-AC-A2QH 
       13.02        10.85         2.66        38.20        26.04         1.02 
TCGA-AC-A2QJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IW TCGA-AC-A8OP 
        2.27         1.55         0.07         1.81         0.69         1.74 
TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A0AJ TCGA-AN-A0AS 
        0.33         0.33         2.96         1.78         8.02         0.33 
TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XO TCGA-AN-A0XP 
        0.33         0.36         0.33         0.33        12.33         0.30 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03V 
       80.28        47.84        66.77        81.63        84.69        29.13 
TCGA-AO-A0J4 TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JI 
       17.65        20.32        53.03        72.00        76.77        38.53 
TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E 
       55.33        71.80        94.59        90.58        77.56        57.30 
TCGA-AO-A12F TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AQ-A1H2 TCGA-AQ-A54O 
       48.36        82.62        61.87         0.53        15.62        21.86 
TCGA-AQ-A7U7 TCGA-AR-A0TQ TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX 
        9.99        49.32        56.88        29.75        24.30        64.83 
TCGA-AR-A0U0 TCGA-AR-A0U2 TCGA-AR-A1AI TCGA-AR-A1AP TCGA-AR-A1AV TCGA-AR-A1AW 
       65.36        83.87        61.84        39.98        42.58        35.24 
TCGA-AR-A24H TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24V TCGA-AR-A24W 
      109.58        66.05        57.40        62.07        54.18        50.96 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
       51.75        56.15        40.64        39.85        34.82        93.83 
TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A5QM TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 
       42.87         7.36        54.74        77.62       143.38       149.59 
TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IO TCGA-B6-A0RE TCGA-B6-A0RH 
      129.57        65.72       112.37       110.14       211.56       189.01 
TCGA-B6-A0RO TCGA-B6-A0RU TCGA-B6-A0WV TCGA-B6-A0WY TCGA-B6-A1KC TCGA-B6-A1KI 
      162.05       131.21        79.63       113.79        43.59        73.51 
TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-BH-A0AU TCGA-BH-A0AW 
       85.35        54.28        49.94        82.88        24.53        20.45 
TCGA-BH-A0B2 TCGA-BH-A0B6 TCGA-BH-A0BA TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BL 
       40.83        56.94        37.22        25.71        24.85        44.05 
TCGA-BH-A0BP TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0DD 
       48.69        45.57        49.94        49.05        44.02        45.83 
TCGA-BH-A0DG TCGA-BH-A0DL TCGA-BH-A0E0 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E9 
       23.44        48.23         4.41        14.30         9.63        46.19 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HB 
       31.00        24.43        30.35        23.08        41.00        26.50 
TCGA-BH-A0HI TCGA-BH-A0HQ TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W5 
       20.38        36.85        27.25        50.79         5.59        42.35 
TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18K TCGA-BH-A18N TCGA-BH-A18Q TCGA-BH-A18T 
       44.81        23.05        90.84        37.74        55.63         7.36 
TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW 
       51.39        69.93        91.99        42.28        12.00        55.69 
TCGA-BH-A1EX TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FH TCGA-BH-A1FN 
       49.58        31.53        97.48        24.66        36.92        72.07 
TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A28Q TCGA-C8-A12L TCGA-C8-A12O TCGA-C8-A12P 
        0.72        38.60         6.44        11.93        12.66        11.77 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A130 TCGA-C8-A131 
        0.07        12.66        12.66        12.66         3.12         1.78 
TCGA-C8-A132 TCGA-C8-A138 TCGA-C8-A1HI TCGA-C8-A1HM TCGA-C8-A26Z TCGA-C8-A274 
        1.45         3.75        11.34         2.30         8.28         0.03 
TCGA-C8-A278 TCGA-C8-A3M8 TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 
        0.03         0.23        20.88        13.97        14.17        13.48 
TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD 
       21.14        19.20        14.17        18.71        15.78        18.15 
TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JP 
       18.90        12.03        12.03        14.01        18.97        21.01 
TCGA-D8-A1JT TCGA-D8-A1X5 TCGA-D8-A1XB TCGA-D8-A1XF TCGA-D8-A1XL TCGA-D8-A1XS 
       13.32        18.58        18.15        15.22        19.92        16.31 
TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       12.99        12.66        16.54        15.32        15.52         3.81 
TCGA-D8-A27I TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27W TCGA-E2-A10B TCGA-E2-A10C 
       14.43        16.41        13.48        12.26        37.51        40.11 
TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14T TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A14Z 
       44.68        40.96        33.30        34.26        31.96        17.03 
TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A159 TCGA-E2-A15C 
       25.41        27.12        23.24        19.43        25.05        22.82 
TCGA-E2-A15H TCGA-E2-A15K TCGA-E2-A15O TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1BD 
       12.92         9.04        13.02        60.53        53.62        17.10 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A1L9 
       33.73        33.70        22.19        20.98        27.42        19.66 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A574 
      106.75       102.61         8.75         7.20        18.05        19.89 
TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF 
       13.48        12.00        13.12        12.59        35.77        20.05 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1RA 
        9.86        11.90         2.10         6.12         1.38        32.09 
TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A226 
       20.81        40.24         6.58        21.27        34.59        34.13 
TCGA-E9-A229 TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 
       13.32        22.75        12.89        27.22         1.94         0.95 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-EW-A1IY 
        0.72        17.75         0.23         0.39         0.26         8.48 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P5 
       16.57        15.68        28.77        29.85        41.13        23.11 
TCGA-EW-A1P6 TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PH TCGA-EW-A2FS 
       18.48        19.99         6.15        13.94        19.96        52.73 
TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DH TCGA-GM-A3XL TCGA-LD-A66U TCGA-LL-A441 
       53.52        43.04        42.28        69.30         8.28         2.99 
TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A6FQ TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LQ-A4E4 
        4.70         3.65         2.63         4.50         5.59        15.91 
TCGA-OL-A5RZ TCGA-OL-A66I TCGA-OL-A66N TCGA-S3-A6ZG TCGA-W8-A86G 
       10.29        23.70        18.21         6.81         5.29 

$`20P GAIN WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SE TCGA-A1-A0SH TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A1-A0SQ 
        8.52        43.43        47.24        31.79        28.01        18.21 
TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V 
      104.81        41.95        82.16        73.84        22.06        63.12 
TCGA-A2-A04W TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
       64.04        36.13       125.59       112.08        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CW TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN 
      107.93        64.04        34.55        28.77       101.72        89.36 
TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EW TCGA-A2-A0EX 
       80.28       107.61        74.40        37.05        29.75        24.72 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T3 
       99.19        54.64        44.28        17.52        17.13        18.71 
TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YE TCGA-A2-A0YF 
       20.52        17.46        18.90        32.55        18.21        15.42 
TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FZ 
       14.50        19.33        14.63        31.73        23.47        22.45 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C 
       19.56        16.47        52.47       107.70        16.31        17.19 
TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KD TCGA-A2-A3XU TCGA-A2-A3XV 
       18.15        91.92        10.59        39.65        29.98        14.07 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW 
       49.48        38.40        34.98        31.99        38.37         7.30 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG 
        8.81         8.91        12.00         3.42        35.31        34.29 
TCGA-A7-A0CH TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H 
       35.47        23.61        29.56        31.36        24.26        23.80 
TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       21.73        22.32        11.34        10.59        10.29        11.28 
TCGA-A7-A3RF TCGA-A7-A426 TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A5ZV 
       13.41        11.97        13.74        21.17        17.92        12.10 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q 
       10.72        11.05        10.42         8.75        13.02         1.02 
TCGA-A8-A06T TCGA-A8-A06X TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E 
       41.06        31.00         1.02         9.01        33.01        19.99 
TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O 
       18.97        18.97        14.01        12.00        17.03         9.99 
TCGA-A8-A07S TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A08A TCGA-A8-A08C 
        7.99        18.05        15.06        36.95         0.99        19.99 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08T TCGA-A8-A08X 
       18.05        19.96         9.99        31.00        93.04        33.99 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B 
       40.01        19.07        12.00         9.99         9.99        12.00 
TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X 
       15.02        25.02        19.04        15.02         0.99        14.01 
TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C 
       19.04        13.02        21.04        17.03        38.04         0.95 
TCGA-AC-A23E TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG 
        2.37         1.48        38.53        40.57        55.43        36.99 
TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD 
       38.79        50.70         0.92         0.99         0.69        14.83 
TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ 
        9.40         1.12         1.81         1.68         1.55         1.32 
TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 
        1.12         1.18         0.43         0.23         0.33         0.62 
TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AT 
        1.71         7.36         6.51         0.16         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN 
        6.44         4.64         7.96         7.00         7.59         7.17 
TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XN TCGA-AN-A0XR 
        6.28         6.02         0.33         0.33         0.33         0.33 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03R 
        0.33         0.33         0.33         5.33         5.59        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J6 
       47.87        59.05        32.78        21.40        24.16        37.48 
TCGA-AO-A0J8 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JF TCGA-AO-A0JG 
       22.36        21.53        50.70        50.86        21.37        26.24 
TCGA-AO-A0JJ TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12D 
       62.04       102.58        99.25        93.70        96.10        64.04 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H 
       41.62        28.37        14.73        70.39        17.79        24.79 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AR-A0TP 
       26.93       130.09         5.65        13.22         2.56        82.88 
TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U3 
        5.26        37.41        55.86        76.14        70.16        76.18 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM 
       55.36        75.55        52.77        51.25        48.82        62.56 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU 
       43.73        43.56        43.07        17.23        40.83        46.32 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       36.26        20.22        50.89        73.02        65.46        68.19 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A251 
       65.69         0.85        53.26        53.36        48.16        45.17 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
      128.65        20.25        40.04        17.10        20.81        16.96 
TCGA-AR-A2LR TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I9 TCGA-B6-A0IA 
       20.38        16.04        20.45        10.59        12.13       220.90 
TCGA-B6-A0IC TCGA-B6-A0IG TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
       50.70       146.50       176.98        18.77       126.12        84.59 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM 
      110.93       140.88        68.45       234.28        81.17        78.02 
TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RV 
      172.96       102.77       140.48       100.70        89.46       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 
       97.48       188.68        17.98        21.47       129.57       129.70 
TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KN 
      186.48        28.27        68.94        58.88       101.52       139.17 
TCGA-B6-A2IU TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 
      170.17        55.00        38.79        25.55        28.50        46.95 
TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC 
       39.55        39.16        48.36        56.98        51.68        32.02 
TCGA-BH-A0BD TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR 
       18.21        21.70        61.68        35.67        27.19        53.69 
TCGA-BH-A0BS TCGA-BH-A0BW TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DE 
       53.95        11.67        41.75        48.13        42.90        31.17 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ 
       38.01        22.13        13.91        17.26        15.65         3.22 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 
        2.56        38.47        45.17        47.41        16.27        15.68 
TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       44.81        32.65        24.49        10.78        15.16        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0HA TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       35.51        24.56        52.96         5.85         2.50        13.61 
TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A18F TCGA-BH-A18G 
       12.89        51.32        23.93        24.95         8.81         2.01 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18R 
        7.23        20.12        26.66        72.56        30.28        37.55 
TCGA-BH-A18S TCGA-BH-A18V TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EY TCGA-BH-A1F0 
       66.05        51.16       113.82        82.85        17.69        25.81 
TCGA-BH-A1F5 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG 
       89.16       120.62       114.15        33.17        74.73       122.89 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 
       63.35        55.00        45.63       144.59        72.07         6.90 
TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A2L8 TCGA-BH-A42T 
       83.31        57.83       130.16        10.65        20.12         0.99 
TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12X TCGA-C8-A134 
      109.28         8.94        11.77        11.77        12.66         0.69 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ 
        0.62         3.85        12.33        10.92        11.34         0.16 
TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X 
       12.03        10.42         3.25         0.30         0.23         0.36 
TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 
        0.43         9.67         0.03        12.20         0.99         0.03 
TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JJ 
       11.90        13.25        20.58        17.49        16.50        20.09 
TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1JU 
       20.12        20.09        19.40        20.38        12.20        14.70 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XC 
       17.79        16.73        25.74        23.90        27.58         2.66 
TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XM TCGA-D8-A1XO 
       17.16        14.73        21.83        14.50        17.69         7.96 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1Y2 TCGA-D8-A1Y3 
       16.41        15.85         6.35        15.16        14.24        14.14 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27K TCGA-D8-A27N 
       17.42        16.04        13.45        13.05         9.44         4.80 
TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 
        0.76        10.09        13.08        12.53        14.50        18.51 
TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A 
        7.33        43.00        34.42        27.52        46.59        40.41 
TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S 
       28.44        28.87        47.15        38.24        38.60        33.17 
TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 
       43.33        32.02        28.60        21.04        23.87        14.79 
TCGA-E2-A15A TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15I 
       23.34        17.29        20.71        21.63        18.21        17.42 
TCGA-E2-A15J TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
       19.40        20.58         7.73        19.56        17.06        14.07 
TCGA-E2-A15T TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC 
       14.99        53.03        29.95        32.35        28.50        16.47 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       38.30        37.41        32.78        28.44        22.65         3.88 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L8 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       11.08        54.18        39.62        24.59        40.47        28.90 
TCGA-E2-A1LG TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A573 
       18.87        43.04        16.93         5.52        15.72        22.26 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1NG TCGA-E9-A1R0 
       19.20        36.82        36.56        39.55        21.57        14.30 
TCGA-E9-A1R2 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RI 
        0.62         2.76        21.21         0.66        34.65        35.64 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A22A TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 
        0.79        12.53        39.09        23.51        24.10        17.06 
TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 
        0.69         0.85        12.56         0.76        26.07        18.41 
TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
        0.62        15.72         0.23        15.39        12.20        39.72 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX 
       18.21        18.90        13.25        25.94        22.82        29.95 
TCGA-EW-A1OZ TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P7 TCGA-EW-A1P8 
       40.41        39.78        52.96        29.82        30.08         7.86 
TCGA-EW-A1PA TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FR TCGA-EW-A2FV 
       18.90        10.52        14.43        34.55        55.00        25.91 
TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 
       22.09        21.27        17.49        10.16        10.59         7.40 
TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DF TCGA-GM-A2DI 
      109.87        59.57       194.27        53.13        42.71        61.91 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
       62.33        90.84        76.64        77.33        53.36       110.50 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX 
       38.20        32.28        53.95        57.63        13.55        18.12 
TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A442 
       11.84        11.57         6.67         4.60         0.66         3.58 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y 
        6.90         5.56         3.19         3.25         3.88         4.14 
TCGA-LL-A740 TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
        4.50         3.22         6.21         2.79         2.10        12.66 
TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW 
       46.55         7.53        44.61        27.65        24.10        26.20 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K 
       16.87        14.10         9.80        14.76        54.51        33.90 
TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P 
       31.07         7.23         4.44 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.03               0.03 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            211.56             234.28 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             21.86              21.37 
[1] "0.0 - 211.6 (21.9)" "0.0 - 234.3 (21.4)"
[1] "hr=" "1.3"
D36V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20P GAIN MUTATED        35       25        1        3       132        78
  20P GAIN WILD-TYPE      45       52        8        6       203       146
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20P GAIN MUTATED           1         64         11         17       10
  20P GAIN WILD-TYPE         1         74         16         42        7
                    vv
clus                 STAGE TIS STAGE X
  20P GAIN MUTATED           1       4
  20P GAIN WILD-TYPE         0      12
D36V3, multiclass
            clus
vv           20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                  35                 45
  STAGE IA                 25                 52
  STAGE IB                  1                  8
  STAGE II                  3                  6
  STAGE IIA               132                203
  STAGE IIB                78                146
  STAGE III                 1                  1
  STAGE IIIA               64                 74
  STAGE IIIB               11                 16
  STAGE IIIC               17                 42
  STAGE IV                 10                  7
  STAGE TIS                 1                  0
  STAGE X                   4                 12
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  20P GAIN MUTATED    96 229  40  16
  20P GAIN WILD-TYPE 162 352  77  20
D36V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1               96                162
  T2              229                352
  T3               40                 77
  T4               16                 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                  N0  N1  N2  N3
  20P GAIN MUTATED   179 119  58  21
  20P GAIN WILD-TYPE 289 211  53  49
D36V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0              179                289
  N1              119                211
  N2               58                 53
  N3               21                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  20P GAIN MUTATED          0 337  10  36
  20P GAIN WILD-TYPE        2 508   7  95
D36V6, multiclass
          clus
vv         20P GAIN MUTATED 20P GAIN WILD-TYPE
  CM0 (I+)                0                  2
  M0                    337                508
  M1                     10                  7
  MX                     36                 95
[1] 4 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   375   8
  20P GAIN WILD-TYPE 609   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    375    8
  20P GAIN WILD-TYPE  609    3
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE              375                609
  MALE                  8                  3
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  20P GAIN MUTATED                            0                           321
  20P GAIN WILD-TYPE                          1                           414
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  20P GAIN MUTATED                               37                   1
  20P GAIN WILD-TYPE                            129                   4
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  20P GAIN MUTATED                                  9                  1
  20P GAIN WILD-TYPE                               20                 13
                    vv
clus                 OTHER  SPECIFY
  20P GAIN MUTATED               13
  20P GAIN WILD-TYPE             31
D36V8, multiclass
                                  clus
vv                                 20P GAIN MUTATED 20P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 321                414
  INFILTRATING LOBULAR CARCINOMA                 37                129
  MEDULLARY CARCINOMA                             1                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                9                 20
  MUCINOUS CARCINOMA                              1                 13
  OTHER  SPECIFY                                 13                 31
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V9, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   125 258
  20P GAIN WILD-TYPE 157 455
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    125  258
  20P GAIN WILD-TYPE  157  455
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO               125                157
  YES              258                455
[1] 2 2
[1] FALSE
D36V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P GAIN MUTATED                                  0    21
  20P GAIN WILD-TYPE                                1    35
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED                          55   268
  20P GAIN WILD-TYPE                        82   440
D36V11, multiclass
                                  clus
vv                                 20P GAIN MUTATED 20P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          21                 35
  BLACK OR AFRICAN AMERICAN                      55                 82
  WHITE                                         268                440
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V12, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    11 308
  20P GAIN WILD-TYPE  25 488
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     11  308
  20P GAIN WILD-TYPE   25  488
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                   11                 25
  NOT HISPANIC OR LATINO              308                488
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED   360  50
  20Q GAIN WILD-TYPE 500  64
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               410                564 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                50                 64 
$`20Q GAIN MUTATED`
TCGA-A1-A0SD TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM 
       14.37        48.10        14.27        20.88        13.68         7.96 
TCGA-A1-A0SP TCGA-A2-A04P TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CL TCGA-A2-A0CM 
       19.20        18.02        64.04        55.43        64.57        24.79 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D0 
       75.55        75.25         5.19        63.45        56.81        21.14 
TCGA-A2-A0D2 TCGA-A2-A0D4 TCGA-A2-A0EQ TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV 
       33.76        25.22        79.76        35.05        34.29        31.82 
TCGA-A2-A0EY TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0T7 TCGA-A2-A0YD TCGA-A2-A0YE 
       24.16        44.88        50.43        20.75        25.28        18.21 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YJ TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX 
       21.90        21.67        18.61        23.77        17.36        36.79 
TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A25B TCGA-A2-A25E TCGA-A2-A3KC TCGA-A2-A3XS 
       20.25        19.20        16.31        91.92        20.88        33.93 
TCGA-A2-A3XT TCGA-A2-A3XX TCGA-A2-A4RX TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CJ 
       83.01        38.40         9.01         6.74        38.30        30.61 
TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A26G 
       37.45        33.11        31.73        10.72        12.72        23.74 
TCGA-A7-A26J TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF 
       20.61        14.70        14.93        14.50        21.17        17.92 
TCGA-A7-A56D TCGA-A7-A6VV TCGA-A8-A06O TCGA-A8-A06R TCGA-A8-A06U TCGA-A8-A06Y 
       14.73        10.29        13.02        17.98        29.03        26.01 
TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07U 
       17.03        53.98         9.01        10.98         8.98         9.96 
TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A086 TCGA-A8-A08B TCGA-A8-A08G TCGA-A8-A08I 
        9.99        28.04        13.02        23.08        19.96        12.00 
TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08X TCGA-A8-A092 
       37.05        31.00         0.99        19.07        33.99        16.01 
TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I 
       17.95        41.98         1.02        13.02        31.00        33.07 
TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A0A1 TCGA-A8-A0A7 
       29.98        15.02         1.02         8.98        12.00         0.99 
TCGA-A8-A0A9 TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2BM TCGA-AC-A2FM TCGA-AC-A2QH 
       13.02        10.85         2.66        38.20        26.04         1.02 
TCGA-AC-A2QJ TCGA-AC-A3W5 TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IW 
        2.27         1.81         1.55         0.07         1.81         0.69 
TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A04C TCGA-AN-A0AJ TCGA-AN-A0AM 
        1.74         0.33         0.33         1.78         8.02         0.16 
TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP 
        0.36         0.33         0.33         0.33        12.33         0.30 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03T TCGA-AO-A03V 
       80.28        47.84        66.77        81.63        47.87        29.13 
TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JI TCGA-AO-A0JL 
       20.32        53.03        72.00        76.77        38.53        55.33 
TCGA-AO-A0JM TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12F 
       71.80        94.59        90.58        77.56        57.30        48.36 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04L TCGA-AQ-A1H2 
       82.62        61.87        17.79        24.79       130.09        15.62 
TCGA-AQ-A7U7 TCGA-AR-A0TQ TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX 
        9.99        49.32        56.88        29.75        24.30        64.83 
TCGA-AR-A0TZ TCGA-AR-A0U2 TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AP TCGA-AR-A1AV 
       76.14        83.87        61.84        51.25        39.98        42.58 
TCGA-AR-A1AW TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S 
       35.24       109.58        73.02        66.05        57.40        62.07 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A255 
       54.18        50.96        51.75        56.15        40.64        34.82 
TCGA-AR-A256 TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LR TCGA-AR-A5QM TCGA-B6-A0I1 
       93.83        42.87         7.36        20.38        54.74        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0IH 
      143.38       149.59        12.13       129.57        65.72       112.37 
TCGA-B6-A0IJ TCGA-B6-A0IO TCGA-B6-A0RE TCGA-B6-A0RL TCGA-B6-A0RO TCGA-B6-A0RU 
      176.98       110.14       211.56        81.17       162.05       131.21 
TCGA-B6-A0WV TCGA-B6-A0WY TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN 
       79.63       113.79        43.59       101.52        73.51       139.17 
TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-BH-A0AU TCGA-BH-A0AW 
       85.35        54.28        49.94        82.88        24.53        20.45 
TCGA-BH-A0AY TCGA-BH-A0B6 TCGA-BH-A0BA TCGA-BH-A0BF TCGA-BH-A0BL TCGA-BH-A0BP 
       25.55        56.94        37.22        25.71        44.05        48.69 
TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0DG 
       45.57        49.94        49.05        44.02        45.83        23.44 
TCGA-BH-A0DL TCGA-BH-A0DQ TCGA-BH-A0E0 TCGA-BH-A0E2 TCGA-BH-A0E9 TCGA-BH-A0EE 
       48.23         3.22         4.41        14.30        46.19        31.00 
TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HB TCGA-BH-A0HI 
       24.43        30.35        23.08        41.00        26.50        20.38 
TCGA-BH-A0HQ TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W5 TCGA-BH-A0W7 
       36.85        27.25        50.79         5.59        42.35        44.81 
TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A18U 
       90.84        26.66        37.74        55.63         7.36        51.39 
TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX 
       69.93        91.99        42.28        12.00        55.69        49.58 
TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FH TCGA-BH-A1FM TCGA-BH-A1FN 
       31.53        97.48        24.66        36.92        45.63        72.07 
TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A28Q TCGA-C8-A12L TCGA-C8-A12O 
        0.72        38.60        57.83         6.44        11.93        12.66 
TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A130 
       11.77         0.07        12.66        12.66        12.66         3.12 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A138 TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HM 
        1.78         1.45         3.75        11.34        11.34         2.30 
TCGA-C8-A1HN TCGA-C8-A26Z TCGA-C8-A274 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A3M8 
        3.25         8.28         0.03         0.03        12.20         0.23 
TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 
       20.88        13.25        13.97        14.17        13.48        21.14 
TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE 
       19.20        14.17        18.71        15.78        18.15        18.90 
TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JP TCGA-D8-A1JT 
       12.03        12.03        14.01        18.97        21.01        13.32 
TCGA-D8-A1X5 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XF TCGA-D8-A1XL TCGA-D8-A1XQ 
       18.58        27.58        18.15        15.22        19.92        16.41 
TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 
       16.31        12.99        12.66        16.54        15.32        15.52 
TCGA-D8-A1Y1 TCGA-D8-A27I TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27R TCGA-D8-A27W 
        3.81        14.43        16.41        13.48        10.09        12.26 
TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14R TCGA-E2-A14S 
       37.51        40.11        44.68        40.96        38.60        33.17 
TCGA-E2-A14T TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 
       33.30        34.26        31.96        25.41        27.12        23.24 
TCGA-E2-A154 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15H TCGA-E2-A15K 
       19.43        25.05        23.34        22.82        12.92         9.04 
TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15R TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1BD 
        7.73        13.02        17.06        60.53        53.62        17.10 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A1L9 
       33.73        33.70        22.19        20.98        27.42        19.66 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 
      106.75       102.61         8.75         7.20        18.05        22.26 
TCGA-E2-A574 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NE 
       19.89        36.82        13.48        12.00        13.12        35.77 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 
        9.86        11.90         0.62         2.10         6.12         1.38 
TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RF 
        2.76        32.09        20.81        40.24        34.65         6.58 
TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A229 TCGA-E9-A22B TCGA-E9-A22E 
       21.27        34.59        34.13        13.32        22.75        12.89 
TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A295 TCGA-E9-A2JS 
        0.69        27.22         1.94         0.95         0.72        17.75 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-EW-A1IY TCGA-EW-A1J3 TCGA-EW-A1J5 
        0.23         0.39         0.26         8.48        16.57        15.68 
TCGA-EW-A1J6 TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P5 TCGA-EW-A1P6 
       28.77        29.85        40.41        41.13        23.11        18.48 
TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A2FS TCGA-EW-A423 TCGA-GI-A2C8 
       19.99         6.15        13.94        52.73        10.16         7.40 
TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A3XL TCGA-JL-A3YW 
       53.52        43.04        42.71        61.91        69.30        11.84 
TCGA-LD-A66U TCGA-LL-A441 TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A6FQ TCGA-LL-A73Y 
        8.28         2.99         4.70         3.65         2.63         4.14 
TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LQ-A4E4 TCGA-OL-A5RZ TCGA-OL-A66I TCGA-OL-A66N 
        5.59         3.22        15.91        10.29        23.70        18.21 
TCGA-S3-A6ZG TCGA-W8-A86G 
        6.81         5.29 

$`20Q GAIN WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SE TCGA-A1-A0SH TCGA-A1-A0SK TCGA-A1-A0SN TCGA-A1-A0SO 
        8.52        43.43        47.24        31.79        39.32        28.01 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U 
       18.21       104.81        41.95        82.16        73.84        22.06 
TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
       63.12        36.13       125.59       112.08        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CW TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN 
      107.93        64.04        34.55        28.77       101.72        89.36 
TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EW TCGA-A2-A0EX 
       80.28       107.61        74.40        37.05        29.75        24.72 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 
       99.19        54.64        27.12        44.28        17.52        17.13 
TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC 
        8.38        18.71        20.52        17.46        18.90        32.55 
TCGA-A2-A0YF TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV 
       15.42        14.50        19.33        14.63        31.73        23.47 
TCGA-A2-A1FZ TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25C 
       22.45        19.56        16.47        52.47       107.70        17.19 
TCGA-A2-A25D TCGA-A2-A25F TCGA-A2-A3KD TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW 
       18.15        10.59        39.65        29.98        14.07        49.48 
TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 
       34.98        31.99        38.37         7.30         8.81         8.91 
TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0DA 
       12.00         3.42        35.31        34.29        35.47        35.67 
TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26I 
       23.61        29.56        31.36        24.26        23.80        21.73 
TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF 
       22.32        11.34        10.59        10.29        11.28        13.41 
TCGA-A7-A426 TCGA-A7-A4SB TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VW 
       11.97        13.74        12.10        10.72        11.05         9.37 
TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06T TCGA-A8-A06X 
       10.42         8.75        13.02         1.02        41.06        31.00 
TCGA-A8-A06Z TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I 
        1.02        33.01        19.99        18.97        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07S TCGA-A8-A082 TCGA-A8-A084 
       12.00        17.03         9.99         7.99        18.05        15.06 
TCGA-A8-A085 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08L TCGA-A8-A08O 
       36.95         0.99        19.99        18.05         9.99        31.00 
TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A 
       93.04        40.01        19.07        12.00         9.99         9.99 
TCGA-A8-A09B TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X 
       12.00        25.02        19.04        15.02         0.99        14.01 
TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C 
       19.04        13.02        21.04        17.03        38.04         0.95 
TCGA-AC-A23E TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG 
        2.37         1.48        38.53        40.57        55.43        36.99 
TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD 
       38.79        50.70         0.92         0.99         0.69        14.83 
TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A62X 
        9.40         1.12         1.68         1.55         1.32         1.12 
TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A 
        1.18         0.43         0.23         0.33         0.62         2.96 
TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT 
        1.71         7.36         6.51         0.33         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN 
        6.44         4.64         7.96         7.00         7.59         7.17 
TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XR 
        6.28         6.02         0.33         0.33         0.33         0.33 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03P 
        0.33         0.33         0.33         5.33         5.59        84.69 
TCGA-AO-A03R TCGA-AO-A03U TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 
       68.75        59.05        32.78        21.40        17.65        24.16 
TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JF 
       37.48        22.36        21.53        50.70        50.86        21.37 
TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 
       26.24        62.04       102.58        99.25        93.70        96.10 
TCGA-AO-A12D TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KR TCGA-AO-A1KS 
       64.04        41.62        28.37        14.73        70.39         0.53 
TCGA-AQ-A04J TCGA-AQ-A0Y5 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0TP 
       26.93         5.65        13.22         2.56        21.86        82.88 
TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TY TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 
        5.26        37.41        55.86        65.36        70.16        76.18 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
       55.36        75.55        52.77        48.82        62.56        43.73 
TCGA-AR-A1AO TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AX 
       43.56        43.07        17.23        40.83        46.32        36.26 
TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
       20.22        50.89        65.46        68.19        65.69         0.85 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A2LE 
       53.26        53.36        48.16        45.17        39.85       128.65 
TCGA-AR-A2LH TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN 
       20.25        40.04        17.10        20.81        16.96        16.04 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IG TCGA-B6-A0IK 
       20.45        10.59       220.90        50.70       146.50        18.77 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RH 
      126.12        84.59       110.93       140.88        68.45       189.01 
TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS 
      234.28        78.02       172.96       102.77       140.48       100.70 
TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX 
       89.46       157.41        97.48       188.68        17.98        21.47 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      129.57       129.70       186.48        28.27        68.94        58.88 
TCGA-B6-A2IU TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 
      170.17        55.00        38.79        28.50        46.95        40.83 
TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC 
       39.55        39.16        48.36        56.98        51.68        32.02 
TCGA-BH-A0BD TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ 
       18.21        24.85        21.70        61.68        35.67        27.19 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BW TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 
       53.69        53.95        11.67        41.75        48.13        42.90 
TCGA-BH-A0DE TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DP 
       31.17        38.01        22.13        13.91        17.26        15.65 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 
        2.56        38.47        45.17        47.41        16.27        15.68 
TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0GZ TCGA-BH-A0H0 
        9.63        44.81        32.65        24.49        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0HA TCGA-BH-A0HK TCGA-BH-A0HO 
       37.78        35.51        24.56        52.96         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0WA 
       13.61        12.89        51.32        23.93        24.95        23.05 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18M TCGA-BH-A18P 
        8.81         2.01         7.23        20.12        72.56        30.28 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18V TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EY 
       37.55        66.05        51.16       113.82        82.85        17.69 
TCGA-BH-A1F0 TCGA-BH-A1F5 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE 
       25.81        89.16       120.62       114.15        33.17        74.73 
TCGA-BH-A1FG TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 
      122.89        63.35        55.00       144.59        72.07         6.90 
TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
       83.31       130.16        10.65        20.12         0.99       109.28 
TCGA-BH-A42V TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12X TCGA-C8-A134 TCGA-C8-A135 
        8.94        11.77        11.77        12.66         0.69         0.62 
TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL 
        3.85        12.33        10.92         0.16        12.03        10.42 
TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A275 
        0.30         0.23         0.36         0.43         9.67         0.03 
TCGA-C8-A27B TCGA-C8-A3M7 TCGA-D8-A13Y TCGA-D8-A141 TCGA-D8-A1J9 TCGA-D8-A1JA 
        0.99         0.03        11.90        20.58        17.49        16.50 
TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JS 
       20.09        20.12        20.09        19.40        20.38        12.20 
TCGA-D8-A1JU TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XC 
       14.70        17.79        16.73        25.74        23.90         2.66 
TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XM TCGA-D8-A1XO 
       17.16        14.73        21.83        14.50        17.69         7.96 
TCGA-D8-A1XR TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E 
       15.85         6.35        15.16        14.24        14.14        17.42 
TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27K TCGA-D8-A27N TCGA-D8-A27P 
       16.04        13.45        13.05         9.44         4.80         0.76 
TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 
       13.08        12.53        14.50        18.51         7.33        43.00 
TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10E TCGA-E2-A10F 
       34.42        27.52        46.59        40.41        28.44        28.87 
TCGA-E2-A14N TCGA-E2-A14Q TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A14Z 
       47.15        38.24        43.33        32.02        28.60        17.03 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F 
       21.04        23.87        14.79        17.29        20.71        21.63 
TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15L TCGA-E2-A15P TCGA-E2-A15S 
       18.21        17.42        19.40        20.58        19.56        14.07 
TCGA-E2-A15T TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC 
       14.99        53.03        29.95        32.35        28.50        16.47 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       38.30        37.41        32.78        28.44        22.65         3.88 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L8 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       11.08        54.18        39.62        24.59        40.47        28.90 
TCGA-E2-A1LG TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E9-A1N4 
       18.87        43.04        16.93         5.52        15.72        19.20 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1R0 
       36.56        39.55        12.59        20.05        21.57        14.30 
TCGA-E9-A1R7 TCGA-E9-A1RD TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A22A 
       21.21         0.66        35.64         0.79        12.53        39.09 
TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A245 TCGA-E9-A24A TCGA-E9-A2JT 
       23.51        24.10        17.06         0.85        12.56         0.76 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A5UO TCGA-E9-A6HE 
       26.07        18.41         0.62        15.72         0.23        15.39 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1OV 
       12.20        39.72        18.21        18.90        13.25        25.94 
TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P7 
       22.82        29.95        39.78        52.96        29.82        30.08 
TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH 
        7.86        18.90        10.52        14.43        34.55        19.96 
TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 
       55.00        25.91        22.09        21.27        17.49        10.59 
TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DH TCGA-GM-A2DK 
      109.87        59.57       194.27        53.13        42.28        62.33 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY 
       90.84        76.64        77.33        53.36       110.50        38.20 
TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YX 
       32.28        53.95        57.63        13.55        18.12        11.57 
TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL 
        6.67         4.60         0.66         3.58         6.90         5.56 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A8F5 
        3.19         3.25         3.88         4.50         4.50         6.21 
TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA 
        2.79         2.10        12.66        46.55         7.53        44.61 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5S0 
       27.65        24.10        26.20        16.87        14.10         9.80 
TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P 
       14.76        54.51        33.90        31.07         7.23         4.44 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.03               0.03 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            211.56             234.28 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            21.785             21.385 
[1] "0.0 - 211.6 (21.8)" "0.0 - 234.3 (21.4)"
[1] "hr=" "1.2"
D37V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20Q GAIN MUTATED        34       27        1        3       143        90
  20Q GAIN WILD-TYPE      46       50        8        6       192       134
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20Q GAIN MUTATED           1         68         14         22        8
  20Q GAIN WILD-TYPE         1         70         13         37        9
                    vv
clus                 STAGE TIS STAGE X
  20Q GAIN MUTATED           1       4
  20Q GAIN WILD-TYPE         0      12
D37V3, multiclass
            clus
vv           20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                  34                 46
  STAGE IA                 27                 50
  STAGE IB                  1                  8
  STAGE II                  3                  6
  STAGE IIA               143                192
  STAGE IIB                90                134
  STAGE III                 1                  1
  STAGE IIIA               68                 70
  STAGE IIIB               14                 13
  STAGE IIIC               22                 37
  STAGE IV                  8                  9
  STAGE TIS                 1                  0
  STAGE X                   4                 12
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  20Q GAIN MUTATED    97 256  42  20
  20Q GAIN WILD-TYPE 161 325  75  16
D37V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1               97                161
  T2              256                325
  T3               42                 75
  T4               20                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  20Q GAIN MUTATED   193 132  60  26
  20Q GAIN WILD-TYPE 275 198  51  44
D37V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0              193                275
  N1              132                198
  N2               60                 51
  N3               26                 44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  20Q GAIN MUTATED          0 367   8  42
  20Q GAIN WILD-TYPE        2 478   9  89
D37V6, multiclass
          clus
vv         20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CM0 (I+)                0                  2
  M0                    367                478
  M1                      8                  9
  MX                     42                 89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   410   7
  20Q GAIN WILD-TYPE 574   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    410    7
  20Q GAIN WILD-TYPE  574    4
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE              410                574
  MALE                  7                  4
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  20Q GAIN MUTATED                            0                           350
  20Q GAIN WILD-TYPE                          1                           385
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  20Q GAIN MUTATED                               41                   1
  20Q GAIN WILD-TYPE                            125                   4
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  20Q GAIN MUTATED                                  9                  1
  20Q GAIN WILD-TYPE                               20                 13
                    vv
clus                 OTHER  SPECIFY
  20Q GAIN MUTATED               15
  20Q GAIN WILD-TYPE             29
D37V8, multiclass
                                  clus
vv                                 20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 350                385
  INFILTRATING LOBULAR CARCINOMA                 41                125
  MEDULLARY CARCINOMA                             1                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                9                 20
  MUCINOUS CARCINOMA                              1                 13
  OTHER  SPECIFY                                 15                 29
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V9, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   129 288
  20Q GAIN WILD-TYPE 153 425
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    129  288
  20Q GAIN WILD-TYPE  153  425
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO               129                153
  YES              288                425
[1] 2 2
[1] FALSE
D37V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q GAIN MUTATED                                  0    25
  20Q GAIN WILD-TYPE                                1    31
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED                          62   287
  20Q GAIN WILD-TYPE                        75   421
D37V11, multiclass
                                  clus
vv                                 20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          25                 31
  BLACK OR AFRICAN AMERICAN                      62                 75
  WHITE                                         287                421
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V12, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    11 338
  20Q GAIN WILD-TYPE  25 458
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     11  338
  20Q GAIN WILD-TYPE   25  458
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   11                 25
  NOT HISPANIC OR LATINO              338                458
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED   151  32
  21Q GAIN WILD-TYPE 709  82
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               183                791 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                32                 82 
$`21Q GAIN MUTATED`
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A04U TCGA-A2-A0CM 
       20.88        13.68        28.01        18.02        22.06        24.79 
TCGA-A2-A0CU TCGA-A2-A0EQ TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SV TCGA-A2-A0T1 
        5.19        79.76        24.16        99.19        27.12        17.13 
TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YM TCGA-A2-A1G1 
        8.38        18.71        18.21        21.90        31.73        19.20 
TCGA-A2-A3KD TCGA-A2-A3XU TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A4S1 TCGA-A7-A0DA 
       39.65        29.98        49.48        38.40        12.00        35.67 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A4SB 
       31.73        10.72        12.72        23.80        21.73        13.74 
TCGA-A7-A4SE TCGA-A7-A6VV TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A06Y TCGA-A8-A075 
       21.17        10.29        13.02         1.02        26.01        17.03 
TCGA-A8-A076 TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A08B 
       53.98         8.98         9.96         9.99        28.04        23.08 
TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08X TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 
        9.99        31.00        33.99        19.07        16.01        17.95 
TCGA-A8-A09K TCGA-A8-A09N TCGA-A8-A09X TCGA-A8-A0AB TCGA-AC-A23G TCGA-AC-A2FM 
       29.98         1.02        14.01        17.03        10.85        26.04 
TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A62Y TCGA-AC-A6IW TCGA-AN-A03Y TCGA-AN-A0AS 
        1.02         2.27         1.81         0.69         0.33         0.33 
TCGA-AN-A0FT TCGA-AN-A0FZ TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A0JM TCGA-AO-A128 
        6.02         0.33        66.77        81.63        71.80        94.59 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A1KT TCGA-AQ-A54O TCGA-AR-A0TW TCGA-AR-A0TY 
       77.56        64.04        17.79        21.86        24.30        55.86 
TCGA-AR-A0U0 TCGA-AR-A1AJ TCGA-AR-A1AR TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A24K 
       65.36        52.77        17.23        42.58        36.26        50.89 
TCGA-AR-A24R TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A2LR TCGA-AR-A5QM TCGA-B6-A0I1 
       57.40        51.75        45.17        20.38        54.74        77.62 
TCGA-B6-A0IH TCGA-B6-A0IK TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IQ TCGA-B6-A0RE 
      112.37        18.77        84.59       110.14       140.88       211.56 
TCGA-B6-A0RO TCGA-B6-A0RU TCGA-B6-A0WY TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A402 
      162.05       131.21       113.79       101.52        73.51        54.28 
TCGA-BH-A0AY TCGA-BH-A0B7 TCGA-BH-A0BL TCGA-BH-A0BR TCGA-BH-A0BT TCGA-BH-A0BZ 
       25.55        56.98        44.05        53.69        45.57        49.05 
TCGA-BH-A0C1 TCGA-BH-A0DS TCGA-BH-A0E6 TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0GY 
       44.02         2.56         9.63        24.49        31.00        30.35 
TCGA-BH-A0HQ TCGA-BH-A18Q TCGA-BH-A1EN TCGA-BH-A1EV TCGA-BH-A1EX TCGA-BH-A1FC 
       36.85        55.63        69.93        12.00        49.58       114.15 
TCGA-BH-A1FU TCGA-BH-A202 TCGA-BH-A203 TCGA-C8-A12P TCGA-C8-A130 TCGA-C8-A131 
       72.07         0.72        38.60        11.77         3.12         1.78 
TCGA-C8-A132 TCGA-C8-A135 TCGA-C8-A1HM TCGA-C8-A26Y TCGA-C8-A275 TCGA-C8-A278 
        1.45         0.62         2.30         0.43         0.03         0.03 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A147 TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JK 
       11.90        20.88        19.20        12.03        14.01        20.12 
TCGA-D8-A1XD TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XU TCGA-D8-A1XW TCGA-E2-A10B 
       17.16        21.83        14.50        12.99        12.66        37.51 
TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A154 
       44.68        40.96        38.60        31.96        17.03        19.43 
TCGA-E2-A159 TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1IN 
       25.05         7.73        13.02        60.53        53.62        22.19 
TCGA-E2-A1L9 TCGA-E2-A1LE TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A573 TCGA-E9-A1R7 
       19.66        28.90         8.75        16.93        22.26        21.21 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RH TCGA-E9-A244 TCGA-E9-A2JS TCGA-E9-A3X8 
        0.66        34.65        34.59         0.69        17.75        15.72 
TCGA-EW-A1OZ TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PC TCGA-EW-A1PH 
       40.41        29.82        23.11         7.86         6.15        19.96 
TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A423 TCGA-GM-A2DC TCGA-GM-A2DF TCGA-LL-A441 
       55.00        25.91        10.16        53.52        42.71         2.99 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A7T0 TCGA-LL-A8F5 
        3.19         3.25         4.14         4.50         3.22         6.21 
TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-W8-A86G 
       26.20         9.80         5.29 

$`21Q GAIN WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N 
       31.79         7.96        39.32        19.20        18.21       104.81 
TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X 
       41.95        82.16        73.84        63.12        64.04        55.43 
TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
       36.13       125.59        64.57       112.08        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX 
      107.93        75.55        75.25        63.45        64.04        56.81 
TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM 
       21.14        34.55        33.76        28.77        25.22       101.72 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET 
       89.36        80.28       107.61        74.40        37.05        35.05 
TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0SU TCGA-A2-A0SW 
       34.29        31.82        29.75        24.72        54.64        44.88 
TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       50.43        44.28        17.52        20.52        17.46        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YH TCGA-A2-A0YI 
       20.75        32.55        25.28        15.42        21.67        14.50 
TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW 
       18.61        19.33        14.63        23.77        23.47        17.36 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       36.79        22.45        20.25        19.56        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
      107.70        16.31        17.19        18.15        91.92        10.59 
TCGA-A2-A3KC TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XY TCGA-A2-A3XZ 
       20.88        33.93        83.01        14.07        34.98        31.99 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 
       38.37         7.30         9.01         8.81         8.91         6.74 
TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ 
        3.42        38.30        35.31        34.29        35.47        30.61 
TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F 
       37.45        33.11        23.61        29.56        31.36        24.26 
TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 
       23.74        20.61        22.32        11.34        10.59        10.29 
TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SD 
       11.28        13.41        14.70        11.97        14.93        14.50 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VW 
       17.92        14.73        12.10        10.72        11.05         9.37 
TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U 
       10.42         8.75        13.02        17.98        41.06        29.03 
TCGA-A8-A06X TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F 
       31.00         1.02         9.01        33.01        19.99        18.97 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P 
       18.97        14.01        12.00        17.03         9.99        10.98 
TCGA-A8-A07S TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A 
        7.99        18.05        15.06        36.95        13.02         0.99 
TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08O 
       19.99        18.05        19.96        12.00        37.05        31.00 
TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A095 TCGA-A8-A097 
        0.99        19.07        93.04        40.01        41.98        12.00 
TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E 
        9.99         9.99        12.00         1.02        13.02        31.00 
TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       33.07        15.02        25.02         8.98        19.04        15.02 
TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 
        0.99        12.00        19.04        13.02        21.04         0.99 
TCGA-A8-A0A9 TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23H TCGA-AC-A2B8 
       13.02        38.04         0.95         2.37         2.66         1.48 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
       38.53        38.20        40.57        55.43        36.99        38.79 
TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
       50.70         0.92         0.99         0.69        14.83         9.40 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS 
        1.12         1.81         1.68         1.55         1.32         1.55 
TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AN-A03X 
        0.07         1.12         1.18         0.43         1.74         0.33 
TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D 
        0.23         0.33         0.62         2.96         1.78         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AT 
        8.02         7.36         6.51         0.16         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN 
        6.44         4.64         7.96         7.00         7.59         7.17 
TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL 
        6.28         0.33         0.36         0.33         0.33         0.33 
TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT 
        0.33        12.33         0.30         0.33         0.33         0.33 
TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03P 
        0.33         5.33         5.59        80.28        47.84        84.69 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 
       68.75        47.87        59.05        29.13        32.78        21.40 
TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 
       17.65        24.16        37.48        20.32        22.36        53.03 
TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF 
       21.53        50.70        50.86        72.00        76.77        21.37 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A125 
       26.24        38.53        62.04        55.33       102.58        99.25 
TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G 
       93.70        96.10        90.58        57.30        48.36        41.62 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS 
       28.37        14.73        82.62        61.87        70.39         0.53 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       24.79        26.93       130.09         5.65        15.62        13.22 
TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS 
        2.56         9.99        82.88        49.32         5.26        37.41 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 
       56.88        29.75        64.83        76.14        70.16        83.87 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AL 
       76.18        55.36        75.55        61.84        51.25        48.82 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS 
       62.56        43.73        43.56        39.98        43.07        40.83 
TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M 
       46.32        35.24        20.22       109.58        73.02        65.46 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24T 
       68.19        65.69         0.85        66.05        62.07        53.26 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A252 
       53.36        54.18        50.96        48.16        56.15        40.64 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LK 
       39.85        34.82        93.83       128.65        20.25        42.87 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN 
        7.36        40.04        17.10        20.81        16.96        16.04 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA 
       20.45        10.59       143.38       149.59        12.13       220.90 
TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IJ TCGA-B6-A0IM 
      129.57        50.70        65.72       146.50       176.98       126.12 
TCGA-B6-A0IP TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM 
      110.93        68.45       189.01       234.28        81.17        78.02 
TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RV 
      172.96       102.77       140.48       100.70        89.46       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WZ 
       97.48       188.68        79.63        17.98        21.47       129.57 
TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC 
      129.70       186.48        28.27        68.94        58.88        43.59 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C 
      139.17       170.17        85.35        49.94        82.88        55.00 
TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 
       24.53        38.79        20.45        28.50        46.95        40.83 
TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B9 TCGA-BH-A0BA 
       39.55        39.16        48.36        56.94        51.68        37.22 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BM 
       32.02        18.21        25.71        24.85        21.70        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW 
       35.67        48.69        27.19        53.95        49.94        11.67 
TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG 
       41.75        48.13        42.90        45.83        31.17        23.44 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP 
       38.01        22.13        13.91        48.23        17.26        15.65 
TCGA-BH-A0DQ TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
        3.22        38.47        45.17        47.41        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EI 
       15.68        14.30        44.81        46.19        32.65        24.43 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 
       10.78        15.16        37.78        35.51        24.56        23.08 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       41.00        52.96        26.50        20.38         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX 
       13.61        12.89        51.32        27.25        50.79         5.59 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F 
       23.93        24.95        42.35        44.81        23.05         8.81 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M 
        2.01         7.23        20.12        90.84        26.66        72.56 
TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U 
       37.74        30.28        37.55        66.05         7.36        51.39 
TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW 
       51.16        91.99       113.82        82.85        42.28        55.69 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 
       17.69        25.81        31.53        89.16        97.48        24.66 
TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
      120.62        33.17        74.73       122.89        36.92        63.35 
TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A204 
       55.00        45.63        72.07       144.59         6.90        83.31 
TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T 
       57.83       130.16        10.65         6.44        20.12         0.99 
TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O 
      109.28         8.94        11.93        11.77        11.77        12.66 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A134 
        0.07        12.66        12.66        12.66        12.66         0.69 
TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI 
        3.85         3.75        12.33        10.92        11.34        11.34 
TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W 
        0.16        12.03        10.42         3.25         0.30         0.23 
TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A27A TCGA-C8-A27B 
        0.36         8.28         9.67         0.03        12.20         0.99 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 
        0.03         0.23        13.25        20.58        13.97        14.17 
TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
       13.48        21.14        14.17        17.49        16.50        18.71 
TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JI TCGA-D8-A1JJ 
       15.78        18.15        18.90        12.03        18.97        20.09 
TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT 
       20.09        19.40        20.38        21.01        12.20        13.32 
TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 
       14.70        18.58        17.79        16.73        25.74        23.90 
TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XL 
       27.58        18.15         2.66        15.22        14.73        19.92 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT 
       17.69         7.96        16.41        15.85        16.31         6.35 
TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 
       15.16        16.54        15.32        15.52         3.81        14.24 
TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I 
       14.14        17.42        16.04        13.45        13.05        14.43 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R 
        9.44        16.41        13.48         4.80         0.76        10.09 
TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 
       13.08        12.53        12.26        14.50        18.51         7.33 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10C 
       43.00        34.42        27.52        46.59        40.41        40.11 
TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14T 
       28.44        28.87        47.15        38.24        33.17        33.30 
TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A152 
       43.33        34.26        32.02        28.60        25.41        27.12 
TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15A TCGA-E2-A15C 
       23.24        21.04        23.87        14.79        23.34        22.82 
TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I 
       17.29        20.71        21.63        18.21        12.92        17.42 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
       19.40         9.04        20.58        19.56        17.06        14.07 
TCGA-E2-A15T TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC 
       14.99        53.03        29.95        32.35        28.50        16.47 
TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II 
       17.10        38.30        37.41        32.78        33.73        33.70 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       28.44        22.65         3.88        20.98        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LG TCGA-E2-A1LH 
       27.42        39.62        24.59        40.47        18.87       106.75 
TCGA-E2-A1LI TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
      102.61        43.04         5.52        15.72         7.20        18.05 
TCGA-E2-A574 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 
       19.89        19.20        36.82        13.48        12.00        13.12 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG 
       36.56        39.55        12.59        35.77        20.05        21.57 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 
        9.86        11.90        14.30         0.62         2.10         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RF 
        1.38         2.76        32.09        20.81        40.24         6.58 
TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
       21.27        35.64        34.13         0.79        12.53        13.32 
TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 
       39.09        22.75        12.89        23.51        24.10        17.06 
TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
        0.85        27.22         1.94         0.95        12.56         0.72 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54Y TCGA-E9-A5FK 
        0.76        26.07        18.41         0.62         0.23         0.39 
TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
        0.26         0.23        15.39        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 
       18.21        18.90        13.25        16.57        15.68        28.77 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P1 
       25.94        22.82        29.95        29.85        41.13        39.78 
TCGA-EW-A1P3 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PD 
       52.96        18.48        30.08        18.90        19.99        13.94 
TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A3E8 
       10.52        14.43        34.55        52.73        22.09        21.27 
TCGA-EW-A3U0 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       17.49        10.59         7.40       109.87        59.57       194.27 
TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       53.13        43.04        42.28        61.91        62.33        90.84 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
       76.64        77.33        53.36       110.50        38.20        32.28 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW 
       69.30        53.95        57.63        13.55        18.12        11.84 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A442 
       11.57         8.28         6.67         4.60         0.66         3.58 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A6FQ TCGA-LL-A6FR 
        6.90         5.56         4.70         3.65         2.63         3.88 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
        4.50         5.59        15.91         2.79         2.10        12.66 
TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX 
       46.55         7.53        44.61        27.65        24.10        16.87 
TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K 
       14.10        10.29        14.76        23.70        54.51        33.90 
TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-S3-A6ZG 
       31.07        18.21         7.23         4.44         6.81 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.03               0.03 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            211.56             234.28 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             21.86              21.27 
[1] "0.0 - 211.6 (21.9)" "0.0 - 234.3 (21.3)"
[1] "hr=" "1.8"
D38V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  21Q GAIN MUTATED        12       11        1        1        69        37
  21Q GAIN WILD-TYPE      68       66        8        8       266       187
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  21Q GAIN MUTATED           0         31          3         14        4
  21Q GAIN WILD-TYPE         2        107         24         45       13
                    vv
clus                 STAGE TIS STAGE X
  21Q GAIN MUTATED           0       4
  21Q GAIN WILD-TYPE         1      12
D38V3, multiclass
            clus
vv           21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                  12                 68
  STAGE IA                 11                 66
  STAGE IB                  1                  8
  STAGE II                  1                  8
  STAGE IIA                69                266
  STAGE IIB                37                187
  STAGE III                 0                  2
  STAGE IIIA               31                107
  STAGE IIIB                3                 24
  STAGE IIIC               14                 45
  STAGE IV                  4                 13
  STAGE TIS                 0                  1
  STAGE X                   4                 12
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  21Q GAIN MUTATED    44 115  22   5
  21Q GAIN WILD-TYPE 214 466  95  31
D38V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1               44                214
  T2              115                466
  T3               22                 95
  T4                5                 31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  21Q GAIN MUTATED    82  64  21  15
  21Q GAIN WILD-TYPE 386 266  90  55
D38V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0               82                386
  N1               64                266
  N2               21                 90
  N3               15                 55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  21Q GAIN MUTATED          0 164   4  19
  21Q GAIN WILD-TYPE        2 681  13 112
D38V6, multiclass
          clus
vv         21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CM0 (I+)                0                  2
  M0                    164                681
  M1                      4                 13
  MX                     19                112
[1] 4 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   185   2
  21Q GAIN WILD-TYPE 799   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED    185    2
  21Q GAIN WILD-TYPE  799    9
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE              185                799
  MALE                  2                  9
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  21Q GAIN MUTATED                            0                           160
  21Q GAIN WILD-TYPE                          1                           575
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  21Q GAIN MUTATED                               15                   2
  21Q GAIN WILD-TYPE                            151                   3
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  21Q GAIN MUTATED                                  0                  1
  21Q GAIN WILD-TYPE                               29                 13
                    vv
clus                 OTHER  SPECIFY
  21Q GAIN MUTATED                9
  21Q GAIN WILD-TYPE             35
D38V8, multiclass
                                  clus
vv                                 21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 160                575
  INFILTRATING LOBULAR CARCINOMA                 15                151
  MEDULLARY CARCINOMA                             2                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)                0                 29
  MUCINOUS CARCINOMA                              1                 13
  OTHER  SPECIFY                                  9                 35
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V9, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    64 123
  21Q GAIN WILD-TYPE 218 590
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     64  123
  21Q GAIN WILD-TYPE  218  590
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                64                218
  YES              123                590
[1] 2 2
[1] FALSE
D38V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q GAIN MUTATED                                  1    10
  21Q GAIN WILD-TYPE                                0    46
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED                          35   118
  21Q GAIN WILD-TYPE                       102   590
D38V11, multiclass
                                  clus
vv                                 21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                          10                 46
  BLACK OR AFRICAN AMERICAN                      35                102
  WHITE                                         118                590
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V12, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     9 143
  21Q GAIN WILD-TYPE  27 653
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      9  143
  21Q GAIN WILD-TYPE   27  653
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    9                 27
  NOT HISPANIC OR LATINO              143                653
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    77  14
  22Q GAIN WILD-TYPE 783 100
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                91                883 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                14                100 
$`22Q GAIN MUTATED`
TCGA-A1-A0SK TCGA-A1-A0SP TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A0CL TCGA-A2-A0CX 
       31.79        19.20        22.06        64.04        64.57        56.81 
TCGA-A2-A0D2 TCGA-A2-A0T1 TCGA-A2-A1FV TCGA-A2-A1G1 TCGA-A7-A0CD TCGA-A7-A13F 
       33.76        17.13        23.47        19.20        38.30        12.72 
TCGA-A7-A6VV TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A079 TCGA-A8-A08B TCGA-A8-A08R 
       10.29        10.42        13.02         9.01        23.08         0.99 
TCGA-A8-A091 TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09X TCGA-AC-A23H TCGA-AC-A2QJ 
       19.07        29.98        15.02        14.01         2.66         2.27 
TCGA-AC-A3W5 TCGA-AC-A62V TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FL 
        1.81         0.07         6.51         0.16         0.33         7.59 
TCGA-AN-A0FX TCGA-AN-A0XN TCGA-AO-A12B TCGA-AO-A12F TCGA-AO-A12G TCGA-AQ-A04L 
        0.33         0.33        77.56        48.36        41.62       130.09 
TCGA-AQ-A0Y5 TCGA-AR-A0TP TCGA-AR-A0TV TCGA-AR-A0U1 TCGA-AR-A24U TCGA-AR-A24V 
        5.65        82.88        29.75        70.16        53.36        54.18 
TCGA-AR-A2LR TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WV TCGA-B6-A1KC TCGA-B6-A402 
       20.38       100.70       131.21        79.63        43.59        54.28 
TCGA-BH-A0BG TCGA-BH-A0C0 TCGA-BH-A0DL TCGA-BH-A0E2 TCGA-BH-A0HY TCGA-BH-A18Q 
       24.85        41.75        48.23        14.30        50.79        55.63 
TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EV TCGA-BH-A1FU TCGA-BH-A202 TCGA-BH-A203 
       51.39        69.93        12.00        72.07         0.72        38.60 
TCGA-BH-A208 TCGA-C8-A12L TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12W TCGA-C8-A1HG 
       57.83        11.93        12.66        11.77        12.66        11.34 
TCGA-D8-A142 TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JK TCGA-D8-A1XJ TCGA-D8-A1XW 
       13.97        15.78        18.90        20.12        21.83        12.66 
TCGA-D8-A1XZ TCGA-D8-A27M TCGA-D8-A27W TCGA-E2-A14X TCGA-E2-A152 TCGA-E2-A1B0 
       15.32        13.48        12.26        31.96        27.12        53.62 
TCGA-E9-A1NC TCGA-E9-A22B TCGA-E9-A243 TCGA-EW-A1OZ TCGA-EW-A424 TCGA-GI-A2C9 
       39.55        22.75        17.06        40.41        10.59       109.87 
TCGA-GM-A2DF TCGA-GM-A3XL TCGA-LL-A5YM TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A7SZ 
       42.71        69.30         4.70         3.25         3.88         5.59 
TCGA-LL-A8F5 
        6.21 

$`22Q GAIN WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ 
       20.88        13.68         7.96        39.32        28.01        18.21 
TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04V 
      104.81        18.02        41.95        82.16        73.84        63.12 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
       55.43        36.13       125.59        24.79       112.08        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV 
       88.60       107.93        75.55        75.25         5.19        63.45 
TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM 
       64.04        21.14        34.55        28.77        25.22       101.72 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES 
       89.36        80.28       107.61        79.76        74.40        37.05 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY 
       35.05        34.29        31.82        29.75        24.72        24.16 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY 
       99.19        54.64        27.12        44.88        50.43        44.28 
TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.52         8.38        18.71        20.52        17.46        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG 
       20.75        32.55        25.28        18.21        15.42        21.90 
TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       21.67        14.50        18.61        19.33        14.63        31.73 
TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 
       23.77        17.36        36.79        22.45        20.25        19.56 
TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D 
       16.47        52.47       107.70        16.31        17.19        18.15 
TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT 
       91.92        10.59        20.88        39.65        33.93        83.01 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ 
       29.98        14.07        49.48        38.40        34.98        31.99 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 
       38.37         7.30         9.01         8.81         8.91        12.00 
TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ 
        6.74         3.42        35.31        34.29        35.47        30.61 
TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13G 
       37.45        35.67        33.11        31.73        10.72        23.61 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I 
       29.56        31.36        24.26        23.74        23.80        21.73 
TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       20.61        22.32        11.34        10.59        10.29        11.28 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD 
       13.41        14.70        11.97        14.93        13.74        14.50 
TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX 
       21.17        17.92        14.73        12.10        10.72        11.05 
TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T 
        9.37         8.75        13.02         1.02        17.98        41.06 
TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 
       29.03        31.00        26.01         1.02        17.03        53.98 
TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J 
       33.01        19.99        18.97        18.97        14.01        12.00 
TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U 
       17.03         9.99        10.98         8.98         7.99         9.96 
TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 
        9.99        28.04        18.05        15.06        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J 
        0.99        19.99        18.05        19.96        12.00        37.05 
TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X 
        9.99        31.00        31.00        19.07        93.04        33.99 
TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 
       40.01        16.01        17.95        41.98        12.00         9.99 
TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I 
        9.99        12.00         1.02        13.02        31.00        33.07 
TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
        1.02        25.02         8.98        19.04        15.02         0.99 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 
       12.00        19.04        13.02        21.04         0.99        13.02 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2B8 
       17.03        38.04         0.95         2.37        10.85         1.48 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
       38.53        38.20        40.57        55.43        36.99        38.79 
TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3HN 
       26.04        50.70         1.02         0.92         0.99         0.69 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ 
       14.83         9.40         1.12         1.68         1.55         1.32 
TCGA-AC-A5XS TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX 
        1.55         1.12         1.81         1.18         0.69         0.43 
TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 
        1.74         0.33         0.33         0.23         0.33         0.62 
TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AR 
        2.96         1.78         1.71         8.02         7.36         0.33 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FN 
        0.33         6.44         4.64         7.96         7.00         7.17 
TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ 
        6.28         6.02         0.33         0.36         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT 
        0.33        12.33         0.30         0.33         0.33         0.33 
TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N 
        0.33         5.33         5.59        80.28        47.84        66.77 
TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V 
       81.63        84.69        68.75        47.87        59.05        29.13 
TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 
       32.78        21.40        17.65        24.16        37.48        20.32 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD 
       22.36        53.03        21.53        50.70        50.86        72.00 
TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL 
       76.77        21.37        26.24        38.53        62.04        55.33 
TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 
       71.80       102.58        99.25        93.70        94.59        96.10 
TCGA-AO-A12A TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       90.58        64.04        57.30        28.37        14.73        82.62 
TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J 
       61.87        70.39         0.53        17.79        24.79        26.93 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TQ 
       15.62        13.22         2.56        21.86         9.99        49.32 
TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
        5.26        37.41        56.88        24.30        64.83        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH 
       76.14        65.36        83.87        76.18        55.36        75.55 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
       61.84        52.77        51.25        48.82        62.56        43.73 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU 
       43.56        39.98        43.07        17.23        40.83        46.32 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K 
       42.58        35.24        36.26        20.22       109.58        50.89 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q 
       73.02        65.46        68.19        65.69         0.85        66.05 
TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
       57.40        62.07        53.26        50.96        48.16        51.75 
TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
       56.15        45.17        40.64        39.85        34.82        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN 
      128.65        20.25        42.87         7.36        40.04        17.10 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       20.81        16.96        54.74        16.04        20.45        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB 
       77.62       143.38       149.59        12.13       220.90       129.57 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK 
       50.70        65.72       146.50       112.37       176.98        18.77 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE 
      126.12        84.59       110.14       110.93       140.88       211.56 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN 
       68.45       189.01       234.28        81.17        78.02       172.96 
TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS 
      162.05       102.77       140.48        89.46       157.41        97.48 
TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 
      188.68        17.98        21.47       113.79       129.57       129.70 
TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KI 
      186.48        28.27        68.94        58.88       101.52        73.51 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C 
      139.17       170.17        85.35        49.94        82.88        55.00 
TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 
       24.53        38.79        20.45        25.55        28.50        46.95 
TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 
       40.83        39.55        39.16        48.36        56.94        56.98 
TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ 
       51.68        37.22        32.02        18.21        25.71        21.70 
TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR 
       44.05        61.68        35.67        48.69        27.19        53.69 
TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 
       53.95        45.57        49.94        11.67        49.05        44.02 
TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH 
       48.13        42.90        45.83        31.17        23.44        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS 
       22.13        13.91        17.26        15.65         3.22         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 
       38.47        45.17        47.41        16.27         4.41        15.68 
TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE 
        9.63        44.81        46.19        32.65        24.49        31.00 
TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       24.43        30.35        10.78        15.16        37.78        35.51 
TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI 
       24.56        23.08        41.00        52.96        26.50        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW 
        5.85         2.50        13.61        36.85        12.89        51.32 
TCGA-BH-A0HX TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       27.25         5.59        23.93        24.95        42.35        44.81 
TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K 
       23.05         8.81         2.01         7.23        20.12        90.84 
TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S 
       26.66        72.56        37.74        30.28        37.55        66.05 
TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU 
        7.36        51.16        91.99       113.82        82.85        42.28 
TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 
       55.69        49.58        17.69        25.81        31.53        89.16 
TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE 
       97.48        24.66       120.62       114.15        33.17        74.73 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN 
      122.89        36.92        63.35        55.00        45.63        72.07 
TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q 
      144.59         6.90        83.31       130.16        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12M TCGA-C8-A12N 
       20.12         0.99       109.28         8.94        11.77        11.77 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A131 
        0.07        12.66        12.66        12.66         3.12         1.78 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE 
        1.45         0.69         0.62         3.85         3.75        12.33 
TCGA-C8-A1HF TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM 
       10.92        11.34         0.16        12.03        10.42         2.30 
TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z 
        3.25         0.30         0.23         0.36         0.43         8.28 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B 
        9.67         0.03         0.03         0.03        12.20         0.99 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 
        0.03         0.23        11.90        20.88        13.25        20.58 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 
       14.17        13.48        21.14        19.20        14.17        17.49 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH 
       16.50        18.71        18.15        12.03        12.03        14.01 
TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP 
       18.97        20.09        20.09        19.40        20.38        21.01 
TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 
       12.20        13.32        14.70        18.58        17.79        16.73 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD 
       25.74        23.90        27.58        18.15         2.66        17.16 
TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO 
       15.22        14.73        14.50        19.92        17.69         7.96 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV 
       16.41        15.85        16.31         6.35        12.99        15.16 
TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E 
       16.54        15.52         3.81        14.24        14.14        17.42 
TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       16.04        13.45        13.05        14.43         9.44        16.41 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 
        4.80         0.76        10.09        13.08        12.53        14.50 
TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 
       18.51         7.33        43.00        34.42        27.52        46.59 
TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N 
       40.41        37.51        40.11        28.44        28.87        47.15 
TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T 
       44.68        40.96        38.24        38.60        33.17        33.30 
TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 
       43.33        34.26        32.02        28.60        17.03        25.41 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 
       23.24        19.43        21.04        23.87        14.79        25.05 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G 
       23.34        22.82        17.29        20.71        21.63        18.21 
TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M 
       12.92        17.42        19.40         9.04        20.58         7.73 
TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ 
       13.02        19.56        17.06        14.07        14.99        60.53 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD 
       53.03        29.95        32.35        28.50        16.47        17.10 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ 
       38.30        37.41        32.78        33.73        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       22.65         3.88        22.19        20.98        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       27.42        39.62        19.66        24.59        40.47        28.90 
TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 
       18.87       106.75       102.61         8.75        43.04        16.93 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 
        5.52        15.72         7.20        18.05        22.26        19.89 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA 
       19.20        36.82        13.48        12.00        13.12        36.56 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ 
       12.59        35.77        20.05        21.57         9.86        11.90 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 
       14.30         0.62         2.10         6.12         1.38         2.76 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE 
       21.21        32.09        20.81        40.24         0.66        34.65 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
        6.58        21.27        34.59        35.64        34.13         0.79 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H 
       12.53        13.32        39.09        12.89        23.51        24.10 
TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A 
        0.69         0.85        27.22         1.94         0.95        12.56 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA 
        0.72        17.75         0.76        26.07        18.41         0.62 
TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE 
       15.72         0.23         0.39         0.26         0.23        15.39 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 
       12.20        39.72         8.48        18.21        18.90        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX 
       16.57        15.68        28.77        25.94        22.82        29.95 
TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 
       29.85        41.13        39.78        52.96        29.82        23.11 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC 
       18.48        30.08         7.86        18.90        19.99         6.15 
TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR 
       13.94        10.52        14.43        34.55        19.96        55.00 
TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 
       52.73        25.91        22.09        21.27        17.49        10.16 
TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD 
        7.40        59.57       194.27        53.13        53.52        43.04 
TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       42.28        61.91        62.33        90.84        76.64        77.33 
TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 
       53.36       110.50        38.20        32.28        53.95        57.63 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U 
       13.55        18.12        11.84        11.57         8.28         6.67 
TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL 
        4.60         0.66         2.99         3.58         6.90         5.56 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 
        3.65         3.19         2.63         4.14         4.50         4.50 
TCGA-LL-A7T0 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 
        3.22        15.91         2.79         2.10        12.66        46.55 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX 
        7.53        44.61        27.65        24.10        26.20        16.87 
TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J 
       14.10        10.29         9.80        14.76        23.70        54.51 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-S3-A6ZG 
       33.90        31.07        18.21         7.23         4.44         6.81 
TCGA-W8-A86G 
        5.29 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.07               0.03 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            131.21             234.28 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             20.12              21.53 
[1] "0.1 - 131.2 (20.1)" "0.0 - 234.3 (21.5)"
[1] "hr=" "1.5"
D39V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  22Q GAIN MUTATED         7        4        0        1        41        18
  22Q GAIN WILD-TYPE      73       73        9        8       294       206
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  22Q GAIN MUTATED           0         13          6          3        1
  22Q GAIN WILD-TYPE         2        125         21         56       16
                    vv
clus                 STAGE TIS STAGE X
  22Q GAIN MUTATED           0       0
  22Q GAIN WILD-TYPE         1      16
D39V3, multiclass
            clus
vv           22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                   7                 73
  STAGE IA                  4                 73
  STAGE IB                  0                  9
  STAGE II                  1                  8
  STAGE IIA                41                294
  STAGE IIB                18                206
  STAGE III                 0                  2
  STAGE IIIA               13                125
  STAGE IIIB                6                 21
  STAGE IIIC                3                 56
  STAGE IV                  1                 16
  STAGE TIS                 0                  1
  STAGE X                   0                 16
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  22Q GAIN MUTATED    17  62   9   6
  22Q GAIN WILD-TYPE 241 519 108  30
D39V4, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1               17                241
  T2               62                519
  T3                9                108
  T4                6                 30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  22Q GAIN MUTATED    51  26  10   4
  22Q GAIN WILD-TYPE 417 304 101  66
D39V5, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0               51                417
  N1               26                304
  N2               10                101
  N3                4                 66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  22Q GAIN MUTATED          0  83   1  10
  22Q GAIN WILD-TYPE        2 762  16 121
D39V6, multiclass
          clus
vv         22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CM0 (I+)                0                  2
  M0                     83                762
  M1                      1                 16
  MX                     10                121
[1] 4 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    93   1
  22Q GAIN WILD-TYPE 891  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     93    1
  22Q GAIN WILD-TYPE  891   10
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               93                891
  MALE                  1                 10
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  22Q GAIN MUTATED                            0                            78
  22Q GAIN WILD-TYPE                          1                           657
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  22Q GAIN MUTATED                                4                   0
  22Q GAIN WILD-TYPE                            162                   5
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  22Q GAIN MUTATED                                  2                  1
  22Q GAIN WILD-TYPE                               27                 13
                    vv
clus                 OTHER  SPECIFY
  22Q GAIN MUTATED                9
  22Q GAIN WILD-TYPE             35
D39V8, multiclass
                                  clus
vv                                 22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                  78                657
  INFILTRATING LOBULAR CARCINOMA                  4                162
  MEDULLARY CARCINOMA                             0                  5
  MIXED HISTOLOGY (PLEASE SPECIFY)                2                 27
  MUCINOUS CARCINOMA                              1                 13
  OTHER  SPECIFY                                  9                 35
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V9, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    21  73
  22Q GAIN WILD-TYPE 261 640
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     21   73
  22Q GAIN WILD-TYPE  261  640
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                21                261
  YES               73                640
[1] 2 2
[1] FALSE
D39V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q GAIN MUTATED                                  1     7
  22Q GAIN WILD-TYPE                                0    49
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED                          17    57
  22Q GAIN WILD-TYPE                       120   651
D39V11, multiclass
                                  clus
vv                                 22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           7                 49
  BLACK OR AFRICAN AMERICAN                      17                120
  WHITE                                          57                651
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V12, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     3  79
  22Q GAIN WILD-TYPE  33 717
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      3   79
  22Q GAIN WILD-TYPE   33  717
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 33
  NOT HISPANIC OR LATINO               79                717
[1] 2 2
[1] FALSE

Clustering(40) Variable = XQ GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED   115  13
  XQ GAIN WILD-TYPE 745 101
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              128               846 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               13               101 
$`XQ GAIN MUTATED`
TCGA-A1-A0SJ TCGA-A1-A0SO TCGA-A2-A04T TCGA-A2-A0CM TCGA-A2-A0CX TCGA-A2-A0D2 
       13.68        28.01        73.84        24.79        56.81        33.76 
TCGA-A2-A0EQ TCGA-A2-A0SW TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0YG TCGA-A2-A0YJ 
       79.76        44.88         8.38        18.71        21.90        18.61 
TCGA-A2-A0YM TCGA-A2-A1G0 TCGA-A2-A25B TCGA-A2-A25E TCGA-A2-A3XX TCGA-A2-A3XY 
       31.73        20.25        16.31        91.92        38.40        34.98 
TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0DB TCGA-A7-A2KD TCGA-A7-A3J0 TCGA-A7-A425 
        6.74        38.30        33.11        22.32        10.29        14.70 
TCGA-A7-A4SD TCGA-A7-A5ZV TCGA-A8-A076 TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A07R 
       14.50        12.10        53.98        17.03        10.98         8.98 
TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A086 TCGA-A8-A08B TCGA-A8-A08C 
        9.96         9.99        28.04        13.02        23.08        19.99 
TCGA-A8-A08F TCGA-A8-A08T TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 
       18.05        93.04        19.07        17.95        41.98        12.00 
TCGA-A8-A09Q TCGA-A8-A09W TCGA-AC-A2BK TCGA-AC-A3OD TCGA-AC-A62X TCGA-AN-A03Y 
       25.02         0.99        38.53        14.83         1.12         0.33 
TCGA-AN-A0FT TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A0J2 
        6.02         0.33         0.33        66.77        81.63        32.78 
TCGA-AO-A0J4 TCGA-AO-A0JM TCGA-AO-A128 TCGA-AO-A12B TCGA-AO-A12F TCGA-AO-A1KR 
       17.65        71.80        94.59        77.56        48.36        70.39 
TCGA-AR-A0TW TCGA-AR-A1AV TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24Z TCGA-AR-A254 
       24.30        42.58        66.05        57.40        51.75        39.85 
TCGA-AR-A255 TCGA-AR-A5QM TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0WZ TCGA-B6-A0X1 
       34.82        54.74       143.38       149.59       129.57       186.48 
TCGA-B6-A1KF TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0BR TCGA-BH-A0DL TCGA-BH-A0DS 
      101.52        20.45        25.55        53.69        48.23         2.56 
TCGA-BH-A0E6 TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0WA 
        9.63        24.43        30.35        36.85        12.89        23.05 
TCGA-BH-A18N TCGA-BH-A18Q TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1F0 TCGA-BH-A1FC 
       37.74        55.63        91.99        82.85        25.81       114.15 
TCGA-BH-A202 TCGA-BH-A209 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A1HG TCGA-C8-A274 
        0.72       130.16        11.93        11.77        11.34         0.03 
TCGA-C8-A275 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A1JD TCGA-D8-A1JT TCGA-D8-A1X5 
        0.03        13.97        14.17        18.15        13.32        18.58 
TCGA-D8-A1XQ TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z6 
       16.41        12.66        15.32        12.53        12.26        18.51 
TCGA-E2-A10B TCGA-E2-A14P TCGA-E2-A14S TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A14Y 
       37.51        40.96        33.17        34.26        31.96        28.60 
TCGA-E2-A15D TCGA-E2-A1B0 TCGA-E2-A56Z TCGA-E9-A1N6 TCGA-E9-A1RC TCGA-E9-A2JS 
       17.29        53.62         7.20        13.48        40.24        17.75 
TCGA-E9-A5FL TCGA-EW-A1IY TCGA-EW-A1P5 TCGA-EW-A1PB TCGA-GI-A2C9 TCGA-LL-A6FQ 
        0.26         8.48        23.11        19.99       109.87         2.63 
TCGA-LL-A73Y TCGA-OL-A66I 
        4.14        23.70 

$`XQ GAIN WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A1-A0SQ 
       20.88        31.79         7.96        39.32        19.20        18.21 
TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04U TCGA-A2-A04V 
      104.81        18.02        41.95        82.16        22.06        63.12 
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO 
       64.04        55.43        36.13       125.59        64.57       112.08 
TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU 
       92.48        88.60       107.93        75.55        75.25         5.19 
TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0D4 
       63.45        64.04        21.14        34.55        28.77        25.22 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES 
      101.72        89.36        80.28       107.61        74.40        37.05 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY 
       35.05        34.29        31.82        29.75        24.72        24.16 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 
       99.19        54.64        27.12        50.43        44.28        17.52 
TCGA-A2-A0T1 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC 
       17.13        20.52        17.46        18.90        20.75        32.55 
TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK 
       25.28        18.21        15.42        21.67        14.50        19.33 
TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ 
       14.63        23.77        23.47        17.36        36.79        22.45 
TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25C 
       19.20        19.56        16.47        52.47       107.70        17.19 
TCGA-A2-A25D TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT 
       18.15        10.59        20.88        39.65        33.93        83.01 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW 
       29.98        14.07        49.48        31.99        38.37         7.30 
TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CE 
        9.01         8.81         8.91        12.00         3.42        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A13D 
       34.29        35.47        30.61        37.45        35.67        31.73 
TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F 
       10.72        12.72        23.61        29.56        31.36        24.26 
TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ 
       23.74        23.80        21.73        20.61        11.34        10.59 
TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SE 
       11.28        13.41        11.97        14.93        13.74        21.17 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW 
       17.92        14.73        10.72        11.05        10.29         9.37 
TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R 
       10.42         8.75        13.02        13.02         1.02        17.98 
TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 
       41.06        29.03        31.00        26.01         1.02        17.03 
TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I 
        9.01        33.01        19.99        18.97        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07O TCGA-A8-A07S TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 
       12.00         9.99         7.99        18.05        15.06        36.95 
TCGA-A8-A08A TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O 
        0.99        19.96        12.00        37.05         9.99        31.00 
TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 
       31.00         0.99        19.07        33.99        40.01        16.01 
TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E 
        9.99         9.99        12.00         1.02        13.02        31.00 
TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T 
       33.07        29.98        15.02         1.02         8.98        19.04 
TCGA-A8-A09V TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 
       15.02        14.01        12.00        19.04        13.02        21.04 
TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E 
        0.99        13.02        17.03        38.04         0.95         2.37 
TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF 
       10.85         2.66         1.48        38.20        40.57        55.43 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI 
       36.99        38.79        26.04        50.70         1.02         0.92 
TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 
        2.27         0.99         0.69         9.40         1.12         1.81 
TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y 
        1.68         1.55         1.32         1.55         0.07         1.81 
TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A041 
        1.18         0.69         0.43         1.74         0.33         0.23 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ 
        0.33         0.62         2.96         1.78         1.71         8.02 
TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT 
        7.36         6.51         0.16         0.33         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN 
        6.44         4.64         7.96         7.00         7.59         7.17 
TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN 
        6.28         0.33         0.36         0.33         0.33         0.33 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU 
       12.33         0.30         0.33         0.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03P TCGA-AO-A03R 
        5.33         5.59        80.28        47.84        84.69        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J6 
       47.87        59.05        29.13        21.40        24.16        37.48 
TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC 
       20.32        22.36        53.03        21.53        50.70        50.86 
TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ 
       72.00        76.77        21.37        26.24        38.53        62.04 
TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12A 
       55.33       102.58        99.25        93.70        96.10        90.58 
TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       64.04        57.30        41.62        28.37        14.73        82.62 
TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       61.87         0.53        17.79        24.79        26.93       130.09 
TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 
        5.65        15.62        13.22         2.56        21.86         9.99 
TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV 
       82.88        49.32         5.26        37.41        56.88        29.75 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 
       64.83        55.86        76.14        65.36        70.16        83.87 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK 
       76.18        55.36        75.55        61.84        52.77        51.25 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ 
       48.82        62.56        43.73        43.56        39.98        43.07 
TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY 
       17.23        40.83        46.32        35.24        36.26        20.22 
TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
      109.58        50.89        73.02        65.46        68.19        65.69 
TCGA-AR-A24P TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W 
        0.85        62.07        53.26        53.36        54.18        50.96 
TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A256 TCGA-AR-A2LE 
       48.16        56.15        45.17        40.64        93.83       128.65 
TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       20.25        42.87         7.36        40.04        17.10        20.81 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       16.96        20.38        16.04        20.45        10.59        77.62 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG 
       12.13       220.90       129.57        50.70        65.72       146.50 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO 
      112.37       176.98        18.77       126.12        84.59       110.14 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
      110.93       140.88       211.56        68.45       189.01       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ 
       81.17        78.02       172.96       162.05       102.77       140.48 
TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT 
      100.70        89.46       131.21       157.41        97.48       188.68 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0X0 TCGA-B6-A0X4 
       79.63        17.98        21.47       113.79       129.70        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU 
       68.94        58.88        43.59        73.51       139.17       170.17 
TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
       85.35        54.28        49.94        82.88        55.00        24.53 
TCGA-BH-A0AV TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 
       38.79        28.50        46.95        40.83        39.55        39.16 
TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC 
       48.36        56.94        56.98        51.68        37.22        32.02 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM 
       18.21        25.71        24.85        21.70        44.05        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV 
       35.67        48.69        27.19        53.95        45.57        49.94 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 
       11.67        49.05        41.75        44.02        48.13        42.90 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       45.83        31.17        23.44        38.01        22.13        13.91 
TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       17.26        15.65         3.22        38.47        45.17        47.41 
TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0E9 
       16.27         4.41        15.68        14.30        44.81        46.19 
TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       32.65        24.49        31.00        10.78        15.16        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB 
       35.51        24.56        23.08        41.00        52.96        26.50 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HW TCGA-BH-A0HX 
       20.38         5.85         2.50        13.61        51.32        27.25 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       50.79         5.59        23.93        24.95        42.35        44.81 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L 
        8.81         2.01         7.23        20.12        90.84        26.66 
TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U 
       72.56        30.28        37.55        66.05         7.36        51.39 
TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW 
       51.16        69.93       113.82        42.28        12.00        55.69 
TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 
       49.58        17.69        31.53        89.16        97.48        24.66 
TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
      120.62        33.17        74.73       122.89        36.92        63.35 
TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 
       55.00        45.63        72.07       144.59        72.07         6.90 
TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
       38.60        83.31        57.83        10.65         6.44        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P 
        0.99       109.28         8.94        11.77        12.66        11.77 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 
        0.07        12.66        12.66        12.66        12.66         3.12 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 
        1.78         1.45         0.69         0.62         3.85         3.75 
TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL 
       12.33        10.92        11.34         0.16        12.03        10.42 
TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y 
        2.30         3.25         0.30         0.23         0.36         0.43 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 
        8.28         9.67         0.03        12.20         0.99         0.03 
TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A145 
        0.23        11.90        20.88        13.25        20.58        13.48 
TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
       21.14        19.20        14.17        17.49        16.50        18.71 
TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI 
       15.78        18.90        12.03        12.03        14.01        18.97 
TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP 
       20.09        20.12        20.09        19.40        20.38        21.01 
TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 
       12.20        14.70        17.79        16.73        25.74        23.90 
TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG 
       27.58        18.15         2.66        17.16        15.22        14.73 
TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR 
       21.83        14.50        19.92        17.69         7.96        15.85 
TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1Y0 
       16.31         6.35        12.99        15.16        16.54        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G 
        3.81        14.24        14.14        17.42        16.04        13.45 
TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N 
       13.05        14.43         9.44        16.41        13.48         4.80 
TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A3Z5 TCGA-D8-A4Z1 TCGA-E2-A105 
        0.76        10.09        13.08        14.50         7.33        43.00 
TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A10E 
       34.42        27.52        46.59        40.41        40.11        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14T 
       28.87        47.15        44.68        38.24        38.60        33.30 
TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 
       43.33        32.02        17.03        25.41        27.12        23.24 
TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A 
       19.43        21.04        23.87        14.79        25.05        23.34 
TCGA-E2-A15C TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I 
       22.82        20.71        21.63        18.21        12.92        17.42 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P 
       19.40         9.04        20.58         7.73        13.02        19.56 
TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B1 TCGA-E2-A1B4 
       17.06        14.07        14.99        60.53        53.03        29.95 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF 
       32.35        28.50        16.47        17.10        38.30        37.41 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       32.78        33.73        33.70        28.44        22.65         3.88 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 
       22.19        20.98        11.08        54.18        27.42        39.62 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH 
       19.66        24.59        40.47        28.90        18.87       106.75 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX 
      102.61         8.75        43.04        16.93         5.52        15.72 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 
       18.05        22.26        19.89        19.20        36.82        12.00 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF 
       13.12        36.56        39.55        12.59        35.77        20.05 
TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 
       21.57         9.86        11.90        14.30         0.62         2.10 
TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB 
        6.12         1.38         2.76        21.21        32.09        20.81 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI 
        0.66        34.65         6.58        21.27        34.59        35.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       34.13         0.79        12.53        13.32        39.09        22.75 
TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A245 
       12.89        23.51        24.10        17.06         0.69         0.85 
TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JT 
       27.22         1.94         0.95        12.56         0.72         0.76 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FK 
       26.07        18.41         0.62        15.72         0.23         0.39 
TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J1 
        0.23        15.39        12.20        39.72        18.21        18.90 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW 
       13.25        16.57        15.68        28.77        25.94        22.82 
TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 
       29.95        29.85        40.41        41.13        39.78        52.96 
TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PC 
       29.82        18.48        30.08         7.86        18.90         6.15 
TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR 
       13.94        10.52        14.43        34.55        19.96        55.00 
TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 
       52.73        25.91        22.09        21.27        17.49        10.16 
TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC 
       10.59         7.40        59.57       194.27        53.13        53.52 
TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       43.04        42.71        42.28        61.91        62.33        90.84 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
       76.64        77.33        53.36       110.50        38.20        32.28 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW 
       69.30        53.95        57.63        13.55        18.12        11.84 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 
       11.57         8.28         6.67         4.60         0.66         2.99 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO 
        3.58         6.90         5.56         4.70         3.65         3.19 
TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 
        3.25         3.88         4.50         4.50         5.59         3.22 
TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 
        6.21        15.91         2.79         2.10        12.66        46.55 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX 
        7.53        44.61        27.65        24.10        26.20        16.87 
TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K 
       14.10        10.29         9.80        14.76        54.51        33.90 
TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-S3-A6ZG TCGA-W8-A86G 
       31.07        18.21         7.23         4.44         6.81         5.29 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.03              0.03 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           186.48            234.28 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           23.095            21.240 
[1] "0.0 - 186.5 (23.1)" "0.0 - 234.3 (21.2)"
[1] "hr=" "1.4"
D40V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XQ GAIN MUTATED         9        8        2        1        51        26
  XQ GAIN WILD-TYPE      71       69        7        8       284       198
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XQ GAIN MUTATED           0         17          3          8        5
  XQ GAIN WILD-TYPE         2        121         24         51       12
                   vv
clus                STAGE TIS STAGE X
  XQ GAIN MUTATED           0       0
  XQ GAIN WILD-TYPE         1      16
D40V3, multiclass
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                  9                71
  STAGE IA                 8                69
  STAGE IB                 2                 7
  STAGE II                 1                 8
  STAGE IIA               51               284
  STAGE IIB               26               198
  STAGE III                0                 2
  STAGE IIIA              17               121
  STAGE IIIB               3                24
  STAGE IIIC               8                51
  STAGE IV                 5                12
  STAGE TIS                0                 1
  STAGE X                  0                16
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  XQ GAIN MUTATED    29  85  13   3
  XQ GAIN WILD-TYPE 229 496 104  33
D40V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1              29               229
  T2              85               496
  T3              13               104
  T4               3                33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  XQ GAIN MUTATED    65  38  16  10
  XQ GAIN WILD-TYPE 403 292  95  60
D40V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              65               403
  N1              38               292
  N2              16                95
  N3              10                60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  XQ GAIN MUTATED          0 112   5  13
  XQ GAIN WILD-TYPE        2 733  12 118
D40V6, multiclass
          clus
vv         XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CM0 (I+)               0                 2
  M0                   112               733
  M1                     5                12
  MX                    13               118
[1] 4 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   129   1
  XQ GAIN WILD-TYPE 855  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED    129    1
  XQ GAIN WILD-TYPE  855   10
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE             129               855
  MALE                 1                10
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  XQ GAIN MUTATED                            1                           110
  XQ GAIN WILD-TYPE                          0                           625
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  XQ GAIN MUTATED                                8                   2
  XQ GAIN WILD-TYPE                            158                   3
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  XQ GAIN MUTATED                                  1                  3
  XQ GAIN WILD-TYPE                               28                 11
                   vv
clus                OTHER  SPECIFY
  XQ GAIN MUTATED                4
  XQ GAIN WILD-TYPE             40
D40V8, multiclass
                                  clus
vv                                 XQ GAIN MUTATED XQ GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                110               625
  INFILTRATING LOBULAR CARCINOMA                 8               158
  MEDULLARY CARCINOMA                            2                 3
  MIXED HISTOLOGY (PLEASE SPECIFY)               1                28
  MUCINOUS CARCINOMA                             3                11
  OTHER  SPECIFY                                 4                40
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V9, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    46  84
  XQ GAIN WILD-TYPE 236 629
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     46   84
  XQ GAIN WILD-TYPE  236  629
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO               46               236
  YES              84               629
[1] 2 2
[1] FALSE
D40V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ GAIN MUTATED                                  0     6
  XQ GAIN WILD-TYPE                                1    50
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED                          24    81
  XQ GAIN WILD-TYPE                       113   627
D40V11, multiclass
                                  clus
vv                                 XQ GAIN MUTATED XQ GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          6                50
  BLACK OR AFRICAN AMERICAN                     24               113
  WHITE                                         81               627
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V12, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     3  98
  XQ GAIN WILD-TYPE  33 698
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      3   98
  XQ GAIN WILD-TYPE   33  698
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                33
  NOT HISPANIC OR LATINO              98               698
[1] 2 2
[1] FALSE

Clustering(41) Variable = 1P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED   185  36
  1P LOSS WILD-TYPE 675  78
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              221               753 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               36                78 
$`1P LOSS MUTATED`
TCGA-A1-A0SN TCGA-A2-A04R TCGA-A2-A0CS TCGA-A2-A0CW TCGA-A2-A0D4 TCGA-A2-A0EN 
       39.32        82.16        75.55        64.04        25.22        89.36 
TCGA-A2-A0EO TCGA-A2-A0EQ TCGA-A2-A0ET TCGA-A2-A0EY TCGA-A2-A0SV TCGA-A2-A0T4 
       80.28        79.76        35.05        24.16        27.12        20.52 
TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A1FW TCGA-A2-A1FX 
       18.21        15.42        21.90        21.67        17.36        36.79 
TCGA-A2-A25C TCGA-A2-A3KC TCGA-A2-A3XU TCGA-A2-A4S3 TCGA-A7-A0CJ TCGA-A7-A56D 
       17.19        20.88        29.98         3.42        30.61        14.73 
TCGA-A7-A5ZV TCGA-A8-A06O TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A075 
       12.10        13.02        41.06        29.03        26.01        17.03 
TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07L TCGA-A8-A07R 
        9.01        33.01        18.97        18.97        17.03         8.98 
TCGA-A8-A084 TCGA-A8-A08B TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A092 
       15.06        23.08        37.05        31.00        19.07        16.01 
TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E 
        9.99         9.99        12.00         1.02        13.02        31.00 
TCGA-A8-A09I TCGA-A8-A09N TCGA-A8-A09X TCGA-A8-A0A2 TCGA-A8-A0A6 TCGA-A8-A0A9 
       33.07         1.02        14.01        19.04        21.04        13.02 
TCGA-A8-A0AB TCGA-AC-A23E TCGA-AC-A2BK TCGA-AC-A2FM TCGA-AC-A3BB TCGA-AC-A8OP 
       17.03         2.37        38.53        26.04         0.99         1.74 
TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A04A TCGA-AN-A0AL 
        0.33         0.33         0.23         0.33         2.96         6.51 
TCGA-AN-A0AR TCGA-AN-A0FD TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0XP TCGA-AN-A0XS 
        0.33         6.44         7.00         7.17         0.30         0.33 
TCGA-AN-A0XU TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A0J5 TCGA-AO-A0J7 
        0.33        80.28        66.77        84.69        24.16        20.32 
TCGA-AO-A0JA TCGA-AO-A0JI TCGA-AO-A12A TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS 
       21.53        38.53        90.58        82.62        61.87         0.53 
TCGA-AQ-A0Y5 TCGA-AR-A0TQ TCGA-AR-A0U2 TCGA-AR-A1AP TCGA-AR-A1AW TCGA-AR-A24H 
        5.65        49.32        83.87        39.98        35.24       109.58 
TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A250 TCGA-AR-A254 TCGA-AR-A2LK TCGA-AR-A2LL 
       57.40        53.26        56.15        39.85        42.87         7.36 
TCGA-AR-A2LO TCGA-AR-A5QN TCGA-B6-A0I9 TCGA-B6-A0IB TCGA-B6-A0IG TCGA-B6-A0IJ 
       20.81        16.04        12.13       129.57       146.50       176.98 
TCGA-B6-A0IO TCGA-B6-A0RL TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RS TCGA-B6-A0WV 
      110.14        81.17       162.05       102.77       100.70        79.63 
TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN 
       17.98        21.47       113.79       101.52        73.51       139.17 
TCGA-B6-A40B TCGA-BH-A0B2 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0BA TCGA-BH-A0BV 
       82.88        40.83        48.36        56.94        37.22        49.94 
TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0E2 TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0GY 
       41.75        44.02        14.30        46.19        24.49        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H7 TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A18F TCGA-BH-A18K 
       10.78        23.08        12.89        51.32         8.81        90.84 
TCGA-BH-A18L TCGA-BH-A18P TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EU 
       26.66        30.28         7.36        51.39        69.93        42.28 
TCGA-BH-A1EV TCGA-BH-A1F8 TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FM TCGA-BH-A204 
       12.00        24.66       114.15        74.73        45.63        83.31 
TCGA-BH-A209 TCGA-BH-A42T TCGA-C8-A12P TCGA-C8-A12W TCGA-C8-A131 TCGA-C8-A138 
      130.16         0.99        11.77        12.66         1.78         3.75 
TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A274 TCGA-C8-A27A 
       12.03        10.42         0.36         8.28         0.03        12.20 
TCGA-C8-A3M7 TCGA-D8-A142 TCGA-D8-A146 TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JI 
        0.03        13.97        21.14        18.90        12.03        18.97 
TCGA-D8-A1JJ TCGA-D8-A1JM TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XQ TCGA-D8-A1XR 
       20.09        19.40        15.22        14.73        16.41        15.85 
TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A1Y3 
       16.31        12.99        15.16        15.32         3.81        14.14 
TCGA-D8-A27I TCGA-D8-A27T TCGA-D8-A27W TCGA-E2-A107 TCGA-E2-A10E TCGA-E2-A14O 
       14.43        13.08        12.26        34.42        28.44        44.68 
TCGA-E2-A14V TCGA-E2-A15R TCGA-E2-A1IH TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-E9-A1NA 
       34.26        17.06        33.73        18.87        16.93        36.56 
TCGA-E9-A1ND TCGA-E9-A1NI TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1RC TCGA-E9-A1RG 
       12.59         9.86         2.10         1.38        40.24        21.27 
TCGA-E9-A22A TCGA-E9-A22E TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A295 
       39.09        12.89         0.69        27.22         0.95         0.72 
TCGA-E9-A2JS TCGA-E9-A3HO TCGA-E9-A54Y TCGA-E9-A5FK TCGA-EW-A1J6 TCGA-EW-A1OY 
       17.75        26.07         0.23         0.39        28.77        29.85 
TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1PC TCGA-EW-A1PE TCGA-EW-A1PH TCGA-EW-A2FR 
       52.96        23.11         6.15        10.52        19.96        55.00 
TCGA-EW-A2FV TCGA-EW-A2FW TCGA-GI-A2C8 TCGA-GM-A3NW TCGA-JL-A3YX TCGA-LL-A5YL 
       25.91        22.09         7.40       110.50        11.57         5.56 
TCGA-LL-A5YM TCGA-OK-A5Q2 TCGA-OL-A5RZ TCGA-OL-A66K TCGA-OL-A66N 
        4.70         2.10        10.29        33.90        18.21 

$`1P LOSS WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SP 
       20.88        13.68        31.79         7.96        28.01        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04T TCGA-A2-A04U 
       18.21       104.81        18.02        41.95        73.84        22.06 
TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL 
       63.12        64.04        55.43        36.13       125.59        64.57 
TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CT 
       24.79       112.08        92.48        88.60       107.93        75.25 
TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 
        5.19        63.45        56.81        21.14        34.55        33.76 
TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EU 
       28.77       101.72       107.61        74.40        37.05        34.29 
TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW 
       31.82        29.75        24.72        99.19        54.64        44.88 
TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 
       50.43        44.28        17.52        17.13         8.38        18.71 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YI 
       17.46        18.90        20.75        32.55        25.28        14.50 
TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV 
       18.61        19.33        14.63        31.73        23.77        23.47 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       22.45        20.25        19.20        19.56        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KD 
      107.70        16.31        18.15        91.92        10.59        39.65 
TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       33.93        83.01        14.07        49.48        38.40        34.98 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       31.99        38.37         7.30         9.01         8.81         8.91 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH 
       12.00         6.74        38.30        35.31        34.29        35.47 
TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F 
       37.45        35.67        33.11        31.73        10.72        12.72 
TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H 
       23.61        29.56        31.36        24.26        23.74        23.80 
TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 
       21.73        20.61        22.32        11.34        10.59        10.29 
TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB 
       11.28        13.41        14.70        11.97        14.93        13.74 
TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV 
       14.50        21.17        17.92        10.72        11.05        10.29 
TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R 
        9.37        10.42         8.75        13.02         1.02        17.98 
TCGA-A8-A06X TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A07E TCGA-A8-A07I TCGA-A8-A07J 
       31.00         1.02        53.98        19.99        14.01        12.00 
TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z 
        9.99        10.98         7.99         9.96         9.99        28.04 
TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08F 
       18.05        36.95        13.02         0.99        19.99        18.05 
TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08T 
       19.96        12.00         9.99        31.00         0.99        93.04 
TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 
       33.99        40.01        19.07        17.95        41.98        12.00 
TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       29.98        15.02        25.02         8.98        19.04        15.02 
TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A4 TCGA-A8-A0A7 TCGA-A8-A0AD TCGA-AC-A23C 
        0.99        12.00        13.02         0.99        38.04         0.95 
TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF 
       10.85         2.66         1.48        38.20        40.57        55.43 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ 
       36.99        38.79        50.70         1.02         0.92         2.27 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 
        0.69        14.83         9.40         1.12         1.81         1.68 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y 
        1.55         1.32         1.55         0.07         1.12         1.81 
TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D 
        1.18         0.69         0.43         0.62         1.78         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FF 
        8.02         7.36         0.16         0.33         0.33         4.64 
TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW 
        7.96         7.59         6.28         6.02         0.33         0.36 
TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO 
        0.33         0.33         0.33         0.33         0.33        12.33 
TCGA-AN-A0XR TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03O 
        0.33         0.33         5.33         5.59        47.84        81.63 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 
       68.75        47.87        59.05        29.13        32.78        21.40 
TCGA-AO-A0J4 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JB TCGA-AO-A0JC 
       17.65        37.48        22.36        53.03        50.70        50.86 
TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A0JL 
       72.00        76.77        21.37        26.24        62.04        55.33 
TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 
       71.80       102.58        99.25        93.70        94.59        96.10 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
       77.56        64.04        57.30        48.36        41.62        28.37 
TCGA-AO-A1KO TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       14.73        70.39        17.79        24.79        26.93       130.09 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP 
       15.62        13.22         2.56        21.86         9.99        82.88 
TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX 
        5.26        37.41        56.88        29.75        24.30        64.83 
TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 
       55.86        76.14        65.36        70.16        76.18        55.36 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM 
       75.55        61.84        52.77        51.25        48.82        62.56 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU 
       43.73        43.56        43.07        17.23        40.83        46.32 
TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M 
       42.58        36.26        20.22        50.89        73.02        65.46 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24U 
       68.19        65.69         0.85        66.05        62.07        53.36 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 
       54.18        50.96        48.16        51.75        45.17        40.64 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LM TCGA-AR-A2LN 
       34.82        93.83       128.65        20.25        40.04        17.10 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       16.96        20.38        54.74        20.45        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IH 
      143.38       149.59       220.90        50.70        65.72       112.37 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE 
       18.77       126.12        84.59       110.93       140.88       211.56 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RQ 
       68.45       189.01       234.28        78.02       172.96       140.48 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WZ 
       89.46       131.21       157.41        97.48       188.68       129.57 
TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC 
      129.70       186.48        28.27        68.94        58.88        43.59 
TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40C TCGA-BH-A0AU 
      170.17        85.35        54.28        49.94        55.00        24.53 
TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 
       38.79        20.45        25.55        28.50        46.95        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       39.16        56.98        51.68        32.02        18.21        25.71 
TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP 
       24.85        21.70        44.05        61.68        35.67        48.69 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BW TCGA-BH-A0BZ 
       27.19        53.69        53.95        45.57        11.67        49.05 
TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH 
       48.13        42.90        45.83        31.17        23.44        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ 
       22.13        13.91        48.23        17.26        15.65         3.22 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
        2.56        38.47        45.17        47.41        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0EI 
       15.68         9.63        44.81        32.65        31.00        24.43 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HA 
       15.16        37.78        35.51        24.56        41.00        52.96 
TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ 
       26.50        20.38         5.85         2.50        13.61        36.85 
TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 
       27.25        50.79         5.59        23.93        24.95        42.35 
TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18M 
       44.81        23.05         2.01         7.23        20.12        72.56 
TCGA-BH-A18N TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18V TCGA-BH-A1EO 
       37.74        55.63        37.55        66.05        51.16        91.99 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 
      113.82        82.85        55.69        49.58        17.69        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FG 
       31.53        89.16        97.48       120.62        33.17       122.89 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU 
       36.92        63.35        55.00        72.07       144.59        72.07 
TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A28O TCGA-BH-A28Q 
        6.90         0.72        38.60        57.83        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N 
       20.12       109.28         8.94        11.93        11.77        11.77 
TCGA-C8-A12O TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A130 
       12.66         0.07        12.66        12.66        12.66         3.12 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF 
        1.45         0.69         0.62         3.85        12.33        10.92 
TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V 
       11.34        11.34         0.16         2.30         3.25         0.30 
TCGA-C8-A26W TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B 
        0.23         0.43         9.67         0.03         0.03         0.99 
TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 
        0.23        11.90        20.88        13.25        20.58        14.17 
TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
       13.48        19.20        14.17        17.49        16.50        18.71 
TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JK TCGA-D8-A1JL 
       15.78        18.15        12.03        14.01        20.12        20.09 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 
       20.38        21.01        12.20        13.32        14.70        18.58 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB 
       17.79        16.73        25.74        23.90        27.58        18.15 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM 
        2.66        17.16        21.83        14.50        19.92        17.69 
TCGA-D8-A1XO TCGA-D8-A1XT TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y2 
        7.96         6.35        12.66        16.54        15.52        14.24 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27K TCGA-D8-A27L 
       17.42        16.04        13.45        13.05         9.44        16.41 
TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27V TCGA-D8-A3Z5 
       13.48         4.80         0.76        10.09        12.53        14.50 
TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A 
       18.51         7.33        43.00        27.52        46.59        40.41 
TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q 
       37.51        40.11        28.87        47.15        40.96        38.24 
TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14X 
       38.60        33.17        33.30        43.33        32.02        31.96 
TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 
       28.60        17.03        25.41        27.12        23.24        19.43 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C 
       21.04        23.87        14.79        25.05        23.34        22.82 
TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I 
       17.29        20.71        21.63        18.21        12.92        17.42 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P 
       19.40         9.04        20.58         7.73        13.02        19.56 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 
       14.07        14.99        60.53        53.62        53.03        29.95 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF 
       32.35        28.50        16.47        17.10        38.30        37.41 
TCGA-E2-A1IG TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN 
       32.78        33.70        28.44        22.65         3.88        22.19 
TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 
       20.98        11.08        54.18        27.42        39.62        19.66 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK 
       24.59        40.47        28.90       106.75       102.61         8.75 
TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 
       43.04         5.52        15.72         7.20        18.05        22.26 
TCGA-E2-A574 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 
       19.89        19.20        36.82        13.48        12.00        13.12 
TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1QZ TCGA-E9-A1R0 
       39.55        35.77        20.05        21.57        11.90        14.30 
TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB 
        0.62         6.12         2.76        21.21        32.09        20.81 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 
        0.66        34.65         6.58        34.59        35.64        34.13 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22B TCGA-E9-A22G TCGA-E9-A22H 
        0.79        12.53        13.32        22.75        23.51        24.10 
TCGA-E9-A243 TCGA-E9-A245 TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3Q9 
       17.06         0.85         1.94        12.56         0.76        18.41 
TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW 
        0.62        15.72         0.26         0.23        15.39        12.20 
TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 
       39.72         8.48        18.21        18.90        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1P0 
       15.68        25.94        22.82        29.95        40.41        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA 
       39.78        29.82        18.48        30.08         7.86        18.90 
TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FS TCGA-EW-A3E8 
       19.99        13.94        14.43        34.55        52.73        21.27 
TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       17.49        10.16        10.59       109.87        59.57       194.27 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI 
       53.13        53.52        43.04        42.71        42.28        61.91 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NY 
       62.33        90.84        76.64        77.33        53.36        38.20 
TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX 
       32.28        69.30        53.95        57.63        13.55        18.12 
TCGA-JL-A3YW TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 
       11.84         8.28         6.67         4.60         0.66         2.99 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FQ 
        3.58         6.90         3.65         3.19         3.25         2.63 
TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 
        3.88         4.14         4.50         4.50         5.59         3.22 
TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 
        6.21        15.91         2.79        12.66        46.55         7.53 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY 
       44.61        27.65        24.10        26.20        16.87        14.10 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66O 
        9.80        14.76        23.70        54.51        31.07         7.23 
TCGA-OL-A66P TCGA-S3-A6ZG TCGA-W8-A86G 
        4.44         6.81         5.29 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.03              0.03 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           176.98            234.28 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            20.32             22.06 
[1] "0.0 - 177.0 (20.3)" "0.0 - 234.3 (22.1)"
[1] "hr=" "1.5"
D41V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1P LOSS MUTATED        12       11        1        3        73        39
  1P LOSS WILD-TYPE      68       66        8        6       262       185
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1P LOSS MUTATED           1         42         16         18        6
  1P LOSS WILD-TYPE         1         96         11         41       11
                   vv
clus                STAGE TIS STAGE X
  1P LOSS MUTATED           0       4
  1P LOSS WILD-TYPE         1      12
D41V3, multiclass
            clus
vv           1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                 12                68
  STAGE IA                11                66
  STAGE IB                 1                 8
  STAGE II                 3                 6
  STAGE IIA               73               262
  STAGE IIB               39               185
  STAGE III                1                 1
  STAGE IIIA              42                96
  STAGE IIIB              16                11
  STAGE IIIC              18                41
  STAGE IV                 6                11
  STAGE TIS                0                 1
  STAGE X                  4                12
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  1P LOSS MUTATED    46 133  27  20
  1P LOSS WILD-TYPE 212 448  90  16
D41V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1              46               212
  T2             133               448
  T3              27                90
  T4              20                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  1P LOSS MUTATED    89  75  35  23
  1P LOSS WILD-TYPE 379 255  76  47
D41V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0              89               379
  N1              75               255
  N2              35                76
  N3              23                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  1P LOSS MUTATED          0 194   6  26
  1P LOSS WILD-TYPE        2 651  11 105
D41V6, multiclass
          clus
vv         1P LOSS MUTATED 1P LOSS WILD-TYPE
  CM0 (I+)               0                 2
  M0                   194               651
  M1                     6                11
  MX                    26               105
[1] 4 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   224   2
  1P LOSS WILD-TYPE 760   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED    224    2
  1P LOSS WILD-TYPE  760    9
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE             224               760
  MALE                 2                 9
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  1P LOSS MUTATED                            1                           169
  1P LOSS WILD-TYPE                          0                           566
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  1P LOSS MUTATED                               39                   2
  1P LOSS WILD-TYPE                            127                   3
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  1P LOSS MUTATED                                  5                  2
  1P LOSS WILD-TYPE                               24                 12
                   vv
clus                OTHER  SPECIFY
  1P LOSS MUTATED                8
  1P LOSS WILD-TYPE             36
D41V8, multiclass
                                  clus
vv                                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                169               566
  INFILTRATING LOBULAR CARCINOMA                39               127
  MEDULLARY CARCINOMA                            2                 3
  MIXED HISTOLOGY (PLEASE SPECIFY)               5                24
  MUCINOUS CARCINOMA                             2                12
  OTHER  SPECIFY                                 8                36
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V9, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    61 165
  1P LOSS WILD-TYPE 221 548
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     61  165
  1P LOSS WILD-TYPE  221  548
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO               61               221
  YES             165               548
[1] 2 2
[1] FALSE
D41V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P LOSS MUTATED                                  0    14
  1P LOSS WILD-TYPE                                1    42
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED                          28   150
  1P LOSS WILD-TYPE                       109   558
D41V11, multiclass
                                  clus
vv                                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         14                42
  BLACK OR AFRICAN AMERICAN                     28               109
  WHITE                                        150               558
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V12, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     6 171
  1P LOSS WILD-TYPE  30 625
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      6  171
  1P LOSS WILD-TYPE   30  625
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                30
  NOT HISPANIC OR LATINO             171               625
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    40   9
  1Q LOSS WILD-TYPE 820 105
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               49               925 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                9               105 
$`1Q LOSS MUTATED`
TCGA-A2-A0CW TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A4S3 
       64.04        18.21        15.42        17.36        36.79         3.42 
TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A079 TCGA-A8-A07L TCGA-A8-A08J TCGA-A8-A08S 
       41.06        29.03         9.01        17.03        37.05        19.07 
TCGA-A8-A09N TCGA-AC-A3BB TCGA-AN-A04A TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0XS 
        1.02         0.99         2.96         6.51         0.33         0.33 
TCGA-AN-A0XU TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A1KP TCGA-AO-A1KS TCGA-AR-A0TQ 
        0.33        66.77        84.69        82.62         0.53        49.32 
TCGA-AR-A0U2 TCGA-AR-A24H TCGA-AR-A24T TCGA-B6-A0IG TCGA-B6-A0RL TCGA-BH-A0B6 
       83.87       109.58        53.26       146.50        81.17        56.94 
TCGA-BH-A0BV TCGA-BH-A0E2 TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0HW TCGA-BH-A1FC 
       49.94        14.30        30.35        10.78        51.32       114.15 
TCGA-BH-A1FE TCGA-BH-A204 TCGA-BH-A42T TCGA-C8-A138 TCGA-C8-A27A TCGA-D8-A1XQ 
       74.73        83.31         0.99         3.75        12.20        16.41 
TCGA-D8-A1XU TCGA-D8-A1XZ TCGA-E2-A15R TCGA-E9-A1ND TCGA-E9-A1RC TCGA-EW-A1J6 
       12.99        15.32        17.06        12.59        40.24        28.77 
TCGA-OL-A5RZ 
       10.29 

$`1Q LOSS WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
       20.88        13.68        31.79         7.96        39.32        28.01 
TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R 
       19.20        18.21       104.81        18.02        41.95        82.16 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
       73.84        22.06        63.12        64.04        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
      125.59        64.57        24.79       112.08        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CX 
      107.93        75.55        75.25         5.19        63.45        56.81 
TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM 
       21.14        34.55        33.76        28.77        25.22       101.72 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES 
       89.36        80.28       107.61        79.76        74.40        37.05 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY 
       35.05        34.29        31.82        29.75        24.72        24.16 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY 
       99.19        54.64        27.12        44.88        50.43        44.28 
TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 
       17.52        17.13         8.38        18.71        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YG TCGA-A2-A0YH 
       18.90        20.75        32.55        25.28        21.90        21.67 
TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT 
       14.50        18.61        19.33        14.63        31.73        23.77 
TCGA-A2-A1FV TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 
       23.47        22.45        20.25        19.20        19.56        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       52.47       107.70        16.31        17.19        18.15        91.92 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU 
       10.59        20.88        39.65        33.93        83.01        29.98 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 
       14.07        49.48        38.40        34.98        31.99        38.37 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 
        7.30         9.01         8.81         8.91        12.00         6.74 
TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 
       38.30        35.31        34.29        35.47        30.61        37.45 
TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G 
       35.67        33.11        31.73        10.72        12.72        23.61 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I 
       29.56        31.36        24.26        23.74        23.80        21.73 
TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       20.61        22.32        11.34        10.59        10.29        11.28 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD 
       13.41        14.70        11.97        14.93        13.74        14.50 
TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX 
       21.17        17.92        14.73        12.10        10.72        11.05 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P 
       10.29         9.37        10.42         8.75        13.02        13.02 
TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 
        1.02        17.98        31.00        26.01         1.02        17.03 
TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I 
       53.98        33.01        19.99        18.97        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U 
       12.00         9.99        10.98         8.98         7.99         9.96 
TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 
        9.99        28.04        18.05        15.06        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I 
        0.99        23.08        19.99        18.05        19.96        12.00 
TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X 
        9.99        31.00        31.00         0.99        93.04        33.99 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 
       40.01        19.07        16.01        17.95        41.98        12.00 
TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E 
        9.99         9.99        12.00         1.02        13.02        31.00 
TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T 
       33.07        29.98        15.02        25.02         8.98        19.04 
TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 
       15.02         0.99        14.01        12.00        19.04        13.02 
TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C 
       21.04         0.99        13.02        17.03        38.04         0.95 
TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM 
        2.37        10.85         2.66         1.48        38.53        38.20 
TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO 
       40.57        55.43        36.99        38.79        26.04        50.70 
TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
        1.02         0.92         2.27         0.69        14.83         9.40 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS 
        1.12         1.81         1.68         1.55         1.32         1.55 
TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX 
        0.07         1.12         1.81         1.18         0.69         0.43 
TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 
        1.74         0.33         0.33         0.23         0.33         0.62 
TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0AS 
        1.78         1.71         8.02         7.36         0.16         0.33 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL 
        0.33         6.44         4.64         7.96         7.00         7.59 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX 
        7.17         6.28         6.02         0.33         0.36         0.33 
TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP 
        0.33         0.33         0.33         0.33        12.33         0.30 
TCGA-AN-A0XR TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M 
        0.33         0.33         5.33         5.59        80.28        47.84 
TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 
       81.63        68.75        47.87        59.05        29.13        32.78 
TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 
       21.40        17.65        24.16        37.48        20.32        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE 
       53.03        21.53        50.70        50.86        72.00        76.77 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM 
       21.37        26.24        38.53        62.04        55.33        71.80 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A 
      102.58        99.25        93.70        94.59        96.10        90.58 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
       77.56        64.04        57.30        48.36        41.62        28.37 
TCGA-AO-A1KO TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J 
       14.73        61.87        70.39        17.79        24.79        26.93 
TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O 
      130.09         5.65        15.62        13.22         2.56        21.86 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV 
        9.99        82.88         5.26        37.41        56.88        29.75 
TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 
       24.30        64.83        55.86        76.14        65.36        70.16 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK 
       76.18        55.36        75.55        61.84        52.77        51.25 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ 
       48.82        62.56        43.73        43.56        39.98        43.07 
TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX 
       17.23        40.83        46.32        42.58        35.24        36.26 
TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       20.22        50.89        73.02        65.46        68.19        65.69 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24U TCGA-AR-A24V 
        0.85        66.05        57.40        62.07        53.36        54.18 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 
       50.96        48.16        51.75        56.15        45.17        40.64 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LK 
       39.85        34.82        93.83       128.65        20.25        42.87 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
        7.36        40.04        17.10        20.81        16.96        20.38 
TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 
       54.74        16.04        20.45        10.59        77.62       143.38 
TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
      149.59        12.13       220.90       129.57        50.70        65.72 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO 
      112.37       176.98        18.77       126.12        84.59       110.14 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
      110.93       140.88       211.56        68.45       189.01       234.28 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS 
       78.02       172.96       162.05       102.77       140.48       100.70 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV 
       89.46       131.21       157.41        97.48       188.68        79.63 
TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 
       17.98        21.47       113.79       129.57       129.70       186.48 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI 
       28.27        68.94        58.88        43.59       101.52        73.51 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B 
      139.17       170.17        85.35        54.28        49.94        82.88 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ 
       55.00        24.53        38.79        20.45        25.55        28.50 
TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 
       46.95        40.83        39.55        39.16        48.36        56.98 
TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG 
       51.68        37.22        32.02        18.21        25.71        24.85 
TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ 
       21.70        44.05        61.68        35.67        48.69        27.19 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 
       53.69        53.95        45.57        11.67        49.05        41.75 
TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG 
       44.02        48.13        42.90        45.83        31.17        23.44 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP 
       38.01        22.13        13.91        48.23        17.26        15.65 
TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ 
        3.22         2.56        38.47        45.17        47.41        16.27 
TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA 
        4.41        15.68         9.63        44.81        46.19        32.65 
TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       24.49        31.00        24.43        15.16        37.78        35.51 
TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI 
       24.56        23.08        41.00        52.96        26.50        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HX 
        5.85         2.50        13.61        36.85        12.89        27.25 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       50.79         5.59        23.93        24.95        42.35        44.81 
TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K 
       23.05         8.81         2.01         7.23        20.12        90.84 
TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R 
       26.66        72.56        37.74        30.28        55.63        37.55 
TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO 
       66.05         7.36        51.39        51.16        69.93        91.99 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX 
      113.82        82.85        42.28        12.00        55.69        49.58 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 
       17.69        25.81        31.53        89.16        97.48        24.66 
TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
      120.62        33.17       122.89        36.92        63.35        55.00 
TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 
       45.63        72.07       144.59        72.07         6.90         0.72 
TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
       38.60        57.83       130.16        10.65         6.44        20.12 
TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O 
      109.28         8.94        11.93        11.77        11.77        12.66 
TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X 
       11.77         0.07        12.66        12.66        12.66        12.66 
TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 
        3.12         1.78         1.45         0.69         0.62         3.85 
TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK 
       12.33        10.92        11.34        11.34         0.16        12.03 
TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X 
       10.42         2.30         3.25         0.30         0.23         0.36 
TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 
        0.43         8.28         9.67         0.03         0.03         0.03 
TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 
        0.99         0.03         0.23        11.90        20.88        13.25 
TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 
       20.58        13.97        14.17        13.48        21.14        19.20 
TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD 
       14.17        17.49        16.50        18.71        15.78        18.15 
TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ 
       18.90        12.03        12.03        14.01        18.97        20.09 
TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS 
       20.12        20.09        19.40        20.38        21.01        12.20 
TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 
       13.32        14.70        18.58        17.79        16.73        25.74 
TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF 
       23.90        27.58        18.15         2.66        17.16        15.22 
TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO 
       14.73        21.83        14.50        19.92        17.69         7.96 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY 
       15.85        16.31         6.35        15.16        12.66        16.54 
TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F 
       15.52         3.81        14.24        14.14        17.42        16.04 
TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M 
       13.45        13.05        14.43         9.44        16.41        13.48 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W 
        4.80         0.76        10.09        13.08        12.53        12.26 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 
       14.50        18.51         7.33        43.00        34.42        27.52 
TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F 
       46.59        40.41        37.51        40.11        28.44        28.87 
TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S 
       47.15        44.68        40.96        38.24        38.60        33.17 
TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y 
       33.30        43.33        34.26        32.02        31.96        28.60 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 
       17.03        25.41        27.12        23.24        19.43        21.04 
TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D 
       23.87        14.79        25.05        23.34        22.82        17.29 
TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J 
       20.71        21.63        18.21        12.92        17.42        19.40 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15S 
        9.04        20.58         7.73        13.02        19.56        14.07 
TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       14.99        60.53        53.62        53.03        29.95        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       28.50        16.47        17.10        38.30        37.41        32.78 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN 
       33.73        33.70        28.44        22.65         3.88        22.19 
TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 
       20.98        11.08        54.18        27.42        39.62        19.66 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI 
       24.59        40.47        28.90        18.87       106.75       102.61 
TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z 
        8.75        43.04        16.93         5.52        15.72         7.20 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 
       18.05        22.26        19.89        19.20        36.82        13.48 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NF 
       12.00        13.12        36.56        39.55        35.77        20.05 
TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 
       21.57         9.86        11.90        14.30         0.62         2.10 
TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB 
        6.12         1.38         2.76        21.21        32.09        20.81 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI 
        0.66        34.65         6.58        21.27        34.59        35.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       34.13         0.79        12.53        13.32        39.09        22.75 
TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A245 
       12.89        23.51        24.10        17.06         0.69         0.85 
TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS 
       27.22         1.94         0.95        12.56         0.72        17.75 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54Y 
        0.76        26.07        18.41         0.62        15.72         0.23 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
        0.39         0.26         0.23        15.39        12.20        39.72 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
        8.48        18.21        18.90        13.25        16.57        15.68 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 
       25.94        22.82        29.95        29.85        40.41        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 
       39.78        52.96        29.82        23.11        18.48        30.08 
TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE 
        7.86        18.90        19.99         6.15        13.94        10.52 
TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV 
       14.43        34.55        19.96        55.00        52.73        25.91 
TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 
       22.09        21.27        17.49        10.16        10.59         7.40 
TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD 
      109.87        59.57       194.27        53.13        53.52        43.04 
TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       42.71        42.28        61.91        62.33        90.84        76.64 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL 
       77.33        53.36       110.50        38.20        32.28        69.30 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX 
       53.95        57.63        13.55        18.12        11.84        11.57 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
        8.28         6.67         4.60         0.66         2.99         3.58 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP 
        6.90         5.56         4.70         3.65         3.19         3.25 
TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ 
        2.63         3.88         4.14         4.50         4.50         5.59 
TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
        3.22         6.21        15.91         2.79         2.10        12.66 
TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW 
       46.55         7.53        44.61        27.65        24.10        26.20 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J 
       16.87        14.10         9.80        14.76        23.70        54.51 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-S3-A6ZG 
       33.90        31.07        18.21         7.23         4.44         6.81 
TCGA-W8-A86G 
        5.29 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.33              0.03 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           146.50            234.28 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            18.21             21.53 
[1] "0.3 - 146.5 (18.2)" "0.0 - 234.3 (21.5)"
[1] "hr=" "1.4"
D42V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1Q LOSS MUTATED         2        4        0        0        15        11
  1Q LOSS WILD-TYPE      78       73        9        9       320       213
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1Q LOSS MUTATED           0         12          2          3        1
  1Q LOSS WILD-TYPE         2        126         25         56       16
                   vv
clus                STAGE TIS STAGE X
  1Q LOSS MUTATED           0       0
  1Q LOSS WILD-TYPE         1      16
D42V3, multiclass
            clus
vv           1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                  2                78
  STAGE IA                 4                73
  STAGE IB                 0                 9
  STAGE II                 0                 9
  STAGE IIA               15               320
  STAGE IIB               11               213
  STAGE III                0                 2
  STAGE IIIA              12               126
  STAGE IIIB               2                25
  STAGE IIIC               3                56
  STAGE IV                 1                16
  STAGE TIS                0                 1
  STAGE X                  0                16
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  1Q LOSS MUTATED    12  27   7   4
  1Q LOSS WILD-TYPE 246 554 110  32
D42V4, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1              12               246
  T2              27               554
  T3               7               110
  T4               4                32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  1Q LOSS MUTATED    15  21   9   5
  1Q LOSS WILD-TYPE 453 309 102  65
D42V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0              15               453
  N1              21               309
  N2               9               102
  N3               5                65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  1Q LOSS MUTATED          0  46   1   3
  1Q LOSS WILD-TYPE        2 799  16 128
D42V6, multiclass
          clus
vv         1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CM0 (I+)               0                 2
  M0                    46               799
  M1                     1                16
  MX                     3               128
[1] 4 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    50   0
  1Q LOSS WILD-TYPE 934  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     50    0
  1Q LOSS WILD-TYPE  934   11
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              50               934
  MALE                 0                11
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  1Q LOSS MUTATED                            0                            43
  1Q LOSS WILD-TYPE                          1                           692
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  1Q LOSS MUTATED                                5                   1
  1Q LOSS WILD-TYPE                            161                   4
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  1Q LOSS MUTATED                                  1                  0
  1Q LOSS WILD-TYPE                               28                 14
                   vv
clus                OTHER  SPECIFY
  1Q LOSS MUTATED                0
  1Q LOSS WILD-TYPE             44
D42V8, multiclass
                                  clus
vv                                 1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                 43               692
  INFILTRATING LOBULAR CARCINOMA                 5               161
  MEDULLARY CARCINOMA                            1                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               1                28
  MUCINOUS CARCINOMA                             0                14
  OTHER  SPECIFY                                 0                44
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V9, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    14  36
  1Q LOSS WILD-TYPE 268 677
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     14   36
  1Q LOSS WILD-TYPE  268  677
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO               14               268
  YES              36               677
[1] 2 2
[1] FALSE
D42V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q LOSS MUTATED                                  0     3
  1Q LOSS WILD-TYPE                                1    53
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED                           9    30
  1Q LOSS WILD-TYPE                       128   678
D42V11, multiclass
                                  clus
vv                                 1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                53
  BLACK OR AFRICAN AMERICAN                      9               128
  WHITE                                         30               678
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V12, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     1  35
  1Q LOSS WILD-TYPE  35 761
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1   35
  1Q LOSS WILD-TYPE   35  761
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                35
  NOT HISPANIC OR LATINO              35               761
[1] 2 2
[1] FALSE

Clustering(43) Variable = 2P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED   148  16
  2P LOSS WILD-TYPE 712  98
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
              164               810 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               16                98 
$`2P LOSS MUTATED`
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0EO TCGA-A2-A0ET TCGA-A2-A0EU 
       75.55        75.25        63.45        80.28        35.05        34.29 
TCGA-A2-A0SV TCGA-A2-A0YH TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A25B TCGA-A2-A4RX 
       27.12        21.67        17.36        36.79        16.31         9.01 
TCGA-A7-A0CE TCGA-A7-A13F TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A6VX TCGA-A8-A06O 
       35.31        12.72        22.32        11.28        10.42        13.02 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07P TCGA-A8-A07R 
       26.01         1.02        33.01        18.97        10.98         8.98 
TCGA-A8-A07W TCGA-A8-A08B TCGA-A8-A08F TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08S 
        9.99        23.08        18.05        37.05        31.00        19.07 
TCGA-A8-A092 TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09T 
       16.01        12.00         1.02         1.02        25.02        19.04 
TCGA-A8-A0A2 TCGA-A8-A0A6 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-AC-A23E TCGA-AC-A2BM 
       19.04        21.04        13.02        17.03         2.37        38.20 
TCGA-AC-A2FF TCGA-AC-A2FM TCGA-AC-A62V TCGA-AN-A03Y TCGA-AN-A0AJ TCGA-AN-A0AS 
       55.43        26.04         0.07         0.33         8.02         0.33 
TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XP 
        7.00         7.59         6.02         0.36         0.33         0.30 
TCGA-AN-A0XT TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03P TCGA-AO-A0J3 TCGA-AO-A0JI 
        0.33        80.28        47.84        84.69        21.40        38.53 
TCGA-AO-A12A TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54O TCGA-AR-A0TZ 
       90.58         0.53        17.79         5.65        21.86        76.14 
TCGA-AR-A0U3 TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AS TCGA-AR-A24H TCGA-AR-A24K 
       76.18        62.56        43.73        40.83       109.58        50.89 
TCGA-AR-A24R TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A2LK TCGA-B6-A0IH TCGA-B6-A0IJ 
       57.40        54.18        50.96        42.87       112.37       176.98 
TCGA-B6-A0RL TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A408 TCGA-BH-A0B2 TCGA-BH-A0BA 
       81.17        43.59        73.51        49.94        40.83        37.22 
TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0C7 TCGA-BH-A0E0 TCGA-BH-A0E2 TCGA-BH-A0EB 
       45.57        49.94        42.90         4.41        14.30        24.49 
TCGA-BH-A0EE TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HU TCGA-BH-A0HW 
       31.00        23.08        41.00        52.96        12.89        51.32 
TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A18I TCGA-BH-A18Q TCGA-BH-A1ES TCGA-BH-A1EU 
       27.25        50.79         7.23        55.63       113.82        42.28 
TCGA-BH-A1FN TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A138 TCGA-C8-A1HG TCGA-C8-A3M7 
       72.07        12.66        12.66         3.75        11.34         0.03 
TCGA-D8-A142 TCGA-D8-A146 TCGA-D8-A1JD TCGA-D8-A1JI TCGA-D8-A1JP TCGA-D8-A1X6 
       13.97        21.14        18.15        18.97        21.01        17.79 
TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XJ TCGA-D8-A1XR TCGA-D8-A1XV TCGA-D8-A1XY 
       27.58        18.15        21.83        15.85        15.16        16.54 
TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27T TCGA-E2-A14O TCGA-E2-A14R TCGA-E2-A14Z 
        3.81        14.14        13.08        44.68        38.60        17.03 
TCGA-E2-A152 TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15S TCGA-E2-A1AZ 
       27.12        20.71        18.21        12.92        14.07        60.53 
TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1IN TCGA-E2-A2P5 TCGA-E9-A1N4 TCGA-E9-A1N6 
       17.10        33.73        22.19        16.93        19.20        13.48 
TCGA-E9-A1NF TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RE TCGA-E9-A1RG 
       20.05         2.76        32.09        20.81        34.65        21.27 
TCGA-E9-A1RI TCGA-E9-A228 TCGA-E9-A22G TCGA-E9-A249 TCGA-E9-A3HO TCGA-E9-A3X8 
       35.64        12.53        23.51         0.95        26.07        15.72 
TCGA-E9-A54Y TCGA-EW-A1J1 TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1P5 
        0.23        18.90        28.77        22.82        29.85        23.11 
TCGA-EW-A1P8 TCGA-EW-A1PE TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A423 TCGA-GI-A2C8 
        7.86        10.52        25.91        22.09        10.16         7.40 
TCGA-LL-A6FR TCGA-LL-A73Y 
        3.88         4.14 

$`2P LOSS WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
       20.88        13.68        31.79         7.96        39.32        28.01 
TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R 
       19.20        18.21       104.81        18.02        41.95        82.16 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
       73.84        22.06        63.12        64.04        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
      125.59        64.57        24.79       112.08        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 
      107.93         5.19        64.04        56.81        21.14        34.55 
TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP 
       33.76        28.77        25.22       101.72        89.36       107.61 
TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
       79.76        74.40        37.05        31.82        29.75        24.72 
TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY 
       24.16        99.19        54.64        44.88        50.43        44.28 
TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 
       17.52        17.13         8.38        18.71        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF 
       18.90        20.75        32.55        25.28        18.21        15.42 
TCGA-A2-A0YG TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       21.90        14.50        18.61        19.33        14.63        31.73 
TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 
       23.77        23.47        22.45        20.25        19.20        19.56 
TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       16.47        52.47       107.70        17.19        18.15        91.92 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU 
       10.59        20.88        39.65        33.93        83.01        29.98 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 
       14.07        49.48        38.40        34.98        31.99        38.37 
TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 
        7.30         8.81         8.91        12.00         6.74         3.42 
TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA 
       38.30        34.29        35.47        30.61        37.45        35.67 
TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       33.11        31.73        10.72        23.61        29.56        31.36 
TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A3IY 
       24.26        23.74        23.80        21.73        20.61        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA 
       10.59        10.29        13.41        14.70        11.97        14.93 
TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV 
       13.74        14.50        21.17        17.92        14.73        12.10 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06P 
       10.72        11.05        10.29         9.37         8.75        13.02 
TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A075 
        1.02        17.98        41.06        29.03        31.00        17.03 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J 
       53.98         9.01        19.99        18.97        14.01        12.00 
TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07Z TCGA-A8-A082 
       17.03         9.99         7.99         9.96        28.04        18.05 
TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08G 
       15.06        36.95        13.02         0.99        19.99        19.96 
TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X 
       12.00         9.99        31.00         0.99        93.04        33.99 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 
       40.01        19.07        17.95        41.98        12.00         9.99 
TCGA-A8-A09A TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M 
        9.99        13.02        31.00        33.07        29.98        15.02 
TCGA-A8-A09R TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A4 
        8.98        15.02         0.99        14.01        12.00        13.02 
TCGA-A8-A0A7 TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 
        0.99        38.04         0.95        10.85         2.66         1.48 
TCGA-AC-A2BK TCGA-AC-A2FB TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH 
       38.53        40.57        36.99        38.79        50.70         1.02 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
        0.92         2.27         0.99         0.69        14.83         9.40 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS 
        1.12         1.81         1.68         1.55         1.32         1.55 
TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A8OP 
        1.12         1.81         1.18         0.69         0.43         1.74 
TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C 
        0.33         0.23         0.33         0.62         2.96         1.78 
TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AT 
        1.71         7.36         6.51         0.16         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FV 
        6.44         4.64         7.96         7.17         6.28         0.33 
TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XR 
        0.33         0.33         0.33         0.33        12.33         0.33 
TCGA-AN-A0XS TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03N TCGA-AO-A03O 
        0.33         0.33         5.33         5.59        66.77        81.63 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J4 
       68.75        47.87        59.05        29.13        32.78        17.65 
TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA 
       24.16        37.48        20.32        22.36        53.03        21.53 
TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG 
       50.70        50.86        72.00        76.77        21.37        26.24 
TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 
       62.04        55.33        71.80       102.58        99.25        93.70 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F 
       94.59        96.10        77.56        64.04        57.30        48.36 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR 
       41.62        28.37        14.73        82.62        61.87        70.39 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N 
       24.79        26.93       130.09        15.62        13.22         2.56 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT 
        9.99        82.88        49.32         5.26        37.41        56.88 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0U0 TCGA-AR-A0U1 
       29.75        24.30        64.83        55.86        65.36        70.16 
TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK 
       83.87        55.36        75.55        61.84        52.77        51.25 
TCGA-AR-A1AL TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AU 
       48.82        43.56        39.98        43.07        17.23        46.32 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24L TCGA-AR-A24M 
       42.58        35.24        36.26        20.22        73.02        65.46 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24T 
       68.19        65.69         0.85        66.05        62.07        53.26 
TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 
       53.36        48.16        51.75        56.15        45.17        40.64 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LL 
       39.85        34.82        93.83       128.65        20.25         7.36 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM 
       40.04        17.10        20.81        16.96        20.38        54.74 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 
       16.04        20.45        10.59        77.62       143.38       149.59 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG 
       12.13       220.90       129.57        50.70        65.72       146.50 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ 
       18.77       126.12        84.59       110.14       110.93       140.88 
TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN 
      211.56        68.45       189.01       234.28        78.02       172.96 
TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU 
      162.05       102.77       140.48       100.70        89.46       131.21 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX 
      157.41        97.48       188.68        79.63        17.98        21.47 
TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
      113.79       129.57       129.70       186.48        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 
       58.88       101.52       139.17       170.17        85.35        54.28 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY 
       82.88        55.00        24.53        38.79        20.45        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 
       28.50        46.95        39.55        39.16        48.36        56.94 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG 
       56.98        51.68        32.02        18.21        25.71        24.85 
TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ 
       21.70        44.05        61.68        35.67        48.69        27.19 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 
       53.69        53.95        11.67        49.05        41.75        44.02 
TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI 
       48.13        45.83        31.17        23.44        38.01        22.13 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS 
       13.91        48.23        17.26        15.65         3.22         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E6 
       38.47        45.17        47.41        16.27        15.68         9.63 
TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ 
       44.81        46.19        32.65        24.43        30.35        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0HB TCGA-BH-A0HI 
       15.16        37.78        35.51        24.56        26.50        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0RX TCGA-BH-A0W3 
        5.85         2.50        13.61        36.85         5.59        23.93 
TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G 
       24.95        42.35        44.81        23.05         8.81         2.01 
TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P 
       20.12        90.84        26.66        72.56        37.74        30.28 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN 
       37.55        66.05         7.36        51.39        51.16        69.93 
TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY 
       91.99        82.85        12.00        55.69        49.58        17.69 
TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB 
       25.81        31.53        89.16        97.48        24.66       120.62 
TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
      114.15        33.17        74.73       122.89        36.92        63.35 
TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 
       55.00        45.63       144.59        72.07         6.90         0.72 
TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q 
       38.60        83.31        57.83       130.16        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12L TCGA-C8-A12M 
       20.12         0.99       109.28         8.94        11.93        11.77 
TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V 
       11.77        12.66        11.77         0.07        12.66        12.66 
TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 
        3.12         1.78         1.45         0.69         0.62         3.85 
TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL 
       12.33        10.92        11.34         0.16        12.03        10.42 
TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y 
        2.30         3.25         0.30         0.23         0.36         0.43 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A 
        8.28         9.67         0.03         0.03         0.03        12.20 
TCGA-C8-A27B TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 
        0.99         0.23        11.90        20.88        13.25        20.58 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA 
       14.17        13.48        19.20        14.17        17.49        16.50 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH 
       18.71        15.78        18.90        12.03        12.03        14.01 
TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JS 
       20.09        20.12        20.09        19.40        20.38        12.20 
TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 
       13.32        14.70        18.58        16.73        25.74        23.90 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XL 
        2.66        17.16        15.22        14.73        14.50        19.92 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU 
       17.69         7.96        16.41        16.31         6.35        12.99 
TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27F 
       12.66        15.32        15.52        14.24        17.42        16.04 
TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M 
       13.45        13.05        14.43         9.44        16.41        13.48 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 
        4.80         0.76        10.09        12.53        12.26        14.50 
TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 
       18.51         7.33        43.00        34.42        27.52        46.59 
TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N 
       40.41        37.51        40.11        28.44        28.87        47.15 
TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V 
       40.96        38.24        33.17        33.30        43.33        34.26 
TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 
       32.02        31.96        28.60        25.41        23.24        19.43 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C 
       21.04        23.87        14.79        25.05        23.34        22.82 
TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       17.29        21.63        17.42        19.40         9.04        20.58 
TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15T TCGA-E2-A1B0 
        7.73        13.02        19.56        17.06        14.99        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE 
       53.03        29.95        32.35        28.50        16.47        38.30 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       37.41        32.78        33.70        28.44        22.65         3.88 
TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 
       20.98        11.08        54.18        27.42        39.62        19.66 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI 
       24.59        40.47        28.90        18.87       106.75       102.61 
TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
        8.75        43.04         5.52        15.72         7.20        18.05 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA 
       22.26        19.89        36.82        12.00        13.12        36.56 
TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ 
       39.55        12.59        35.77        21.57         9.86        11.90 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 
       14.30         0.62         2.10         6.12         1.38        21.21 
TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A227 
       40.24         0.66         6.58        34.59        34.13         0.79 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 
       13.32        39.09        22.75        12.89        24.10        17.06 
TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A295 
        0.69         0.85        27.22         1.94        12.56         0.72 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A5FK TCGA-E9-A5FL 
       17.75         0.76        18.41         0.62         0.39         0.26 
TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
        0.23        15.39        12.20        39.72         8.48        18.21 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OZ 
       13.25        16.57        15.68        25.94        29.95        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 
       41.13        39.78        52.96        29.82        18.48        30.08 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PF TCGA-EW-A1PG 
       18.90        19.99         6.15        13.94        14.43        34.55 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 
       19.96        55.00        52.73        21.27        17.49        10.59 
TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD 
      109.87        59.57       194.27        53.13        53.52        43.04 
TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       42.71        42.28        61.91        62.33        90.84        76.64 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL 
       77.33        53.36       110.50        38.20        32.28        69.30 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX 
       53.95        57.63        13.55        18.12        11.84        11.57 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
        8.28         6.67         4.60         0.66         2.99         3.58 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP 
        6.90         5.56         4.70         3.65         3.19         3.25 
TCGA-LL-A6FQ TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 
        2.63         4.50         4.50         5.59         3.22         6.21 
TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 
       15.91         2.79         2.10        12.66        46.55         7.53 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY 
       44.61        27.65        24.10        26.20        16.87        14.10 
TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K 
       10.29         9.80        14.76        23.70        54.51        33.90 
TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-S3-A6ZG TCGA-W8-A86G 
       31.07        18.21         7.23         4.44         6.81         5.29 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             0.03              0.03 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           176.98            234.28 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            21.09             21.60 
[1] "0.0 - 177.0 (21.1)" "0.0 - 234.3 (21.6)"
[1] "hr=" "1.1"
D43V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2P LOSS MUTATED        11       11        0        2        53        34
  2P LOSS WILD-TYPE      69       66        9        7       282       190
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2P LOSS MUTATED           1         30          6         12        6
  2P LOSS WILD-TYPE         1        108         21         47       11
                   vv
clus                STAGE TIS STAGE X
  2P LOSS MUTATED           0       2
  2P LOSS WILD-TYPE         1      14
D43V3, multiclass
            clus
vv           2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                 11                69
  STAGE IA                11                66
  STAGE IB                 0                 9
  STAGE II                 2                 7
  STAGE IIA               53               282
  STAGE IIB               34               190
  STAGE III                1                 1
  STAGE IIIA              30               108
  STAGE IIIB               6                21
  STAGE IIIC              12                47
  STAGE IV                 6                11
  STAGE TIS                0                 1
  STAGE X                  2                14
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2P LOSS MUTATED    37 104  19   8
  2P LOSS WILD-TYPE 221 477  98  28
D43V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1              37               221
  T2             104               477
  T3              19                98
  T4               8                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                 N0  N1  N2  N3
  2P LOSS MUTATED    74  50  28  15
  2P LOSS WILD-TYPE 394 280  83  55
D43V5, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0              74               394
  N1              50               280
  N2              28                83
  N3              15                55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  2P LOSS MUTATED          1 138   6  23
  2P LOSS WILD-TYPE        1 707  11 108
D43V6, multiclass
          clus
vv         2P LOSS MUTATED 2P LOSS WILD-TYPE
  CM0 (I+)               1                 1
  M0                   138               707
  M1                     6                11
  MX                    23               108
[1] 4 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   166   2
  2P LOSS WILD-TYPE 818   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED    166    2
  2P LOSS WILD-TYPE  818    9
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE             166               818
  MALE                 2                 9
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  2P LOSS MUTATED                            0                           134
  2P LOSS WILD-TYPE                          1                           601
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  2P LOSS MUTATED                               19                   0
  2P LOSS WILD-TYPE                            147                   5
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  2P LOSS MUTATED                                  7                  2
  2P LOSS WILD-TYPE                               22                 12
                   vv
clus                OTHER  SPECIFY
  2P LOSS MUTATED                6
  2P LOSS WILD-TYPE             38
D43V8, multiclass
                                  clus
vv                                 2P LOSS MUTATED 2P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                134               601
  INFILTRATING LOBULAR CARCINOMA                19               147
  MEDULLARY CARCINOMA                            0                 5
  MIXED HISTOLOGY (PLEASE SPECIFY)               7                22
  MUCINOUS CARCINOMA                             2                12
  OTHER  SPECIFY                                 6                38
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V9, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    60 108
  2P LOSS WILD-TYPE 222 605
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     60  108
  2P LOSS WILD-TYPE  222  605
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO               60               222
  YES             108               605
[1] 2 2
[1] FALSE
D43V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P LOSS MUTATED                                  0    10
  2P LOSS WILD-TYPE                                1    46
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED                          16   117
  2P LOSS WILD-TYPE                       121   591
D43V11, multiclass
                                  clus
vv                                 2P LOSS MUTATED 2P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         10                46
  BLACK OR AFRICAN AMERICAN                     16               121
  WHITE                                        117               591
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V12, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    10 117
  2P LOSS WILD-TYPE  26 679
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     10  117
  2P LOSS WILD-TYPE   26  679
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                  10                26
  NOT HISPANIC OR LATINO             117               679
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2Q LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED   164  23
  2Q LOSS WILD-TYPE 696  91
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
              187               787 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               23                91 
$`2Q LOSS MUTATED`
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0EO TCGA-A2-A0ET TCGA-A2-A0EU 
       75.55        75.25        63.45        80.28        35.05        34.29 
TCGA-A2-A0SV TCGA-A2-A0YH TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A3XS TCGA-A2-A4RX 
       27.12        21.67        17.36        36.79        33.93         9.01 
TCGA-A7-A0CE TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A3J1 TCGA-A7-A6VX TCGA-A8-A06O 
       35.31        10.72        12.72        11.28        10.42        13.02 
TCGA-A8-A06T TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07P 
       41.06        26.01         1.02        33.01        18.97        10.98 
TCGA-A8-A07R TCGA-A8-A07W TCGA-A8-A08B TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08J 
        8.98         9.99        23.08        18.05        12.00        37.05 
TCGA-A8-A08O TCGA-A8-A08S TCGA-A8-A092 TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09N 
       31.00        19.07        16.01        12.00         1.02         1.02 
TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A0A2 TCGA-A8-A0A6 TCGA-A8-A0A9 TCGA-A8-A0AB 
       25.02        19.04        19.04        21.04        13.02        17.03 
TCGA-AC-A23E TCGA-AC-A2BM TCGA-AC-A2FF TCGA-AC-A2FM TCGA-AC-A62V TCGA-AC-A6IW 
        2.37        38.20        55.43        26.04         0.07         0.69 
TCGA-AN-A03Y TCGA-AN-A0AJ TCGA-AN-A0AS TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FT 
        0.33         8.02         0.33         7.00         7.59         6.02 
TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FZ TCGA-AN-A0XP TCGA-AN-A0XT TCGA-AO-A03L 
        0.36         0.33         0.33         0.30         0.33        80.28 
TCGA-AO-A03M TCGA-AO-A03P TCGA-AO-A0J3 TCGA-AO-A0JD TCGA-AO-A0JI TCGA-AO-A12A 
       47.84        84.69        21.40        72.00        38.53        90.58 
TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0TS 
        0.53        17.79         5.65         2.56        21.86        37.41 
TCGA-AR-A0TV TCGA-AR-A0U3 TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AS TCGA-AR-A1AY 
       29.75        76.18        62.56        43.73        40.83        20.22 
TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24R TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A2LK 
      109.58        50.89        57.40        54.18        50.96        42.87 
TCGA-B6-A0I9 TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0RL TCGA-B6-A0RU TCGA-B6-A1KC 
       12.13       112.37       176.98        81.17       131.21        43.59 
TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A408 TCGA-BH-A0B2 TCGA-BH-A0BA TCGA-BH-A0BT 
       73.51       139.17        49.94        40.83        37.22        45.57 
TCGA-BH-A0BV TCGA-BH-A0C7 TCGA-BH-A0E0 TCGA-BH-A0E2 TCGA-BH-A0EB TCGA-BH-A0EE 
       49.94        42.90         4.41        14.30        24.49        31.00 
TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX 
       23.08        41.00        52.96        12.89        51.32        27.25 
TCGA-BH-A18I TCGA-BH-A18Q TCGA-BH-A1ES TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1F6 
        7.23        55.63       113.82        42.28        12.00        97.48 
TCGA-BH-A1FC TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A202 TCGA-C8-A12W TCGA-C8-A12X 
      114.15        45.63        72.07         0.72        12.66        12.66 
TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HK TCGA-C8-A26Z TCGA-C8-A3M7 
        3.75        10.92        11.34        12.03         8.28         0.03 
TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A146 TCGA-D8-A1JI TCGA-D8-A1X6 TCGA-D8-A1XA 
       20.88        13.97        21.14        18.97        17.79        27.58 
TCGA-D8-A1XB TCGA-D8-A1XJ TCGA-D8-A1XR TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1Y1 
       18.15        21.83        15.85        15.16        16.54         3.81 
TCGA-D8-A1Y3 TCGA-D8-A27T TCGA-E2-A14O TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Z 
       14.14        13.08        44.68        38.60        31.96        17.03 
TCGA-E2-A152 TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15S TCGA-E2-A1AZ 
       27.12        20.71        18.21        12.92        14.07        60.53 
TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IN TCGA-E2-A2P5 TCGA-E9-A1N4 
       17.10        33.73        33.70        22.19        16.93        19.20 
TCGA-E9-A1N6 TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB 
       13.48        20.05         9.86         2.76        32.09        20.81 
TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A228 TCGA-E9-A22G TCGA-E9-A249 
       34.65        21.27        35.64        12.53        23.51         0.95 
TCGA-E9-A3HO TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-EW-A1J1 TCGA-EW-A1J6 TCGA-EW-A1OW 
       26.07        15.72         0.23        18.90        28.77        22.82 
TCGA-EW-A1OY TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PE TCGA-EW-A2FV TCGA-EW-A2FW 
       29.85        23.11         7.86        10.52        25.91        22.09 
TCGA-EW-A423 TCGA-GM-A2DF TCGA-GM-A4E0 TCGA-LL-A6FR TCGA-LL-A7SZ TCGA-LL-A7T0 
       10.16        42.71        57.63         3.88         5.59         3.22 
TCGA-OL-A5RZ 
       10.29 

$`2Q LOSS WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
       20.88        13.68        31.79         7.96        39.32        28.01 
TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R 
       19.20        18.21       104.81        18.02        41.95        82.16 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
       73.84        22.06        63.12        64.04        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
      125.59        64.57        24.79       112.08        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 
      107.93         5.19        64.04        56.81        21.14        34.55 
TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP 
       33.76        28.77        25.22       101.72        89.36       107.61 
TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
       79.76        74.40        37.05        31.82        29.75        24.72 
TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY 
       24.16        99.19        54.64        44.88        50.43        44.28 
TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 
       17.52        17.13         8.38        18.71        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF 
       18.90        20.75        32.55        25.28        18.21        15.42 
TCGA-A2-A0YG TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       21.90        14.50        18.61        19.33        14.63        31.73 
TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 
       23.77        23.47        22.45        20.25        19.20        19.56 
TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D 
       16.47        52.47       107.70        16.31        17.19        18.15 
TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XU 
       91.92        10.59        20.88        39.65        83.01        29.98 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 
       14.07        49.48        38.40        34.98        31.99        38.37 
TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 
        7.30         8.81         8.91        12.00         6.74         3.42 
TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA 
       38.30        34.29        35.47        30.61        37.45        35.67 
TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F 
       33.11        31.73        23.61        29.56        31.36        24.26 
TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY 
       23.74        23.80        21.73        20.61        22.32        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA 
       10.59        10.29        13.41        14.70        11.97        14.93 
TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV 
       13.74        14.50        21.17        17.92        14.73        12.10 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06P 
       10.72        11.05        10.29         9.37         8.75        13.02 
TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A076 
        1.02        17.98        29.03        31.00        17.03        53.98 
TCGA-A8-A079 TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
        9.01        19.99        18.97        14.01        12.00        17.03 
TCGA-A8-A07O TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 
        9.99         7.99         9.96        28.04        18.05        15.06 
TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08L 
       36.95        13.02         0.99        19.99        19.96         9.99 
TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 
       31.00         0.99        93.04        33.99        40.01        19.07 
TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09D 
       17.95        41.98        12.00         9.99         9.99        13.02 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09R TCGA-A8-A09V 
       31.00        33.07        29.98        15.02         8.98        15.02 
TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A4 TCGA-A8-A0A7 TCGA-A8-A0AD 
        0.99        14.01        12.00        13.02         0.99        38.04 
TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2FB 
        0.95        10.85         2.66         1.48        38.53        40.57 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ 
       36.99        38.79        50.70         1.02         0.92         2.27 
TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 
        0.99         0.69        14.83         9.40         1.12         1.81 
TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62X TCGA-AC-A62Y 
        1.68         1.55         1.32         1.55         1.12         1.81 
TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 
        1.18         0.43         1.74         0.33         0.23         0.33 
TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL 
        0.62         2.96         1.78         1.71         7.36         6.51 
TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ 
        0.16         0.33         0.33         6.44         4.64         7.96 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN 
        7.17         6.28         0.33         0.33         0.33         0.33 
TCGA-AN-A0XO TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW 
       12.33         0.33         0.33         0.33         5.33         5.59 
TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V 
       66.77        81.63        68.75        47.87        59.05        29.13 
TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 
       32.78        17.65        24.16        37.48        20.32        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF 
       53.03        21.53        50.70        50.86        76.77        21.37 
TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 
       26.24        62.04        55.33        71.80       102.58        99.25 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
       93.70        94.59        96.10        77.56        64.04        57.30 
TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ 
       48.36        41.62        28.37        14.73        82.62        61.87 
TCGA-AO-A1KR TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       70.39        24.79        26.93       130.09        15.62        13.22 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TW 
        9.99        82.88        49.32         5.26        56.88        24.30 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 
       64.83        55.86        76.14        65.36        70.16        83.87 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL 
       55.36        75.55        61.84        52.77        51.25        48.82 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AU TCGA-AR-A1AV 
       43.56        39.98        43.07        17.23        46.32        42.58 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       35.24        36.26        73.02        65.46        68.19        65.69 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X 
        0.85        66.05        62.07        53.26        53.36        48.16 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 
       51.75        56.15        45.17        40.64        39.85        34.82 
TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN 
       93.83       128.65        20.25         7.36        40.04        17.10 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP 
       20.81        16.96        20.38        54.74        16.04        20.45 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IB 
       10.59        77.62       143.38       149.59       220.90       129.57 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
       50.70        65.72       146.50        18.77       126.12        84.59 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH 
      110.14       110.93       140.88       211.56        68.45       189.01 
TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ 
      234.28        78.02       172.96       162.05       102.77       140.48 
TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV 
      100.70        89.46       157.41        97.48       188.68        79.63 
TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 
       17.98        21.47       113.79       129.57       129.70       186.48 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A2IU TCGA-B6-A401 
       28.27        68.94        58.88       101.52       170.17        85.35 
TCGA-B6-A402 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW 
       54.28        82.88        55.00        24.53        38.79        20.45 
TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 
       25.55        28.50        46.95        39.55        39.16        48.36 
TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       56.94        56.98        51.68        32.02        18.21        25.71 
TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP 
       24.85        21.70        44.05        61.68        35.67        48.69 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 
       27.19        53.69        53.95        11.67        49.05        41.75 
TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH 
       44.02        48.13        45.83        31.17        23.44        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ 
       22.13        13.91        48.23        17.26        15.65         3.22 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 
        2.56        38.47        45.17        47.41        16.27        15.68 
TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EI TCGA-BH-A0GY 
        9.63        44.81        46.19        32.65        24.43        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0HB 
       10.78        15.16        37.78        35.51        24.56        26.50 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HY 
       20.38         5.85         2.50        13.61        36.85        50.79 
TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA 
        5.59        23.93        24.95        42.35        44.81        23.05 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M 
        8.81         2.01        20.12        90.84        26.66        72.56 
TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U 
       37.74        30.28        37.55        66.05         7.36        51.39 
TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1EW TCGA-BH-A1EX 
       51.16        69.93        91.99        82.85        55.69        49.58 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F8 TCGA-BH-A1FB 
       17.69        25.81        31.53        89.16        24.66       120.62 
TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
       33.17        74.73       122.89        36.92        63.35        55.00 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 
      144.59        72.07         6.90        38.60        83.31        57.83 
TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
      130.16        10.65         6.44        20.12         0.99       109.28 
TCGA-BH-A42V TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P 
        8.94        11.93        11.77        11.77        12.66        11.77 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 
        0.07        12.66        12.66         3.12         1.78         1.45 
TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HI TCGA-C8-A1HJ 
        0.69         0.62         3.85        12.33        11.34         0.16 
TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X 
       10.42         2.30         3.25         0.30         0.23         0.36 
TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A 
        0.43         9.67         0.03         0.03         0.03        12.20 
TCGA-C8-A27B TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 
        0.99         0.23        11.90        13.25        20.58        14.17 
TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
       13.48        19.20        14.17        17.49        16.50        18.71 
TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH 
       15.78        18.15        18.90        12.03        12.03        14.01 
TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP 
       20.09        20.12        20.09        19.40        20.38        21.01 
TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X7 TCGA-D8-A1X8 
       12.20        13.32        14.70        18.58        16.73        25.74 
TCGA-D8-A1X9 TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XK 
       23.90         2.66        17.16        15.22        14.73        14.50 
TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1XT 
       19.92        17.69         7.96        16.41        16.31         6.35 
TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A27E 
       12.99        12.66        15.32        15.52        14.24        17.42 
TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       16.04        13.45        13.05        14.43         9.44        16.41 
TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27V TCGA-D8-A27W 
       13.48         4.80         0.76        10.09        12.53        12.26 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 
       14.50        18.51         7.33        43.00        34.42        27.52 
TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F 
       46.59        40.41        37.51        40.11        28.44        28.87 
TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U 
       47.15        40.96        38.24        33.17        33.30        43.33 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 
       34.26        32.02        28.60        25.41        23.24        19.43 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C 
       21.04        23.87        14.79        25.05        23.34        22.82 
TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       17.29        21.63        17.42        19.40         9.04        20.58 
TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15T TCGA-E2-A1B0 
        7.73        13.02        19.56        17.06        14.99        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE 
       53.03        29.95        32.35        28.50        16.47        38.30 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IO 
       37.41        32.78        28.44        22.65         3.88        20.98 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA 
       11.08        54.18        27.42        39.62        19.66        24.59 
TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK 
       40.47        28.90        18.87       106.75       102.61         8.75 
TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 
       43.04         5.52        15.72         7.20        18.05        22.26 
TCGA-E2-A574 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC 
       19.89        36.82        12.00        13.12        36.56        39.55 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       12.59        35.77        21.57        11.90        14.30         0.62 
TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RC TCGA-E9-A1RD 
        2.10         6.12         1.38        21.21        40.24         0.66 
TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A229 TCGA-E9-A22A 
        6.58        34.59        34.13         0.79        13.32        39.09 
TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A245 
       22.75        12.89        24.10        17.06         0.69         0.85 
TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT 
       27.22         1.94        12.56         0.72        17.75         0.76 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE 
       18.41         0.62         0.39         0.26         0.23        15.39 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1J3 
       12.20        39.72         8.48        18.21        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 
       15.68        25.94        29.95        40.41        41.13        39.78 
TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB 
       52.96        29.82        18.48        30.08        18.90        19.99 
TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR 
        6.15        13.94        14.43        34.55        19.96        55.00 
TCGA-EW-A2FS TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 
       52.73        21.27        17.49        10.59         7.40       109.87 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DH 
       59.57       194.27        53.13        53.52        43.04        42.28 
TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO 
       61.91        62.33        90.84        76.64        77.33        53.36 
TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A5PV 
      110.50        38.20        32.28        69.30        53.95        13.55 
TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 
       18.12        11.84        11.57         8.28         6.67         4.60 
TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM 
        0.66         2.99         3.58         6.90         5.56         4.70 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A73Z 
        3.65         3.19         3.25         2.63         4.14         4.50 
TCGA-LL-A740 TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
        4.50         6.21        15.91         2.79         2.10        12.66 
TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW 
       46.55         7.53        44.61        27.65        24.10        26.20 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J 
       16.87        14.10         9.80        14.76        23.70        54.51 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-S3-A6ZG 
       33.90        31.07        18.21         7.23         4.44         6.81 
TCGA-W8-A86G 
        5.29 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.03              0.03 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           176.98            234.28 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            21.04             21.63 
[1] "0.0 - 177.0 (21.0)" "0.0 - 234.3 (21.6)"
[1] "hr=" "1.3"
D44V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2Q LOSS MUTATED        12       11        0        3        62        37
  2Q LOSS WILD-TYPE      68       66        9        6       273       187
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2Q LOSS MUTATED           1         34          6         13        7
  2Q LOSS WILD-TYPE         1        104         21         46       10
                   vv
clus                STAGE TIS STAGE X
  2Q LOSS MUTATED           0       3
  2Q LOSS WILD-TYPE         1      13
D44V3, multiclass
            clus
vv           2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                 12                68
  STAGE IA                11                66
  STAGE IB                 0                 9
  STAGE II                 3                 6
  STAGE IIA               62               273
  STAGE IIB               37               187
  STAGE III                1                 1
  STAGE IIIA              34               104
  STAGE IIIB               6                21
  STAGE IIIC              13                46
  STAGE IV                 7                10
  STAGE TIS                0                 1
  STAGE X                  3                13
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2Q LOSS MUTATED    41 116  24   9
  2Q LOSS WILD-TYPE 217 465  93  27
D44V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1              41               217
  T2             116               465
  T3              24                93
  T4               9                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                 N0  N1  N2  N3
  2Q LOSS MUTATED    82  59  31  16
  2Q LOSS WILD-TYPE 386 271  80  54
D44V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0              82               386
  N1              59               271
  N2              31                80
  N3              16                54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  2Q LOSS MUTATED          1 157   7  25
  2Q LOSS WILD-TYPE        1 688  10 106
D44V6, multiclass
          clus
vv         2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CM0 (I+)               1                 1
  M0                   157               688
  M1                     7                10
  MX                    25               106
[1] 4 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   188   2
  2Q LOSS WILD-TYPE 796   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED    188    2
  2Q LOSS WILD-TYPE  796    9
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE             188               796
  MALE                 2                 9
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  2Q LOSS MUTATED                            0                           152
  2Q LOSS WILD-TYPE                          1                           583
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  2Q LOSS MUTATED                               20                   1
  2Q LOSS WILD-TYPE                            146                   4
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  2Q LOSS MUTATED                                  8                  2
  2Q LOSS WILD-TYPE                               21                 12
                   vv
clus                OTHER  SPECIFY
  2Q LOSS MUTATED                7
  2Q LOSS WILD-TYPE             37
D44V8, multiclass
                                  clus
vv                                 2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                152               583
  INFILTRATING LOBULAR CARCINOMA                20               146
  MEDULLARY CARCINOMA                            1                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               8                21
  MUCINOUS CARCINOMA                             2                12
  OTHER  SPECIFY                                 7                37
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V9, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    63 127
  2Q LOSS WILD-TYPE 219 586
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     63  127
  2Q LOSS WILD-TYPE  219  586
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO               63               219
  YES             127               586
[1] 2 2
[1] FALSE
D44V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q LOSS MUTATED                                  0    13
  2Q LOSS WILD-TYPE                                1    43
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED                          22   128
  2Q LOSS WILD-TYPE                       115   580
D44V11, multiclass
                                  clus
vv                                 2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         13                43
  BLACK OR AFRICAN AMERICAN                     22               115
  WHITE                                        128               580
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V12, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    11 135
  2Q LOSS WILD-TYPE  25 661
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     11  135
  2Q LOSS WILD-TYPE   25  661
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                  11                25
  NOT HISPANIC OR LATINO             135               661
[1] 2 2
[1] FALSE

Clustering(45) Variable = 3P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED   145  23
  3P LOSS WILD-TYPE 715  91
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              168               806 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               23                91 
$`3P LOSS MUTATED`
TCGA-A1-A0SK TCGA-A1-A0SP TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A0CL TCGA-A2-A0CT 
       31.79        19.20        73.84        22.06        64.57        75.25 
TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D4 TCGA-A2-A0EO 
       64.04        56.81        21.14        34.55        25.22        80.28 
TCGA-A2-A0EQ TCGA-A2-A0T3 TCGA-A2-A0YE TCGA-A2-A0YT TCGA-A2-A1G1 TCGA-A2-A3XX 
       79.76        18.71        18.21        23.77        19.20        38.40 
TCGA-A2-A4S1 TCGA-A7-A0CE TCGA-A7-A0CJ TCGA-A7-A13D TCGA-A7-A26F TCGA-A7-A2KD 
       12.00        35.31        30.61        31.73        24.26        22.32 
TCGA-A7-A4SF TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06U TCGA-A8-A06Z 
       17.92         9.37        10.42         8.75        29.03         1.02 
TCGA-A8-A07F TCGA-A8-A07J TCGA-A8-A08O TCGA-A8-A09M TCGA-AC-A2BK TCGA-AC-A2FO 
       18.97        12.00        31.00        15.02        38.53        50.70 
TCGA-AC-A3OD TCGA-AN-A041 TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AR TCGA-AN-A0FJ 
       14.83         0.23         1.78         1.71         0.33         7.96 
TCGA-AN-A0FL TCGA-AN-A0FT TCGA-AN-A0XU TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03P 
        7.59         6.02         0.33        80.28        47.84        84.69 
TCGA-AO-A03T TCGA-AO-A0J3 TCGA-AO-A0JA TCGA-AO-A0JG TCGA-AO-A124 TCGA-AO-A1KS 
       47.87        21.40        21.53        26.24       102.58         0.53 
TCGA-AQ-A04L TCGA-AR-A0TP TCGA-AR-A0TT TCGA-AR-A0TX TCGA-AR-A0U1 TCGA-AR-A0U2 
      130.09        82.88        56.88        64.83        70.16        83.87 
TCGA-AR-A1AH TCGA-AR-A1AQ TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A251 TCGA-AR-A255 
       75.55        43.07        62.07        53.26        45.17        34.82 
TCGA-AR-A256 TCGA-AR-A2LO TCGA-B6-A0IB TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ 
       93.83        20.81       129.57       146.50       112.37       176.98 
TCGA-B6-A0WS TCGA-B6-A0WW TCGA-B6-A0WY TCGA-B6-A1KI TCGA-BH-A0B9 TCGA-BH-A0BG 
       97.48        17.98       113.79        73.51        51.68        24.85 
TCGA-BH-A0BJ TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0DI TCGA-BH-A0DL 
       21.70        11.67        49.05        44.02        22.13        48.23 
TCGA-BH-A0E0 TCGA-BH-A0HA TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0RX TCGA-BH-A18F 
        4.41        52.96        12.89        51.32         5.59         8.81 
TCGA-BH-A18L TCGA-BH-A18T TCGA-BH-A1EN TCGA-BH-A1F8 TCGA-BH-A1FM TCGA-BH-A1FU 
       26.66         7.36        69.93        24.66        45.63        72.07 
TCGA-BH-A208 TCGA-BH-A42T TCGA-C8-A12L TCGA-C8-A12P TCGA-C8-A135 TCGA-C8-A137 
       57.83         0.99        11.93        11.77         0.62         3.85 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A26W 
       10.92        11.34         0.16        12.03         2.30         0.23 
TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JD TCGA-D8-A1JG TCGA-D8-A1JJ TCGA-D8-A1JK 
       14.17        17.49        18.15        12.03        20.09        20.12 
TCGA-D8-A1JM TCGA-D8-A1X5 TCGA-D8-A1XB TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL 
       19.40        18.58        18.15        21.83        14.50        19.92 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A27M 
        6.35        12.99        16.54        15.32         3.81        13.48 
TCGA-D8-A27N TCGA-E2-A10C TCGA-E2-A14R TCGA-E2-A14V TCGA-E2-A150 TCGA-E2-A152 
        4.80        40.11        38.60        34.26        25.41        27.12 
TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A1II TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A1LE 
       25.05        23.34        33.70        20.98        27.42        28.90 
TCGA-E2-A574 TCGA-E9-A1N8 TCGA-E9-A1NC TCGA-E9-A1NF TCGA-E9-A1R4 TCGA-E9-A226 
       19.89        12.00        39.55        20.05         6.12        34.13 
TCGA-E9-A229 TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A295 TCGA-E9-A2JS TCGA-EW-A1OW 
       13.32        23.51         0.69         0.72        17.75        22.82 
TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1PC TCGA-EW-A2FS TCGA-EW-A423 TCGA-GI-A2C8 
       29.82        23.11         6.15        52.73        10.16         7.40 
TCGA-GI-A2C9 TCGA-GM-A2DB TCGA-GM-A2DH TCGA-JL-A3YX TCGA-LL-A5YL TCGA-LL-A7T0 
      109.87        53.13        42.28        11.57         5.56         3.22 
TCGA-LL-A8F5 TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66K TCGA-OL-A66N TCGA-S3-A6ZG 
        6.21        14.10         9.80        33.90        18.21         6.81 

$`3P LOSS WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ 
       20.88        13.68         7.96        39.32        28.01        18.21 
TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04W 
      104.81        18.02        41.95        82.16        63.12        64.04 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
       55.43        36.13       125.59        24.79       112.08        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0D2 
       88.60       107.93        75.55         5.19        63.45        33.76 
TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES 
       28.77       101.72        89.36       107.61        74.40        37.05 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY 
       35.05        34.29        31.82        29.75        24.72        24.16 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY 
       99.19        54.64        27.12        44.88        50.43        44.28 
TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.52        17.13         8.38        20.52        17.46        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH 
       20.75        32.55        25.28        15.42        21.90        21.67 
TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV 
       14.50        18.61        19.33        14.63        31.73        23.47 
TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 
       17.36        36.79        22.45        20.25        19.56        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       52.47       107.70        16.31        17.19        18.15        91.92 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU 
       10.59        20.88        39.65        33.93        83.01        29.98 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW 
       14.07        49.48        34.98        31.99        38.37         7.30 
TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD 
        9.01         8.81         8.91         6.74         3.42        38.30 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13E 
       34.29        35.47        37.45        35.67        33.11        10.72 
TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26G TCGA-A7-A26H 
       12.72        23.61        29.56        31.36        23.74        23.80 
TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       21.73        20.61        11.34        10.59        10.29        11.28 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD 
       13.41        14.70        11.97        14.93        13.74        14.50 
TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV 
       21.17        14.73        12.10        10.72        11.05        10.29 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06X 
       13.02        13.02         1.02        17.98        41.06        31.00 
TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E 
       26.01        17.03        53.98         9.01        33.01        19.99 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R 
       18.97        14.01        17.03         9.99        10.98         8.98 
TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 
        7.99         9.96         9.99        28.04        18.05        15.06 
TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F 
       36.95        13.02         0.99        23.08        19.99        18.05 
TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08R 
       19.96        12.00        37.05         9.99        31.00         0.99 
TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 
       19.07        93.04        33.99        40.01        19.07        16.01 
TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B 
       17.95        41.98        12.00         9.99         9.99        12.00 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09N 
        1.02        13.02        31.00        33.07        29.98         1.02 
TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X 
       25.02         8.98        19.04        15.02         0.99        14.01 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 
       12.00        19.04        13.02        21.04         0.99        13.02 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H 
       17.03        38.04         0.95         2.37        10.85         2.66 
TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
        1.48        38.20        40.57        55.43        36.99        38.79 
TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN 
       26.04         1.02         0.92         2.27         0.99         0.69 
TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ 
        9.40         1.12         1.81         1.68         1.55         1.32 
TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW 
        1.55         0.07         1.12         1.81         1.18         0.69 
TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A046 TCGA-AN-A049 
        0.43         1.74         0.33         0.33         0.33         0.62 
TCGA-AN-A04A TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AS 
        2.96         8.02         7.36         6.51         0.16         0.33 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0FS 
        0.33         6.44         4.64         7.00         7.17         6.28 
TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL 
        0.33         0.36         0.33         0.33         0.33         0.33 
TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT 
        0.33        12.33         0.30         0.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03U 
        5.33         5.59        66.77        81.63        68.75        59.05 
TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 
       29.13        32.78        17.65        24.16        37.48        20.32 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE 
       22.36        53.03        50.70        50.86        72.00        76.77 
TCGA-AO-A0JF TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A125 
       21.37        38.53        62.04        55.33        71.80        99.25 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D 
       93.70        94.59        96.10        90.58        77.56        64.04 
TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       57.30        48.36        41.62        28.37        14.73        82.62 
TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A0Y5 
       61.87        70.39        17.79        24.79        26.93         5.65 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TQ 
       15.62        13.22         2.56        21.86         9.99        49.32 
TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0TZ 
        5.26        37.41        29.75        24.30        55.86        76.14 
TCGA-AR-A0U0 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK 
       65.36        76.18        55.36        61.84        52.77        51.25 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AR 
       48.82        62.56        43.73        43.56        39.98        17.23 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY 
       40.83        46.32        42.58        35.24        36.26        20.22 
TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
      109.58        50.89        73.02        65.46        68.19        65.69 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W 
        0.85        66.05        57.40        53.36        54.18        50.96 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A2LE 
       48.16        51.75        56.15        40.64        39.85       128.65 
TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ 
       20.25        42.87         7.36        40.04        17.10        16.96 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       20.38        54.74        16.04        20.45        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IE 
      143.38       149.59        12.13       220.90        50.70        65.72 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ 
       18.77       126.12        84.59       110.14       110.93       140.88 
TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM 
      211.56        68.45       189.01       234.28        81.17        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT 
      172.96       162.05       102.77       140.48       100.70        89.46 
TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WX TCGA-B6-A0WZ 
      131.21       157.41       188.68        79.63        21.47       129.57 
TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC 
      129.70       186.48        28.27        68.94        58.88        43.59 
TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 
      101.52       139.17       170.17        85.35        54.28        49.94 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY 
       82.88        55.00        24.53        38.79        20.45        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 
       28.50        46.95        40.83        39.55        39.16        48.36 
TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       56.94        56.98        37.22        32.02        18.21        25.71 
TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR 
       44.05        61.68        35.67        48.69        27.19        53.69 
TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 
       53.95        45.57        49.94        41.75        48.13        42.90 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DK TCGA-BH-A0DO 
       45.83        31.17        23.44        38.01        13.91        17.26 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       15.65         3.22         2.56        38.47        45.17        47.41 
TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 
       16.27        15.68        14.30         9.63        44.81        46.19 
TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ 
       32.65        24.49        31.00        24.43        30.35        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 
       15.16        37.78        35.51        24.56        23.08        41.00 
TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ 
       26.50        20.38         5.85         2.50        13.61        36.85 
TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       27.25        50.79        23.93        24.95        42.35        44.81 
TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M 
       23.05         2.01         7.23        20.12        90.84        72.56 
TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U 
       37.74        30.28        55.63        37.55        66.05        51.39 
TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV 
       51.16        91.99       113.82        82.85        42.28        12.00 
TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 
       55.69        49.58        17.69        25.81        31.53        89.16 
TCGA-BH-A1F6 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG 
       97.48       120.62       114.15        33.17        74.73       122.89 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A201 
       36.92        63.35        55.00        72.07       144.59         6.90 
TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q 
        0.72        38.60        83.31       130.16        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O 
       20.12       109.28         8.94        11.77        11.77        12.66 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 
        0.07        12.66        12.66        12.66        12.66         3.12 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HI 
        1.78         1.45         0.69         3.75        12.33        11.34 
TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z 
       10.42         3.25         0.30         0.36         0.43         8.28 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B 
        9.67         0.03         0.03         0.03        12.20         0.99 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 
        0.03         0.23        11.90        20.88        13.25        20.58 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1JA 
       13.97        14.17        13.48        21.14        19.20        16.50 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JI 
       18.71        15.78        18.90        12.03        14.01        18.97 
TCGA-D8-A1JL TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU 
       20.09        20.38        21.01        12.20        13.32        14.70 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XC 
       17.79        16.73        25.74        23.90        27.58         2.66 
TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ 
       17.16        15.22        14.73        17.69         7.96        16.41 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1Y0 TCGA-D8-A1Y2 
       15.85        16.31        15.16        12.66        15.52        14.24 
TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I 
       14.14        17.42        16.04        13.45        13.05        14.43 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V 
        9.44        16.41         0.76        10.09        13.08        12.53 
TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A107 
       12.26        14.50        18.51         7.33        43.00        34.42 
TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F 
       27.52        46.59        40.41        37.51        28.44        28.87 
TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14T 
       47.15        44.68        40.96        38.24        33.17        33.30 
TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A153 
       43.33        32.02        31.96        28.60        17.03        23.24 
TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15C TCGA-E2-A15D 
       19.43        21.04        23.87        14.79        22.82        17.29 
TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J 
       20.71        21.63        18.21        12.92        17.42        19.40 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R 
        9.04        20.58         7.73        13.02        19.56        17.06 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 
       14.07        14.99        60.53        53.62        53.03        29.95 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF 
       32.35        28.50        16.47        17.10        38.30        37.41 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN 
       32.78        33.73        28.44        22.65         3.88        22.19 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB 
       11.08        54.18        39.62        19.66        24.59        40.47 
TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 
       18.87       106.75       102.61         8.75        43.04        16.93 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E9-A1N4 
        5.52        15.72         7.20        18.05        22.26        19.20 
TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1ND TCGA-E9-A1NE 
       36.82        13.48        13.12        36.56        12.59        35.77 
TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 
       21.57         9.86        11.90        14.30         0.62         2.10 
TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC 
        1.38         2.76        21.21        32.09        20.81        40.24 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI 
        0.66        34.65         6.58        21.27        34.59        35.64 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22H 
        0.79        12.53        39.09        22.75        12.89        24.10 
TCGA-E9-A243 TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A 
       17.06         0.85        27.22         1.94         0.95        12.56 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54Y 
        0.76        26.07        18.41         0.62        15.72         0.23 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
        0.39         0.26         0.23        15.39        12.20        39.72 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
        8.48        18.21        18.90        13.25        16.57        15.68 
TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 
       28.77        25.94        29.95        29.85        40.41        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA 
       39.78        52.96        18.48        30.08         7.86        18.90 
TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH 
       19.99        13.94        10.52        14.43        34.55        19.96 
TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 
       55.00        25.91        22.09        21.27        17.49        10.59 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DI 
       59.57       194.27        53.52        43.04        42.71        61.91 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
       62.33        90.84        76.64        77.33        53.36       110.50 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV 
       38.20        32.28        69.30        53.95        57.63        13.55 
TCGA-GM-A5PX TCGA-JL-A3YW TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 
       18.12        11.84         8.28         6.67         4.60         0.66 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO 
        2.99         3.58         6.90         4.70         3.65         3.19 
TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 
        3.25         2.63         3.88         4.14         4.50         4.50 
TCGA-LL-A7SZ TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 
        5.59        15.91         2.79         2.10        12.66        46.55 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX 
        7.53        44.61        27.65        24.10        26.20        16.87 
TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66O 
       10.29        14.76        23.70        54.51        31.07         7.23 
TCGA-OL-A66P TCGA-W8-A86G 
        4.44         5.29 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.16              0.03 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           176.98            234.28 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           21.765            21.270 
[1] "0.2 - 177.0 (21.8)" "0.0 - 234.3 (21.3)"
[1] "hr=" "1.2"
D45V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3P LOSS MUTATED        10       12        2        1        61        48
  3P LOSS WILD-TYPE      70       65        7        8       274       176
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3P LOSS MUTATED           0         20          3          8        3
  3P LOSS WILD-TYPE         2        118         24         51       14
                   vv
clus                STAGE TIS STAGE X
  3P LOSS MUTATED           0       2
  3P LOSS WILD-TYPE         1      14
D45V3, multiclass
            clus
vv           3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                 10                70
  STAGE IA                12                65
  STAGE IB                 2                 7
  STAGE II                 1                 8
  STAGE IIA               61               274
  STAGE IIB               48               176
  STAGE III                0                 2
  STAGE IIIA              20               118
  STAGE IIIB               3                24
  STAGE IIIC               8                51
  STAGE IV                 3                14
  STAGE TIS                0                 1
  STAGE X                  2                14
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  3P LOSS MUTATED    28 122  17   3
  3P LOSS WILD-TYPE 230 459 100  33
D45V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1              28               230
  T2             122               459
  T3              17               100
  T4               3                33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  3P LOSS MUTATED    84  57  17  10
  3P LOSS WILD-TYPE 384 273  94  60
D45V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0              84               384
  N1              57               273
  N2              17                94
  N3              10                60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  3P LOSS MUTATED          0 141   3  26
  3P LOSS WILD-TYPE        2 704  14 105
D45V6, multiclass
          clus
vv         3P LOSS MUTATED 3P LOSS WILD-TYPE
  CM0 (I+)               0                 2
  M0                   141               704
  M1                     3                14
  MX                    26               105
[1] 4 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   170   0
  3P LOSS WILD-TYPE 814  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED    170    0
  3P LOSS WILD-TYPE  814   11
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE             170               814
  MALE                 0                11
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  3P LOSS MUTATED                            0                           144
  3P LOSS WILD-TYPE                          1                           591
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  3P LOSS MUTATED                               15                   1
  3P LOSS WILD-TYPE                            151                   4
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  3P LOSS MUTATED                                  2                  0
  3P LOSS WILD-TYPE                               27                 14
                   vv
clus                OTHER  SPECIFY
  3P LOSS MUTATED                8
  3P LOSS WILD-TYPE             36
D45V8, multiclass
                                  clus
vv                                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                144               591
  INFILTRATING LOBULAR CARCINOMA                15               151
  MEDULLARY CARCINOMA                            1                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               2                27
  MUCINOUS CARCINOMA                             0                14
  OTHER  SPECIFY                                 8                36
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V9, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    62 108
  3P LOSS WILD-TYPE 220 605
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     62  108
  3P LOSS WILD-TYPE  220  605
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               62               220
  YES             108               605
[1] 2 2
[1] FALSE
D45V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P LOSS MUTATED                                  0    15
  3P LOSS WILD-TYPE                                1    41
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED                          30   116
  3P LOSS WILD-TYPE                       107   592
D45V11, multiclass
                                  clus
vv                                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         15                41
  BLACK OR AFRICAN AMERICAN                     30               107
  WHITE                                        116               592
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V12, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     2 148
  3P LOSS WILD-TYPE  34 648
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      2  148
  3P LOSS WILD-TYPE   34  648
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                34
  NOT HISPANIC OR LATINO             148               648
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    78  14
  3Q LOSS WILD-TYPE 782 100
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               92               882 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               14               100 
$`3Q LOSS MUTATED`
TCGA-A1-A0SK TCGA-A1-A0SP TCGA-A2-A04T TCGA-A2-A0CT TCGA-A2-A0CW TCGA-A2-A0CX 
       31.79        19.20        73.84        75.25        64.04        56.81 
TCGA-A2-A0D1 TCGA-A2-A0D4 TCGA-A2-A0EO TCGA-A2-A0EQ TCGA-A2-A0YE TCGA-A2-A0YT 
       34.55        25.22        80.28        79.76        18.21        23.77 
TCGA-A2-A3XX TCGA-A2-A4S1 TCGA-A7-A26F TCGA-A7-A2KD TCGA-A7-A4SF TCGA-A7-A6VY 
       38.40        12.00        24.26        22.32        17.92         8.75 
TCGA-A8-A06U TCGA-A8-A06Z TCGA-A8-A07F TCGA-A8-A08O TCGA-AC-A2FO TCGA-AC-A3OD 
       29.03         1.02        18.97        31.00        50.70        14.83 
TCGA-AN-A04C TCGA-AN-A0AR TCGA-AN-A0FJ TCGA-AN-A0FT TCGA-AN-A0XU TCGA-AO-A03P 
        1.78         0.33         7.96         6.02         0.33        84.69 
TCGA-AO-A0JA TCGA-AO-A124 TCGA-AO-A1KS TCGA-AR-A0TT TCGA-AR-A0U2 TCGA-AR-A1AH 
       21.53       102.58         0.53        56.88        83.87        75.55 
TCGA-AR-A1AQ TCGA-AR-A251 TCGA-B6-A0IG TCGA-B6-A1KI TCGA-BH-A0B9 TCGA-BH-A0BJ 
       43.07        45.17       146.50        73.51        51.68        21.70 
TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0HW TCGA-BH-A18F TCGA-BH-A18L TCGA-BH-A18T 
       49.05        44.02        51.32         8.81        26.66         7.36 
TCGA-BH-A1EN TCGA-BH-A1FM TCGA-BH-A1FU TCGA-BH-A208 TCGA-C8-A12L TCGA-C8-A12P 
       69.93        45.63        72.07        57.83        11.93        11.77 
TCGA-C8-A135 TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HK TCGA-C8-A1HM TCGA-D8-A1J8 
        0.62        10.92        11.34        12.03         2.30        14.17 
TCGA-D8-A1J9 TCGA-D8-A1JD TCGA-D8-A1JG TCGA-D8-A1JJ TCGA-D8-A1JM TCGA-D8-A1XB 
       17.49        18.15        12.03        20.09        19.40        18.15 
TCGA-D8-A1XT TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A27N TCGA-E2-A10C 
        6.35        16.54        15.32         3.81         4.80        40.11 
TCGA-E2-A14R TCGA-E2-A14T TCGA-E2-A150 TCGA-E2-A15A TCGA-E2-A1IO TCGA-E2-A1L7 
       38.60        33.30        25.41        23.34        20.98        27.42 
TCGA-E2-A574 TCGA-E9-A1R4 TCGA-E9-A226 TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A247 
       19.89         6.12        34.13        23.51         0.69        27.22 
TCGA-E9-A295 TCGA-EW-A1P5 TCGA-GI-A2C9 TCGA-JL-A3YX TCGA-LL-A7T0 TCGA-OL-A66K 
        0.72        23.11       109.87        11.57         3.22        33.90 
TCGA-OL-A66N TCGA-S3-A6ZG 
       18.21         6.81 

$`3Q LOSS WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ 
       20.88        13.68         7.96        39.32        28.01        18.21 
TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04U TCGA-A2-A04V 
      104.81        18.02        41.95        82.16        22.06        63.12 
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM 
       64.04        55.43        36.13       125.59        64.57        24.79 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CU 
      112.08        92.48        88.60       107.93        75.55         5.19 
TCGA-A2-A0CV TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN 
       63.45        21.14        33.76        28.77       101.72        89.36 
TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV 
      107.61        74.40        37.05        35.05        34.29        31.82 
TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV 
       29.75        24.72        24.16        99.19        54.64        27.12 
TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 
       44.88        50.43        44.28        17.52        17.13         8.38 
TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC 
       18.71        20.52        17.46        18.90        20.75        32.55 
TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ 
       25.28        15.42        21.90        21.67        14.50        18.61 
TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX 
       19.33        14.63        31.73        23.47        17.36        36.79 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       22.45        20.25        19.20        19.56        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
      107.70        16.31        17.19        18.15        91.92        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV 
       20.88        39.65        33.93        83.01        29.98        14.07 
TCGA-A2-A3XW TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX 
       49.48        34.98        31.99        38.37         7.30         9.01 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE 
        8.81         8.91         6.74         3.42        38.30        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB 
       34.29        35.47        30.61        37.45        35.67        33.11 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       31.73        10.72        12.72        23.61        29.56        31.36 
TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ 
       23.74        23.80        21.73        20.61        11.34        10.59 
TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA 
       10.29        11.28        13.41        14.70        11.97        14.93 
TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW 
       13.74        14.50        21.17        14.73        12.10        10.72 
TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A06P 
       11.05        10.29         9.37        10.42        13.02        13.02 
TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A075 
        1.02        17.98        41.06        31.00        26.01        17.03 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07I 
       53.98         9.01        33.01        19.99        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S 
       12.00        17.03         9.99        10.98         8.98         7.99 
TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 
        9.96         9.99        28.04        18.05        15.06        36.95 
TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G 
       13.02         0.99        23.08        19.99        18.05        19.96 
TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S 
       12.00        37.05         9.99        31.00         0.99        19.07 
TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 
       93.04        33.99        40.01        19.07        16.01        17.95 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C 
       41.98        12.00         9.99         9.99        12.00         1.02 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N 
       13.02        31.00        33.07        29.98        15.02         1.02 
TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X 
       25.02         8.98        19.04        15.02         0.99        14.01 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 
       12.00        19.04        13.02        21.04         0.99        13.02 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H 
       17.03        38.04         0.95         2.37        10.85         2.66 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG 
        1.48        38.53        38.20        40.57        55.43        36.99 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB 
       38.79        26.04         1.02         0.92         2.27         0.99 
TCGA-AC-A3HN TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI 
        0.69         9.40         1.12         1.81         1.68         1.55 
TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV 
        1.32         1.55         0.07         1.12         1.81         1.18 
TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 
        0.69         0.43         1.74         0.33         0.33         0.23 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK 
        0.33         0.62         2.96         1.71         8.02         7.36 
TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF 
        6.51         0.16         0.33         0.33         6.44         4.64 
TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0FW 
        7.00         7.59         7.17         6.28         0.33         0.36 
TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO 
        0.33         0.33         0.33         0.33         0.33        12.33 
TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AN-A0XW 
        0.30         0.33         0.33         0.33         5.33         5.59 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T 
       80.28        47.84        66.77        81.63        68.75        47.87 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 
       59.05        29.13        32.78        21.40        17.65        24.16 
TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JB TCGA-AO-A0JC 
       37.48        20.32        22.36        53.03        50.70        50.86 
TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ 
       72.00        76.77        21.37        26.24        38.53        62.04 
TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 
       55.33        71.80        99.25        93.70        94.59        96.10 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G 
       90.58        77.56        64.04        57.30        48.36        41.62 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KT 
       28.37        14.73        82.62        61.87        70.39        17.79 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       24.79        26.93       130.09         5.65        15.62        13.22 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
        2.56        21.86         9.99        82.88        49.32         5.26 
TCGA-AR-A0TS TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
       37.41        29.75        24.30        64.83        55.86        76.14 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AJ 
       65.36        70.16        76.18        55.36        61.84        52.77 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP 
       51.25        48.82        62.56        43.73        43.56        39.98 
TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX 
       17.23        40.83        46.32        42.58        35.24        36.26 
TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       20.22       109.58        50.89        73.02        65.46        68.19 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T 
       65.69         0.85        66.05        57.40        62.07        53.26 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 
       53.36        54.18        50.96        48.16        51.75        56.15 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH 
       40.64        39.85        34.82        93.83       128.65        20.25 
TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       42.87         7.36        40.04        17.10        20.81        16.96 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       20.38        54.74        16.04        20.45        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC 
      143.38       149.59        12.13       220.90       129.57        50.70 
TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
       65.72       112.37       176.98        18.77       126.12        84.59 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH 
      110.14       110.93       140.88       211.56        68.45       189.01 
TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP 
      234.28        81.17        78.02       172.96       162.05       102.77 
TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS 
      140.48       100.70        89.46       131.21       157.41        97.48 
TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ 
      188.68        79.63        17.98        21.47       113.79       129.57 
TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC 
      129.70       186.48        28.27        68.94        58.88        43.59 
TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 
      101.52       139.17       170.17        85.35        54.28        49.94 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY 
       82.88        55.00        24.53        38.79        20.45        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 
       28.50        46.95        40.83        39.55        39.16        48.36 
TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       56.94        56.98        37.22        32.02        18.21        25.71 
TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ 
       24.85        44.05        61.68        35.67        48.69        27.19 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0C0 
       53.69        53.95        45.57        49.94        11.67        41.75 
TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH 
       48.13        42.90        45.83        31.17        23.44        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ 
       22.13        13.91        48.23        17.26        15.65         3.22 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
        2.56        38.47        45.17        47.41        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA 
       15.68        14.30         9.63        44.81        46.19        32.65 
TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 
       24.49        31.00        24.43        30.35        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA 
       37.78        35.51        24.56        23.08        41.00        52.96 
TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ 
       26.50        20.38         5.85         2.50        13.61        36.85 
TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 
       12.89        27.25        50.79         5.59        23.93        24.95 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J 
       42.35        44.81        23.05         2.01         7.23        20.12 
TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R 
       90.84        72.56        37.74        30.28        55.63        37.55 
TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET 
       66.05        51.39        51.16        91.99       113.82        82.85 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 
       42.28        12.00        55.69        49.58        17.69        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC 
       31.53        89.16        97.48        24.66       120.62       114.15 
TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
       33.17        74.73       122.89        36.92        63.35        55.00 
TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 
       72.07       144.59         6.90         0.72        38.60        83.31 
TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
      130.16        10.65         6.44        20.12         0.99       109.28 
TCGA-BH-A42V TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12Q TCGA-C8-A12U 
        8.94        11.77        11.77        12.66         0.07        12.66 
TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 
       12.66        12.66        12.66         3.12         1.78         1.45 
TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HI TCGA-C8-A1HJ 
        0.69         3.85         3.75        12.33        11.34         0.16 
TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y 
       10.42         3.25         0.30         0.23         0.36         0.43 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A 
        8.28         9.67         0.03         0.03         0.03        12.20 
TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 
        0.99         0.03         0.23        11.90        20.88        13.25 
TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 
       20.58        13.97        14.17        13.48        21.14        19.20 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JH 
       16.50        18.71        15.78        18.90        12.03        14.01 
TCGA-D8-A1JI TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS 
       18.97        20.12        20.09        20.38        21.01        12.20 
TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 
       13.32        14.70        18.58        17.79        16.73        25.74 
TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG 
       23.90        27.58         2.66        17.16        15.22        14.73 
TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ 
       21.83        14.50        19.92        17.69         7.96        16.41 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1Y0 
       15.85        16.31        12.99        15.16        12.66        15.52 
TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H 
       14.24        14.14        17.42        16.04        13.45        13.05 
TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27P TCGA-D8-A27R 
       14.43         9.44        16.41        13.48         0.76        10.09 
TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 
       13.08        12.53        12.26        14.50        18.51         7.33 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B 
       43.00        34.42        27.52        46.59        40.41        37.51 
TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q 
       28.44        28.87        47.15        44.68        40.96        38.24 
TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y 
       33.17        43.33        34.26        32.02        31.96        28.60 
TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 
       17.03        27.12        23.24        19.43        21.04        23.87 
TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F 
       14.79        25.05        22.82        17.29        20.71        21.63 
TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       18.21        12.92        17.42        19.40         9.04        20.58 
TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
        7.73        13.02        19.56        17.06        14.07        14.99 
TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       60.53        53.62        53.03        29.95        32.35        28.50 
TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       16.47        17.10        38.30        37.41        32.78        33.73 
TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IU 
       33.70        28.44        22.65         3.88        22.19        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       54.18        39.62        19.66        24.59        40.47        28.90 
TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 
       18.87       106.75       102.61         8.75        43.04        16.93 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E9-A1N4 
        5.52        15.72         7.20        18.05        22.26        19.20 
TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC 
       36.82        13.48        12.00        13.12        36.56        39.55 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ 
       12.59        35.77        20.05        21.57         9.86        11.90 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 
       14.30         0.62         2.10         1.38         2.76        21.21 
TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF 
       32.09        20.81        40.24         0.66        34.65         6.58 
TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
       21.27        34.59        35.64         0.79        12.53        13.32 
TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A245 
       39.09        22.75        12.89        24.10        17.06         0.85 
TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO 
        1.94         0.95        12.56        17.75         0.76        26.07 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL 
       18.41         0.62        15.72         0.23         0.39         0.26 
TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
        0.23        15.39        12.20        39.72         8.48        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV 
       18.90        13.25        16.57        15.68        28.77        25.94 
TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 
       22.82        29.95        29.85        40.41        41.13        39.78 
TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA 
       52.96        29.82        18.48        30.08         7.86        18.90 
TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
       19.99         6.15        13.94        10.52        14.43        34.55 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 
       19.96        55.00        52.73        25.91        22.09        21.27 
TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA 
       17.49        10.16        10.59         7.40        59.57       194.27 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI 
       53.13        53.52        43.04        42.71        42.28        61.91 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
       62.33        90.84        76.64        77.33        53.36       110.50 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV 
       38.20        32.28        69.30        53.95        57.63        13.55 
TCGA-GM-A5PX TCGA-JL-A3YW TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 
       18.12        11.84         8.28         6.67         4.60         0.66 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN 
        2.99         3.58         6.90         5.56         4.70         3.65 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z 
        3.19         3.25         2.63         3.88         4.14         4.50 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 
        4.50         5.59         6.21        15.91         2.79         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
       12.66        46.55         7.53        44.61        27.65        24.10 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H 
       26.20        16.87        14.10        10.29         9.80        14.76 
TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P TCGA-W8-A86G 
       23.70        54.51        31.07         7.23         4.44         5.29 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.33              0.03 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           146.50            234.28 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            22.01             21.32 
[1] "0.3 - 146.5 (22.0)" "0.0 - 234.3 (21.3)"
[1] "hr=" "1.5"
D46V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3Q LOSS MUTATED         2        8        0        0        37        27
  3Q LOSS WILD-TYPE      78       69        9        9       298       197
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3Q LOSS MUTATED           0         13          1          3        2
  3Q LOSS WILD-TYPE         2        125         26         56       15
                   vv
clus                STAGE TIS STAGE X
  3Q LOSS MUTATED           0       0
  3Q LOSS WILD-TYPE         1      16
D46V3, multiclass
            clus
vv           3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                  2                78
  STAGE IA                 8                69
  STAGE IB                 0                 9
  STAGE II                 0                 9
  STAGE IIA               37               298
  STAGE IIB               27               197
  STAGE III                0                 2
  STAGE IIIA              13               125
  STAGE IIIB               1                26
  STAGE IIIC               3                56
  STAGE IV                 2                15
  STAGE TIS                0                 1
  STAGE X                  0                16
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  3Q LOSS MUTATED    12  73   7   1
  3Q LOSS WILD-TYPE 246 508 110  35
D46V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1              12               246
  T2              73               508
  T3               7               110
  T4               1                35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  3Q LOSS MUTATED    46  30  12   4
  3Q LOSS WILD-TYPE 422 300  99  66
D46V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0              46               422
  N1              30               300
  N2              12                99
  N3               4                66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  3Q LOSS MUTATED          0  82   2   9
  3Q LOSS WILD-TYPE        2 763  15 122
D46V6, multiclass
          clus
vv         3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CM0 (I+)               0                 2
  M0                    82               763
  M1                     2                15
  MX                     9               122
[1] 4 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    93   0
  3Q LOSS WILD-TYPE 891  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     93    0
  3Q LOSS WILD-TYPE  891   11
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              93               891
  MALE                 0                11
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  3Q LOSS MUTATED                            0                            81
  3Q LOSS WILD-TYPE                          1                           654
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  3Q LOSS MUTATED                                8                   0
  3Q LOSS WILD-TYPE                            158                   5
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  3Q LOSS MUTATED                                  0                  0
  3Q LOSS WILD-TYPE                               29                 14
                   vv
clus                OTHER  SPECIFY
  3Q LOSS MUTATED                4
  3Q LOSS WILD-TYPE             40
D46V8, multiclass
                                  clus
vv                                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                 81               654
  INFILTRATING LOBULAR CARCINOMA                 8               158
  MEDULLARY CARCINOMA                            0                 5
  MIXED HISTOLOGY (PLEASE SPECIFY)               0                29
  MUCINOUS CARCINOMA                             0                14
  OTHER  SPECIFY                                 4                40
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V9, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    36  57
  3Q LOSS WILD-TYPE 246 656
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     36   57
  3Q LOSS WILD-TYPE  246  656
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO               36               246
  YES              57               656
[1] 2 2
[1] FALSE
D46V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q LOSS MUTATED                                  0    10
  3Q LOSS WILD-TYPE                                1    46
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED                          13    64
  3Q LOSS WILD-TYPE                       124   644
D46V11, multiclass
                                  clus
vv                                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         10                46
  BLACK OR AFRICAN AMERICAN                     13               124
  WHITE                                         64               644
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V12, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     0  83
  3Q LOSS WILD-TYPE  36 713
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0   83
  3Q LOSS WILD-TYPE   36  713
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                36
  NOT HISPANIC OR LATINO              83               713
[1] 2 2
[1] FALSE

Clustering(47) Variable = 4P LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED   274  44
  4P LOSS WILD-TYPE 586  70
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              318               656 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               44                70 
$`4P LOSS MUTATED`
TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A0CL 
       20.88        31.79        39.32        28.01        18.02        64.57 
TCGA-A2-A0CM TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0EQ 
       24.79        75.55        63.45        64.04        21.14        79.76 
TCGA-A2-A0SV TCGA-A2-A0T1 TCGA-A2-A0T3 TCGA-A2-A0T7 TCGA-A2-A0YE TCGA-A2-A0YH 
       27.12        17.13        18.71        20.75        18.21        21.67 
TCGA-A2-A0YJ TCGA-A2-A1FW TCGA-A2-A1G1 TCGA-A2-A25C TCGA-A2-A3XS TCGA-A2-A3XT 
       18.61        17.36        19.20        17.19        33.93        83.01 
TCGA-A2-A3XZ TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A7-A0CE TCGA-A7-A0CJ TCGA-A7-A0DA 
       31.99         7.30         9.01        35.31        30.61        35.67 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A26G TCGA-A7-A26I TCGA-A7-A2KD 
       31.73        10.72        12.72        23.74        21.73        22.32 
TCGA-A7-A4SD TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX 
       14.50        14.73        12.10        10.29         9.37        10.42 
TCGA-A7-A6VY TCGA-A8-A06Q TCGA-A8-A06T TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A07B 
        8.75         1.02        41.06        31.00        26.01        33.01 
TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A08B TCGA-A8-A08F 
        9.99         8.98        15.06        36.95        23.08        18.05 
TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A092 TCGA-A8-A09C 
       12.00         9.99         0.99        33.99        16.01         1.02 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09X TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A2BK 
       31.00        33.07        14.01         0.95         2.37        38.53 
TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y 
        0.92         0.99         1.55         0.07         1.12         1.81 
TCGA-AC-A6IW TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D 
        0.69         0.23         0.33         0.62         2.96         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD 
        8.02         0.16         0.33         0.33         0.33         6.44 
TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX 
        7.96         7.00         6.02         0.33         0.36         0.33 
TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU 
        0.33        12.33         0.30         0.33         0.33         0.33 
TCGA-AN-A0XW TCGA-AO-A03N TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J7 
        5.59        66.77        32.78        21.40        17.65        20.32 
TCGA-AO-A0JE TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12D 
       76.77        71.80       102.58        96.10        90.58        64.04 
TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04J TCGA-AQ-A04L 
       48.36        61.87         0.53        17.79        26.93       130.09 
TCGA-AQ-A0Y5 TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TY TCGA-AR-A0U0 TCGA-AR-A0U1 
        5.65        82.88         5.26        55.86        65.36        70.16 
TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AQ 
       76.18        75.55        61.84        62.56        43.73        43.07 
TCGA-AR-A1AR TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24O TCGA-AR-A24Q 
       17.23        20.22       109.58        50.89        65.69        66.05 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A251 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LO 
       54.18        50.96        45.17        34.82        93.83        20.81 
TCGA-AR-A5QN TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IG 
       16.04        10.59        77.62       220.90       129.57       146.50 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IQ 
      112.37       176.98        18.77        84.59       110.14       140.88 
TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RL TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WV 
      211.56       189.01        81.17       100.70       131.21        79.63 
TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A401 TCGA-B6-A402 
       21.47       113.79        43.59        73.51        85.35        54.28 
TCGA-B6-A408 TCGA-B6-A40B TCGA-BH-A0AW TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B5 
       49.94        82.88        20.45        46.95        39.55        48.36 
TCGA-BH-A0BA TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BP 
       37.22        25.71        24.85        21.70        44.05        48.69 
TCGA-BH-A0BR TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C7 
       53.69        45.57        49.94        41.75        44.02        42.90 
TCGA-BH-A0DX TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0H7 
       47.41         4.41         9.63        46.19        24.49        23.08 
TCGA-BH-A0HI TCGA-BH-A0HU TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0WA 
       20.38        12.89        50.79         5.59        23.93        23.05 
TCGA-BH-A18F TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EU 
        8.81        55.63         7.36        51.39        51.16        42.28 
TCGA-BH-A1EV TCGA-BH-A1F0 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FD TCGA-BH-A1FU 
       12.00        25.81        97.48        24.66        33.17        72.07 
TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A209 TCGA-C8-A12L TCGA-C8-A12P TCGA-C8-A135 
       38.60        57.83       130.16        11.93        11.77         0.62 
TCGA-C8-A138 TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A26Y 
        3.75         0.16        12.03        10.42         2.30         0.43 
TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A142 
        0.03         0.03         0.99        11.90        20.88        13.97 
TCGA-D8-A147 TCGA-D8-A1JA TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JJ TCGA-D8-A1JK 
       19.20        16.50        18.90        12.03        20.09        20.12 
TCGA-D8-A1JM TCGA-D8-A1XA TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK 
       19.40        27.58        15.22        14.73        21.83        14.50 
TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1Y3 TCGA-D8-A27F 
        7.96        15.85        12.99        12.66        14.14        16.04 
TCGA-D8-A27H TCGA-D8-A27T TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q 
       13.05        13.08        47.15        44.68        40.96        38.24 
TCGA-E2-A14R TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A154 TCGA-E2-A158 TCGA-E2-A159 
       38.60        17.03        25.41        19.43        14.79        25.05 
TCGA-E2-A15H TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1II 
       12.92        60.53        53.62        17.10        33.73        33.70 
TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A573 TCGA-E2-A574 
       39.62        18.87       106.75       102.61        22.26        19.89 
TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1NI 
       13.48        12.00        39.55        12.59        20.05         9.86 
TCGA-E9-A1R3 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A22E TCGA-E9-A22G 
        2.10        21.21        32.09        20.81        12.89        23.51 
TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A3HO TCGA-E9-A3X8 TCGA-E9-A54Y 
        0.69         1.94         0.95        26.07        15.72         0.23 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-EW-A1IX TCGA-EW-A1J1 TCGA-EW-A1OV TCGA-EW-A1OW 
        0.39         0.26        39.72        18.90        25.94        22.82 
TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PC TCGA-EW-A1PD 
       29.85        40.41        23.11         7.86         6.15        13.94 
TCGA-EW-A1PE TCGA-EW-A2FR TCGA-EW-A3U0 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2DB 
       10.52        55.00        17.49         7.40       109.87        53.13 
TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DL TCGA-GM-A3XL TCGA-JL-A3YW 
       42.71        42.28        61.91        90.84        69.30        11.84 
TCGA-JL-A3YX TCGA-LL-A441 TCGA-LL-A5YM TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Z 
       11.57         2.99         4.70         3.25         3.88         4.50 
TCGA-LL-A8F5 TCGA-OL-A5D7 TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-OL-A66I TCGA-OL-A66K 
        6.21        46.55        26.20         9.80        23.70        33.90 

$`4P LOSS WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04Q 
       13.68         7.96        19.20        18.21       104.81        41.95 
TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X 
       82.16        73.84        22.06        63.12        64.04        55.43 
TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
       36.13       125.59       112.08        92.48        88.60       107.93 
TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 
       75.25         5.19        56.81        34.55        33.76        28.77 
TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER 
       25.22       101.72        89.36        80.28       107.61        74.40 
TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
       37.05        35.05        34.29        31.82        29.75        24.72 
TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY 
       24.16        99.19        54.64        44.88        50.43        44.28 
TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC 
       17.52         8.38        20.52        17.46        18.90        32.55 
TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL 
       25.28        15.42        21.90        14.50        19.33        14.63 
TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 
       31.73        23.77        23.47        36.79        22.45        20.25 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25D 
       19.56        16.47        52.47       107.70        16.31        18.15 
TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XU TCGA-A2-A3XV 
       91.92        10.59        20.88        39.65        29.98        14.07 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RY TCGA-A2-A4S0 
       49.48        38.40        34.98        38.37         8.81         8.91 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH 
       12.00         6.74         3.42        38.30        34.29        35.47 
TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F 
       37.45        33.11        23.61        29.56        31.36        24.26 
TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       23.80        20.61        11.34        10.59        10.29        11.28 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SE 
       13.41        14.70        11.97        14.93        13.74        21.17 
TCGA-A7-A4SF TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06R 
       17.92        10.72        11.05        13.02        13.02        17.98 
TCGA-A8-A06U TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07E 
       29.03         1.02        17.03        53.98         9.01        19.99 
TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07P 
       18.97        18.97        14.01        12.00        17.03        10.98 
TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A086 
        7.99         9.96         9.99        28.04        18.05        13.02 
TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08P 
        0.99        19.99        19.96        37.05        31.00        31.00 
TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 
       19.07        93.04        40.01        19.07        17.95        41.98 
TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09K 
       12.00         9.99         9.99        12.00        13.02        29.98 
TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       15.02         1.02        25.02         8.98        19.04        15.02 
TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 
        0.99        12.00        19.04        13.02        21.04         0.99 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 
       13.02        17.03        38.04        10.85         2.66         1.48 
TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM 
       38.20        40.57        55.43        36.99        38.79        26.04 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
       50.70         1.02         2.27         0.69        14.83         9.40 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A6IV 
        1.12         1.81         1.68         1.55         1.32         1.18 
TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A04C TCGA-AN-A0AK 
        0.43         1.74         0.33         0.33         1.78         7.36 
TCGA-AN-A0AL TCGA-AN-A0FF TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FY 
        6.51         4.64         7.59         7.17         6.28         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XR TCGA-AN-A0XV TCGA-AO-A03L TCGA-AO-A03M 
        0.33         0.33         0.33         5.33        80.28        47.84 
TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V 
       81.63        84.69        68.75        47.87        59.05        29.13 
TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB 
       24.16        37.48        22.36        53.03        21.53        50.70 
TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ 
       50.86        72.00        21.37        26.24        38.53        62.04 
TCGA-AO-A0JL TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12B TCGA-AO-A12E 
       55.33        99.25        93.70        94.59        77.56        57.30 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AQ-A04H 
       41.62        28.37        14.73        82.62        70.39        24.79 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TQ 
       15.62        13.22         2.56        21.86         9.99        49.32 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TZ 
       37.41        56.88        29.75        24.30        64.83        76.14 
TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AO 
       83.87        55.36        52.77        51.25        48.82        43.56 
TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX 
       39.98        40.83        46.32        42.58        35.24        36.26 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S 
       73.02        65.46        68.19         0.85        57.40        62.07 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 
       53.26        53.36        48.16        51.75        56.15        40.64 
TCGA-AR-A254 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM 
       39.85       128.65        20.25        42.87         7.36        40.04 
TCGA-AR-A2LN TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QP TCGA-B6-A0I2 
       17.10        16.96        20.38        54.74        20.45       143.38 
TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IM TCGA-B6-A0IP 
      149.59        12.13        50.70        65.72       126.12       110.93 
TCGA-B6-A0RG TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP 
       68.45       234.28        78.02       172.96       162.05       102.77 
TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW 
      140.48        89.46       157.41        97.48       188.68        17.98 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      129.57       129.70       186.48        28.27        68.94        58.88 
TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV 
      101.52       139.17       170.17        55.00        24.53        38.79 
TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0B7 
       25.55        28.50        40.83        39.16        56.94        56.98 
TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ 
       51.68        32.02        18.21        61.68        35.67        27.19 
TCGA-BH-A0BS TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE 
       53.95        11.67        49.05        48.13        45.83        31.17 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO 
       23.44        38.01        22.13        13.91        48.23        17.26 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DZ 
       15.65         3.22         2.56        38.47        45.17        16.27 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0EI 
       15.68        14.30        44.81        32.65        31.00        24.43 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       30.35        10.78        15.16        37.78        35.51        24.56 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       41.00        52.96        26.50         5.85         2.50        13.61 
TCGA-BH-A0HQ TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       36.85        51.32        27.25        24.95        42.35        44.81 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M 
        2.01         7.23        20.12        90.84        26.66        72.56 
TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A1EN TCGA-BH-A1EO 
       37.74        30.28        37.55        66.05        69.93        91.99 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F2 
      113.82        82.85        55.69        49.58        17.69        31.53 
TCGA-BH-A1F5 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH 
       89.16       120.62       114.15        74.73       122.89        36.92 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A201 
       63.35        55.00        45.63        72.07       144.59         6.90 
TCGA-BH-A202 TCGA-BH-A204 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T 
        0.72        83.31        10.65         6.44        20.12         0.99 
TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12Q 
      109.28         8.94        11.77        11.77        12.66         0.07 
TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A131 
       12.66        12.66        12.66        12.66         3.12         1.78 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG 
        1.45         0.69         3.85        12.33        10.92        11.34 
TCGA-C8-A1HI TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Z 
       11.34         3.25         0.30         0.23         0.36         8.28 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A27A TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A140 
        9.67         0.03        12.20         0.03         0.23        13.25 
TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 
       20.58        14.17        13.48        21.14        14.17        17.49 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI 
       18.71        15.78        18.15        12.03        14.01        18.97 
TCGA-D8-A1JL TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU 
       20.09        20.38        21.01        12.20        13.32        14.70 
TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XB 
       18.58        17.79        16.73        25.74        23.90        18.15 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XQ TCGA-D8-A1XS 
        2.66        17.16        19.92        17.69        16.41        16.31 
TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 
        6.35        15.16        16.54        15.32        15.52         3.81 
TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       14.24        17.42        13.45        14.43         9.44        16.41 
TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27V TCGA-D8-A27W 
       13.48         4.80         0.76        10.09        12.53        12.26 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 
       14.50        18.51         7.33        43.00        34.42        27.52 
TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F 
       46.59        40.41        37.51        40.11        28.44        28.87 
TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X 
       33.17        33.30        43.33        34.26        32.02        31.96 
TCGA-E2-A14Y TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15A 
       28.60        27.12        23.24        21.04        23.87        23.34 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15I 
       22.82        17.29        20.71        21.63        18.21        17.42 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P 
       19.40         9.04        20.58         7.73        13.02        19.56 
TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       17.06        14.07        14.99        53.03        29.95        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IJ 
       28.50        16.47        38.30        37.41        32.78        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       22.65         3.88        22.19        20.98        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LK 
       27.42        19.66        24.59        40.47        28.90         8.75 
TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
       43.04        16.93         5.52        15.72         7.20        18.05 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NE TCGA-E9-A1NG 
       19.20        36.82        13.12        36.56        35.77        21.57 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 
       11.90        14.30         0.62         6.12         1.38         2.76 
TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH 
       40.24         0.66        34.65         6.58        21.27        34.59 
TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       35.64        34.13         0.79        12.53        13.32        39.09 
TCGA-E9-A22B TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A24A 
       22.75        24.10        17.06         0.85        27.22        12.56 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A5UO 
        0.72        17.75         0.76        18.41         0.62         0.23 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1J3 
       15.39        12.20         8.48        18.21        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OX TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 
       15.68        28.77        29.95        41.13        39.78        52.96 
TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PF 
       29.82        18.48        30.08        18.90        19.99        14.43 
TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 
       34.55        19.96        52.73        25.91        22.09        21.27 
TCGA-EW-A423 TCGA-EW-A424 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DC TCGA-GM-A2DD 
       10.16        10.59        59.57       194.27        53.52        43.04 
TCGA-GM-A2DK TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY 
       62.33        76.64        77.33        53.36       110.50        38.20 
TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-LD-A66U 
       32.28        53.95        57.63        13.55        18.12         8.28 
TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL 
        6.67         4.60         0.66         3.58         6.90         5.56 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A740 TCGA-LL-A7SZ 
        3.65         3.19         2.63         4.14         4.50         5.59 
TCGA-LL-A7T0 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 
        3.22        15.91         2.79         2.10        12.66         7.53 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       44.61        27.65        24.10        16.87        14.10        10.29 
TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P 
       14.76        54.51        31.07        18.21         7.23         4.44 
TCGA-S3-A6ZG TCGA-W8-A86G 
        6.81         5.29 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.03              0.03 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           220.90            234.28 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           21.305            21.550 
[1] "0.0 - 220.9 (21.3)" "0.0 - 234.3 (21.6)"
[1] "hr=" "1.2"
D47V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4P LOSS MUTATED        24       15        1        3       119        74
  4P LOSS WILD-TYPE      56       62        8        6       216       150
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4P LOSS MUTATED           0         49          8         18        6
  4P LOSS WILD-TYPE         2         89         19         41       11
                   vv
clus                STAGE TIS STAGE X
  4P LOSS MUTATED           0       6
  4P LOSS WILD-TYPE         1      10
D47V3, multiclass
            clus
vv           4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                 24                56
  STAGE IA                15                62
  STAGE IB                 1                 8
  STAGE II                 3                 6
  STAGE IIA              119               216
  STAGE IIB               74               150
  STAGE III                0                 2
  STAGE IIIA              49                89
  STAGE IIIB               8                19
  STAGE IIIC              18                41
  STAGE IV                 6                11
  STAGE TIS                0                 1
  STAGE X                  6                10
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  4P LOSS MUTATED    67 209  35  12
  4P LOSS WILD-TYPE 191 372  82  24
D47V4, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1              67               191
  T2             209               372
  T3              35                82
  T4              12                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                 N0  N1  N2  N3
  4P LOSS MUTATED   150 109  41  20
  4P LOSS WILD-TYPE 318 221  70  50
D47V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0             150               318
  N1             109               221
  N2              41                70
  N3              20                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  4P LOSS MUTATED          0 282   6  36
  4P LOSS WILD-TYPE        2 563  11  95
D47V6, multiclass
          clus
vv         4P LOSS MUTATED 4P LOSS WILD-TYPE
  CM0 (I+)               0                 2
  M0                   282               563
  M1                     6                11
  MX                    36                95
[1] 4 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   320   4
  4P LOSS WILD-TYPE 664   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED    320    4
  4P LOSS WILD-TYPE  664    7
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE             320               664
  MALE                 4                 7
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  4P LOSS MUTATED                            1                           271
  4P LOSS WILD-TYPE                          0                           464
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  4P LOSS MUTATED                               27                   2
  4P LOSS WILD-TYPE                            139                   3
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  4P LOSS MUTATED                                  7                  0
  4P LOSS WILD-TYPE                               22                 14
                   vv
clus                OTHER  SPECIFY
  4P LOSS MUTATED               15
  4P LOSS WILD-TYPE             29
D47V8, multiclass
                                  clus
vv                                 4P LOSS MUTATED 4P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                271               464
  INFILTRATING LOBULAR CARCINOMA                27               139
  MEDULLARY CARCINOMA                            2                 3
  MIXED HISTOLOGY (PLEASE SPECIFY)               7                22
  MUCINOUS CARCINOMA                             0                14
  OTHER  SPECIFY                                15                29
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V9, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    94 230
  4P LOSS WILD-TYPE 188 483
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     94  230
  4P LOSS WILD-TYPE  188  483
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               94               188
  YES             230               483
[1] 2 2
[1] FALSE
D47V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P LOSS MUTATED                                  1    19
  4P LOSS WILD-TYPE                                0    37
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED                          59   221
  4P LOSS WILD-TYPE                        78   487
D47V11, multiclass
                                  clus
vv                                 4P LOSS MUTATED 4P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         19                37
  BLACK OR AFRICAN AMERICAN                     59                78
  WHITE                                        221               487
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V12, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    10 265
  4P LOSS WILD-TYPE  26 531
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     10  265
  4P LOSS WILD-TYPE   26  531
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                  10                26
  NOT HISPANIC OR LATINO             265               531
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4Q LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED   247  36
  4Q LOSS WILD-TYPE 613  78
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              283               691 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               36                78 
$`4Q LOSS MUTATED`
TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A04W 
       20.88        31.79        39.32        28.01        18.02        64.04 
TCGA-A2-A0CL TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0EQ 
       64.57        75.55        63.45        64.04        21.14        79.76 
TCGA-A2-A0SV TCGA-A2-A0SX TCGA-A2-A0T1 TCGA-A2-A0T7 TCGA-A2-A0YE TCGA-A2-A0YJ 
       27.12        50.43        17.13        20.75        18.21        18.61 
TCGA-A2-A1FW TCGA-A2-A1G1 TCGA-A2-A25C TCGA-A2-A3XT TCGA-A2-A3XZ TCGA-A2-A4RX 
       17.36        19.20        17.19        83.01        31.99         9.01 
TCGA-A7-A0CE TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A26G 
       35.31        30.61        35.67        31.73        12.72        23.74 
TCGA-A7-A26I TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A6VV 
       21.73        14.50        21.17        17.92        14.73        10.29 
TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A8-A06Q TCGA-A8-A06T TCGA-A8-A06X TCGA-A8-A06Y 
        9.37        10.42         1.02        41.06        31.00        26.01 
TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07R TCGA-A8-A084 
        1.02        17.03        33.01        19.99         8.98        15.06 
TCGA-A8-A08B TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08R TCGA-A8-A08X 
       23.08        18.05        12.00         9.99         0.99        33.99 
TCGA-A8-A092 TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09R TCGA-A8-A09X TCGA-AC-A23E 
       16.01         1.02        31.00         8.98        14.01         2.37 
TCGA-AC-A2BK TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X 
       38.53         0.92         0.99         1.55         0.07         1.12 
TCGA-AC-A62Y TCGA-AC-A6IW TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A 
        1.81         0.69         0.23         0.33         0.62         2.96 
TCGA-AN-A0AJ TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FJ 
        8.02         0.33         0.33         0.33         6.44         7.96 
TCGA-AN-A0FK TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0XN TCGA-AN-A0XP 
        7.00         0.33         0.36         0.33         0.33         0.30 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XW TCGA-AO-A03N TCGA-AO-A0J2 
        0.33         0.33         0.33         5.59        66.77        32.78 
TCGA-AO-A0J4 TCGA-AO-A0J7 TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JM TCGA-AO-A124 
       17.65        20.32        72.00        76.77        71.80       102.58 
TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KS 
       96.10        90.58        64.04        48.36        61.87         0.53 
TCGA-AO-A1KT TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AR-A0TR TCGA-AR-A0TY TCGA-AR-A0U0 
       17.79       130.09         5.65         5.26        55.86        65.36 
TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AQ 
       70.16        76.18        75.55        62.56        43.73        43.07 
TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24O TCGA-AR-A24Q TCGA-AR-A24S 
       20.22       109.58        50.89        65.69        66.05        62.07 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A251 TCGA-AR-A256 TCGA-AR-A5QQ TCGA-B6-A0I1 
       54.18        50.96        45.17        93.83        10.59        77.62 
TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IN 
      220.90       129.57       112.37       176.98        18.77        84.59 
TCGA-B6-A0IO TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RL TCGA-B6-A0RU 
      110.14       140.88       211.56       189.01        81.17       131.21 
TCGA-B6-A0WV TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A401 
       79.63        21.47       113.79        43.59        73.51        85.35 
TCGA-B6-A408 TCGA-B6-A40B TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0B0 TCGA-BH-A0B3 
       49.94        82.88        38.79        20.45        46.95        39.55 
TCGA-BH-A0B5 TCGA-BH-A0BA TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BP 
       48.36        37.22        25.71        21.70        44.05        48.69 
TCGA-BH-A0BR TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0E0 
       53.69        45.57        49.94        41.75        44.02         4.41 
TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0GZ TCGA-BH-A0H7 TCGA-BH-A0HI 
        9.63        46.19        24.49        10.78        23.08        20.38 
TCGA-BH-A0HU TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0WA TCGA-BH-A18F 
       12.89        50.79         5.59        23.93        23.05         8.81 
TCGA-BH-A18Q TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EU TCGA-BH-A1EV 
       55.63        51.39        51.16        69.93        42.28        12.00 
TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FD TCGA-BH-A1FU TCGA-BH-A203 TCGA-BH-A208 
       97.48        24.66        33.17        72.07        38.60        57.83 
TCGA-BH-A209 TCGA-C8-A12L TCGA-C8-A12P TCGA-C8-A138 TCGA-C8-A1HJ TCGA-C8-A1HK 
      130.16        11.93        11.77         3.75         0.16        12.03 
TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A26Y TCGA-C8-A278 TCGA-C8-A27B TCGA-D8-A13Y 
       10.42         2.30         0.43         0.03         0.99        11.90 
TCGA-D8-A13Z TCGA-D8-A1JA TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JJ TCGA-D8-A1JK 
       20.88        16.50        18.90        12.03        20.09        20.12 
TCGA-D8-A1JM TCGA-D8-A1JP TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XO 
       19.40        21.01        14.73        21.83        14.50         7.96 
TCGA-D8-A1XR TCGA-D8-A1XU TCGA-D8-A27H TCGA-D8-A27T TCGA-E2-A14N TCGA-E2-A14O 
       15.85        12.99        13.05        13.08        47.15        44.68 
TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A150 TCGA-E2-A154 TCGA-E2-A159 TCGA-E2-A15H 
       38.24        38.60        25.41        19.43        25.05        12.92 
TCGA-E2-A15S TCGA-E2-A1B0 TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1L8 
       14.07        53.62        17.10        33.73        33.70        39.62 
TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N6 
       18.87       106.75       102.61        22.26        19.89        13.48 
TCGA-E9-A1N8 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1R3 
       12.00        39.55        12.59        20.05         9.86         2.10 
TCGA-E9-A1R4 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A226 TCGA-E9-A22E TCGA-E9-A22G 
        6.12        32.09        20.81        34.13        12.89        23.51 
TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A3HO TCGA-E9-A3X8 TCGA-E9-A54Y 
        0.69         1.94         0.95        26.07        15.72         0.23 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-EW-A1IX TCGA-EW-A1J1 TCGA-EW-A1OV TCGA-EW-A1OW 
        0.39         0.26        39.72        18.90        25.94        22.82 
TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PC TCGA-EW-A1PE 
       29.85        40.41        23.11         7.86         6.15        10.52 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A3U0 TCGA-GI-A2C8 TCGA-GM-A2DF TCGA-GM-A2DH 
       19.96        55.00        17.49         7.40        42.71        42.28 
TCGA-GM-A2DI TCGA-GM-A3XL TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LL-A441 TCGA-LL-A5YM 
       61.91        69.30        11.84        11.57         2.99         4.70 
TCGA-LL-A6FR TCGA-LL-A73Z TCGA-LL-A8F5 TCGA-OL-A5D7 TCGA-OL-A5RW TCGA-OL-A5S0 
        3.88         4.50         6.21        46.55        26.20         9.80 
TCGA-OL-A66K 
       33.90 

$`4Q LOSS WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04Q 
       13.68         7.96        19.20        18.21       104.81        41.95 
TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04X TCGA-A2-A04Y 
       82.16        73.84        22.06        63.12        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
      125.59        24.79       112.08        92.48        88.60       107.93 
TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 
       75.25         5.19        56.81        34.55        33.76        28.77 
TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER 
       25.22       101.72        89.36        80.28       107.61        74.40 
TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
       37.05        35.05        34.29        31.82        29.75        24.72 
TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 
       24.16        99.19        54.64        44.88        44.28        17.52 
TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC 
        8.38        18.71        20.52        17.46        18.90        32.55 
TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK 
       25.28        15.42        21.90        21.67        14.50        19.33 
TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ 
       14.63        31.73        23.77        23.47        36.79        22.45 
TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B 
       20.25        19.56        16.47        52.47       107.70        16.31 
TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS 
       18.15        91.92        10.59        20.88        39.65        33.93 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 
       29.98        14.07        49.48        38.40        34.98        38.37 
TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 
        7.30         8.81         8.91        12.00         6.74         3.42 
TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13E 
       38.30        34.29        35.47        37.45        33.11        10.72 
TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26J 
       23.61        29.56        31.36        24.26        23.80        20.61 
TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF 
       22.32        11.34        10.59        10.29        11.28        13.41 
TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A5ZV TCGA-A7-A5ZW 
       14.70        11.97        14.93        13.74        12.10        10.72 
TCGA-A7-A5ZX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06R TCGA-A8-A06U 
       11.05         8.75        13.02        13.02        17.98        29.03 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J 
       53.98         9.01        18.97        18.97        14.01        12.00 
TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W 
       17.03         9.99        10.98         7.99         9.96         9.99 
TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C 
       28.04        18.05        36.95        13.02         0.99        19.99 
TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08T 
       19.96        37.05        31.00        31.00        19.07        93.04 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 
       40.01        19.07        17.95        41.98        12.00         9.99 
TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M 
        9.99        12.00        13.02        33.07        29.98        15.02 
TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A1 
        1.02        25.02        19.04        15.02         0.99        12.00 
TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB 
       19.04        13.02        21.04         0.99        13.02        17.03 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BM 
       38.04         0.95        10.85         2.66         1.48        38.20 
TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO 
       40.57        55.43        36.99        38.79        26.04        50.70 
TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN 
        1.02         2.27         0.69        14.83         9.40         1.12 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A6IV TCGA-AC-A6IX 
        1.81         1.68         1.55         1.32         1.18         0.43 
TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AK 
        1.74         0.33         0.33         1.78         1.71         7.36 
TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0FF TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        6.51         0.16         4.64         7.59         7.17         6.28 
TCGA-AN-A0FT TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XO TCGA-AN-A0XR 
        6.02         0.33         0.33         0.33        12.33         0.33 
TCGA-AN-A0XV TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R 
        5.33        80.28        47.84        81.63        84.69        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J6 
       47.87        59.05        29.13        21.40        24.16        37.48 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JF 
       22.36        53.03        21.53        50.70        50.86        21.37 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A125 TCGA-AO-A126 
       26.24        38.53        62.04        55.33        99.25        93.70 
TCGA-AO-A128 TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
       94.59        77.56        57.30        41.62        28.37        14.73 
TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       82.62        70.39        24.79        26.93        15.62        13.22 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS 
        2.56        21.86         9.99        82.88        49.32        37.41 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TZ TCGA-AR-A0U2 
       56.88        29.75        24.30        64.83        76.14        83.87 
TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AO 
       55.36        61.84        52.77        51.25        48.82        43.56 
TCGA-AR-A1AP TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       39.98        17.23        40.83        46.32        42.58        35.24 
TCGA-AR-A1AX TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24P TCGA-AR-A24R 
       36.26        73.02        65.46        68.19         0.85        57.40 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 
       53.26        53.36        48.16        51.75        56.15        40.64 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LL 
       39.85        34.82       128.65        20.25        42.87         7.36 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM 
       40.04        17.10        20.81        16.96        20.38        54.74 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IC 
       16.04        20.45       143.38       149.59        12.13        50.70 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IM TCGA-B6-A0IP TCGA-B6-A0RG TCGA-B6-A0RI 
       65.72       146.50       126.12       110.93        68.45       234.28 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS 
       78.02       172.96       162.05       102.77       140.48       100.70 
TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WZ 
       89.46       157.41        97.48       188.68        17.98       129.57 
TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF 
      129.70       186.48        28.27        68.94        58.88       101.52 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A402 TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AY 
      139.17       170.17        54.28        55.00        24.53        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 
       28.50        40.83        39.16        56.94        56.98        51.68 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BG TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ 
       32.02        18.21        24.85        61.68        35.67        27.19 
TCGA-BH-A0BS TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD 
       53.95        11.67        49.05        48.13        42.90        45.83 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL 
       31.17        23.44        38.01        22.13        13.91        48.23 
TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       17.26        15.65         3.22         2.56        38.47        45.17 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0EA 
       47.41        16.27        15.68        14.30        44.81        32.65 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       31.00        24.43        30.35        15.16        37.78        35.51 
TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HK TCGA-BH-A0HO 
       24.56        41.00        52.96        26.50         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0W4 TCGA-BH-A0W5 
       13.61        36.85        51.32        27.25        24.95        42.35 
TCGA-BH-A0W7 TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L 
       44.81         2.01         7.23        20.12        90.84        26.66 
TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T 
       72.56        37.74        30.28        37.55        66.05         7.36 
TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY 
       91.99       113.82        82.85        55.69        49.58        17.69 
TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FE 
       25.81        31.53        89.16       120.62       114.15        74.73 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN 
      122.89        36.92        63.35        55.00        45.63        72.07 
TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A204 TCGA-BH-A28O TCGA-BH-A28Q 
      144.59         6.90         0.72        83.31        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12M TCGA-C8-A12N 
       20.12         0.99       109.28         8.94        11.77        11.77 
TCGA-C8-A12O TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X 
       12.66         0.07        12.66        12.66        12.66        12.66 
TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 
        3.12         1.78         1.45         0.69         0.62         3.85 
TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HN TCGA-C8-A26V 
       12.33        10.92        11.34        11.34         3.25         0.30 
TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
        0.23         0.36         8.28         9.67         0.03         0.03 
TCGA-C8-A27A TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 
       12.20         0.03         0.23        13.25        20.58        13.97 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 
       14.17        13.48        21.14        19.20        14.17        17.49 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI 
       18.71        15.78        18.15        12.03        14.01        18.97 
TCGA-D8-A1JL TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 
       20.09        20.38        12.20        13.32        14.70        18.58 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB 
       17.79        16.73        25.74        23.90        27.58        18.15 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XQ 
        2.66        17.16        15.22        19.92        17.69        16.41 
TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ 
       16.31         6.35        15.16        12.66        16.54        15.32 
TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F 
       15.52         3.81        14.24        14.14        17.42        16.04 
TCGA-D8-A27G TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N 
       13.45        14.43         9.44        16.41        13.48         4.80 
TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 
        0.76        10.09        12.53        12.26        14.50        18.51 
TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A 
        7.33        43.00        34.42        27.52        46.59        40.41 
TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14P TCGA-E2-A14S 
       37.51        40.11        28.44        28.87        40.96        33.17 
TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y 
       33.30        43.33        34.26        32.02        31.96        28.60 
TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 
       17.03        27.12        23.24        21.04        23.87        14.79 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G 
       23.34        22.82        17.29        20.71        21.63        18.21 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O 
       17.42        19.40         9.04        20.58         7.73        13.02 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B1 TCGA-E2-A1B4 
       19.56        17.06        14.99        60.53        53.03        29.95 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       32.35        28.50        16.47        38.30        37.41        32.78 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       28.44        22.65         3.88        22.19        20.98        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       54.18        27.42        19.66        24.59        40.47        28.90 
TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z 
        8.75        43.04        16.93         5.52        15.72         7.20 
TCGA-E2-A570 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NE 
       18.05        19.20        36.82        13.12        36.56        35.77 
TCGA-E9-A1NG TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R5 TCGA-E9-A1R6 
       21.57        11.90        14.30         0.62         1.38         2.76 
TCGA-E9-A1R7 TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG 
       21.21        40.24         0.66        34.65         6.58        21.27 
TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       34.59        35.64         0.79        12.53        13.32        39.09 
TCGA-E9-A22B TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A24A 
       22.75        24.10        17.06         0.85        27.22        12.56 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A5UO 
        0.72        17.75         0.76        18.41         0.62         0.23 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1J3 
       15.39        12.20         8.48        18.21        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OX TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 
       15.68        28.77        29.95        41.13        39.78        52.96 
TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PD 
       29.82        18.48        30.08        18.90        19.99        13.94 
TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 
       14.43        34.55        52.73        25.91        22.09        21.27 
TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       10.16        10.59       109.87        59.57       194.27        53.13 
TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       53.52        43.04        62.33        90.84        76.64        77.33 
TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 
       53.36       110.50        38.20        32.28        53.95        57.63 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 
       13.55        18.12         8.28         6.67         4.60         0.66 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP 
        3.58         6.90         5.56         3.65         3.19         3.25 
TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LQ-A4E4 
        2.63         4.14         4.50         5.59         3.22        15.91 
TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.79         2.10        12.66         7.53        44.61        27.65 
TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I 
       24.10        16.87        14.10        10.29        14.76        23.70 
TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-S3-A6ZG 
       54.51        31.07        18.21         7.23         4.44         6.81 
TCGA-W8-A86G 
        5.29 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.03              0.03 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           220.90            234.28 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            21.17             21.53 
[1] "0.0 - 220.9 (21.2)" "0.0 - 234.3 (21.5)"
[1] "hr=" "1"  
D48V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4Q LOSS MUTATED        20       17        0        2       104        64
  4Q LOSS WILD-TYPE      60       60        9        7       231       160
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4Q LOSS MUTATED           0         45          8         15        6
  4Q LOSS WILD-TYPE         2         93         19         44       11
                   vv
clus                STAGE TIS STAGE X
  4Q LOSS MUTATED           0       6
  4Q LOSS WILD-TYPE         1      10
D48V3, multiclass
            clus
vv           4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                 20                60
  STAGE IA                17                60
  STAGE IB                 0                 9
  STAGE II                 2                 7
  STAGE IIA              104               231
  STAGE IIB               64               160
  STAGE III                0                 2
  STAGE IIIA              45                93
  STAGE IIIB               8                19
  STAGE IIIC              15                44
  STAGE IV                 6                11
  STAGE TIS                0                 1
  STAGE X                  6                10
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  4Q LOSS MUTATED    59 180  35  13
  4Q LOSS WILD-TYPE 199 401  82  23
D48V4, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1              59               199
  T2             180               401
  T3              35                82
  T4              13                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                 N0  N1  N2  N3
  4Q LOSS MUTATED   133  96  36  18
  4Q LOSS WILD-TYPE 335 234  75  52
D48V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0             133               335
  N1              96               234
  N2              36                75
  N3              18                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  4Q LOSS MUTATED          0 251   6  31
  4Q LOSS WILD-TYPE        2 594  11 100
D48V6, multiclass
          clus
vv         4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CM0 (I+)               0                 2
  M0                   251               594
  M1                     6                11
  MX                    31               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED   286   2
  4Q LOSS WILD-TYPE 698   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    286    2
  4Q LOSS WILD-TYPE  698    9
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE             286               698
  MALE                 2                 9
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  4Q LOSS MUTATED                            0                           240
  4Q LOSS WILD-TYPE                          1                           495
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  4Q LOSS MUTATED                               24                   1
  4Q LOSS WILD-TYPE                            142                   4
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  4Q LOSS MUTATED                                  7                  0
  4Q LOSS WILD-TYPE                               22                 14
                   vv
clus                OTHER  SPECIFY
  4Q LOSS MUTATED               15
  4Q LOSS WILD-TYPE             29
D48V8, multiclass
                                  clus
vv                                 4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                240               495
  INFILTRATING LOBULAR CARCINOMA                24               142
  MEDULLARY CARCINOMA                            1                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               7                22
  MUCINOUS CARCINOMA                             0                14
  OTHER  SPECIFY                                15                29
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V9, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    86 202
  4Q LOSS WILD-TYPE 196 511
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     86  202
  4Q LOSS WILD-TYPE  196  511
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO               86               196
  YES             202               511
[1] 2 2
[1] FALSE
D48V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q LOSS MUTATED                                  1    16
  4Q LOSS WILD-TYPE                                0    40
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED                          53   193
  4Q LOSS WILD-TYPE                        84   515
D48V11, multiclass
                                  clus
vv                                 4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         16                40
  BLACK OR AFRICAN AMERICAN                     53                84
  WHITE                                        193               515
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V12, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     9 228
  4Q LOSS WILD-TYPE  27 568
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      9  228
  4Q LOSS WILD-TYPE   27  568
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   9                27
  NOT HISPANIC OR LATINO             228               568
[1] 2 2
[1] FALSE

Clustering(49) Variable = 5P LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED   107  21
  5P LOSS WILD-TYPE 753  93
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              128               846 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               21                93 
$`5P LOSS MUTATED`
TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A0CM 
       31.79        28.01        18.02        73.84        22.06        24.79 
TCGA-A2-A0D0 TCGA-A2-A0EY TCGA-A2-A0SX TCGA-A2-A0YH TCGA-A2-A0YJ TCGA-A2-A0YM 
       21.14        24.16        50.43        21.67        18.61        31.73 
TCGA-A2-A1G1 TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A7-A0DA 
       19.20        33.93        83.01        38.40        34.98        35.67 
TCGA-A7-A13E TCGA-A7-A26I TCGA-A7-A4SE TCGA-A7-A6VY TCGA-A8-A06T TCGA-A8-A075 
       10.72        21.73        21.17         8.75        41.06        17.03 
TCGA-A8-A076 TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A084 TCGA-A8-A08X TCGA-AC-A2BK 
       53.98         9.99         8.98        15.06        33.99        38.53 
TCGA-AC-A6IW TCGA-AN-A041 TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AT 
        0.69         0.23         7.36         6.51         0.33         0.33 
TCGA-AN-A0FL TCGA-AN-A0FT TCGA-AN-A0FZ TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0JB 
        7.59         6.02         0.33        17.65        24.16        50.70 
TCGA-AO-A124 TCGA-AO-A129 TCGA-AO-A12F TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AR-A0U0 
      102.58        96.10        48.36        26.93       130.09        65.36 
TCGA-AR-A0U2 TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A24K 
       83.87        75.55        52.77        43.07        17.23        50.89 
TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A250 TCGA-AR-A251 TCGA-B6-A0IB TCGA-B6-A0IG 
       66.05        62.07        56.15        45.17       129.57       146.50 
TCGA-B6-A0IO TCGA-B6-A0RP TCGA-B6-A0RU TCGA-B6-A402 TCGA-BH-A0B4 TCGA-BH-A0BG 
      110.14       102.77       131.21        54.28        39.16        24.85 
TCGA-BH-A0BL TCGA-BH-A0BT TCGA-BH-A0C0 TCGA-BH-A0E0 TCGA-BH-A0HA TCGA-BH-A0WA 
       44.05        45.57        41.75         4.41        52.96        23.05 
TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FN TCGA-BH-A1FU 
        7.36        51.16       114.15        74.73        72.07        72.07 
TCGA-BH-A209 TCGA-C8-A12O TCGA-C8-A134 TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A26W 
      130.16        12.66         0.69         3.75        10.92         0.23 
TCGA-C8-A26X TCGA-C8-A278 TCGA-C8-A27A TCGA-D8-A147 TCGA-D8-A1JB TCGA-D8-A1JF 
        0.36         0.03        12.20        19.20        18.71        12.03 
TCGA-D8-A1XF TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XQ TCGA-D8-A1XZ 
       15.22        21.83        14.50        19.92        16.41        15.32 
TCGA-D8-A1Y3 TCGA-D8-A27R TCGA-E2-A14N TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A1AZ 
       14.14        10.09        47.15        25.05        23.34        60.53 
TCGA-E2-A1B6 TCGA-E2-A1L7 TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A573 
       28.50        27.42       102.61         8.75        43.04        22.26 
TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A3QA 
       39.55        12.59        20.05        23.51         0.69         0.62 
TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P8 TCGA-EW-A2FV TCGA-GM-A2DD 
       22.82        29.85        41.13         7.86        25.91        43.04 
TCGA-GM-A2DF TCGA-GM-A3XL TCGA-JL-A3YW TCGA-LL-A441 TCGA-OL-A5D7 TCGA-OL-A5RW 
       42.71        69.30        11.84         2.99        46.55        26.20 
TCGA-OL-A66I TCGA-OL-A66J 
       23.70        54.51 

$`5P LOSS WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A1-A0SQ 
       20.88        13.68         7.96        39.32        19.20        18.21 
TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X 
      104.81        41.95        82.16        63.12        64.04        55.43 
TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
       36.13       125.59        64.57       112.08        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW 
      107.93        75.55        75.25         5.19        63.45        64.04 
TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM 
       56.81        34.55        33.76        28.77        25.22       101.72 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES 
       89.36        80.28       107.61        79.76        74.40        37.05 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST 
       35.05        34.29        31.82        29.75        24.72        99.19 
TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 
       54.64        27.12        44.88        44.28        17.52        17.13 
TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 
        8.38        18.71        20.52        17.46        18.90        20.75 
TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YI 
       32.55        25.28        18.21        15.42        21.90        14.50 
TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX 
       19.33        14.63        23.77        23.47        17.36        36.79 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A 
       22.45        20.25        19.56        16.47        52.47       107.70 
TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
       16.31        17.19        18.15        91.92        10.59        20.88 
TCGA-A2-A3KD TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XZ TCGA-A2-A3Y0 
       39.65        29.98        14.07        49.48        31.99        38.37 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 
        7.30         9.01         8.81         8.91        12.00         6.74 
TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ 
        3.42        38.30        35.31        34.29        35.47        30.61 
TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H 
       37.45        33.11        31.73        12.72        23.61        29.56 
TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD 
       31.36        24.26        23.74        23.80        20.61        22.32 
TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 
       11.34        10.59        10.29        11.28        13.41        14.70 
TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A56D 
       11.97        14.93        13.74        14.50        17.92        14.73 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX 
       12.10        10.72        11.05        10.29         9.37        10.42 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06U TCGA-A8-A06X 
       13.02        13.02         1.02        17.98        29.03        31.00 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F 
       26.01         1.02         9.01        33.01        19.99        18.97 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A07S 
       18.97        14.01        12.00        17.03        10.98         7.99 
TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A086 
        9.96         9.99        28.04        18.05        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I 
        0.99        23.08        19.99        18.05        19.96        12.00 
TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S 
       37.05         9.99        31.00        31.00         0.99        19.07 
TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 
       93.04        40.01        19.07        16.01        17.95        41.98 
TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D 
       12.00         9.99         9.99        12.00         1.02        13.02 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q 
       31.00        33.07        29.98        15.02         1.02        25.02 
TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 
        8.98        19.04        15.02         0.99        14.01        12.00 
TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB 
       19.04        13.02        21.04         0.99        13.02        17.03 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 
       38.04         0.95         2.37        10.85         2.66         1.48 
TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM 
       38.20        40.57        55.43        36.99        38.79        26.04 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN 
       50.70         1.02         0.92         2.27         0.99         0.69 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI 
       14.83         9.40         1.12         1.81         1.68         1.55 
TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV 
        1.32         1.55         0.07         1.12         1.81         1.18 
TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A046 TCGA-AN-A049 
        0.43         1.74         0.33         0.33         0.33         0.62 
TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AM TCGA-AN-A0AS 
        2.96         1.78         1.71         8.02         0.16         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0FS 
        6.44         4.64         7.96         7.00         7.17         6.28 
TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN 
        0.33         0.36         0.33         0.33         0.33         0.33 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU 
       12.33         0.30         0.33         0.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O 
        5.33         5.59        80.28        47.84        66.77        81.63 
TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 
       84.69        68.75        47.87        59.05        29.13        32.78 
TCGA-AO-A0J3 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA 
       21.40        37.48        20.32        22.36        53.03        21.53 
TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI 
       50.86        72.00        76.77        21.37        26.24        38.53 
TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 
       62.04        55.33        71.80        99.25        93.70        94.59 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H 
       90.58        77.56        64.04        57.30        41.62        28.37 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT 
       14.73        82.62        61.87        70.39         0.53        17.79 
TCGA-AQ-A04H TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O 
       24.79         5.65        15.62        13.22         2.56        21.86 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT 
        9.99        82.88        49.32         5.26        37.41        56.88 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 
       29.75        24.30        64.83        55.86        76.14        70.16 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM 
       76.18        55.36        61.84        51.25        48.82        62.56 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
       43.73        43.56        39.98        40.83        46.32        42.58 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M 
       35.24        36.26        20.22       109.58        73.02        65.46 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24U 
       68.19        65.69         0.85        57.40        53.26        53.36 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A252 TCGA-AR-A254 
       54.18        50.96        48.16        51.75        40.64        39.85 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LL 
       34.82        93.83       128.65        20.25        42.87         7.36 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM 
       40.04        17.10        20.81        16.96        20.38        54.74 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 
       16.04        20.45        10.59        77.62       143.38       149.59 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IJ 
       12.13       220.90        50.70        65.72       112.37       176.98 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE 
       18.77       126.12        84.59       110.93       140.88       211.56 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN 
       68.45       189.01       234.28        81.17        78.02       172.96 
TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS 
      162.05       140.48       100.70        89.46       157.41        97.48 
TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ 
      188.68        79.63        17.98        21.47       113.79       129.57 
TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC 
      129.70       186.48        28.27        68.94        58.88        43.59 
TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A408 
      101.52        73.51       139.17       170.17        85.35        49.94 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY 
       82.88        55.00        24.53        38.79        20.45        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0B6 
       28.50        46.95        40.83        39.55        48.36        56.94 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       56.98        51.68        37.22        32.02        18.21        25.71 
TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR 
       21.70        61.68        35.67        48.69        27.19        53.69 
TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C3 
       53.95        49.94        11.67        49.05        44.02        48.13 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI 
       42.90        45.83        31.17        23.44        38.01        22.13 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS 
       13.91        48.23        17.26        15.65         3.22         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 
       38.47        45.17        47.41        16.27        15.68        14.30 
TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE 
        9.63        44.81        46.19        32.65        24.49        31.00 
TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       24.43        30.35        10.78        15.16        37.78        35.51 
TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK 
       24.56        23.08        41.00        26.50        20.38         5.85 
TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX 
        2.50        13.61        36.85        12.89        51.32        27.25 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       50.79         5.59        23.93        24.95        42.35        44.81 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L 
        8.81         2.01         7.23        20.12        90.84        26.66 
TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S 
       72.56        37.74        30.28        55.63        37.55        66.05 
TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU 
       51.39        69.93        91.99       113.82        82.85        42.28 
TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 
       12.00        55.69        49.58        17.69        25.81        31.53 
TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FG 
       89.16        97.48        24.66       120.62        33.17       122.89 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A201 
       36.92        63.35        55.00        45.63       144.59         6.90 
TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A28O TCGA-BH-A28Q 
        0.72        38.60        83.31        57.83        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12L TCGA-C8-A12M 
       20.12         0.99       109.28         8.94        11.93        11.77 
TCGA-C8-A12N TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W 
       11.77        11.77         0.07        12.66        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A135 TCGA-C8-A137 
       12.66         3.12         1.78         1.45         0.62         3.85 
TCGA-C8-A1HE TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL 
       12.33        11.34        11.34         0.16        12.03        10.42 
TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 
        2.30         3.25         0.30         0.43         8.28         9.67 
TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y 
        0.03         0.03         0.99         0.03         0.23        11.90 
TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 
       20.88        13.25        20.58        13.97        14.17        13.48 
TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JC TCGA-D8-A1JD 
       21.14        14.17        17.49        16.50        15.78        18.15 
TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK 
       18.90        12.03        14.01        18.97        20.09        20.12 
TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT 
       20.09        19.40        20.38        21.01        12.20        13.32 
TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 
       14.70        18.58        17.79        16.73        25.74        23.90 
TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XM 
       27.58        18.15         2.66        17.16        14.73        17.69 
TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV 
        7.96        15.85        16.31         6.35        12.99        15.16 
TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E 
       12.66        16.54        15.52         3.81        14.24        17.42 
TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       16.04        13.45        13.05        14.43         9.44        16.41 
TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W 
       13.48         4.80         0.76        13.08        12.53        12.26 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 
       14.50        18.51         7.33        43.00        34.42        27.52 
TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F 
       46.59        40.41        37.51        40.11        28.44        28.87 
TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T 
       44.68        40.96        38.24        38.60        33.17        33.30 
TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z 
       43.33        34.26        32.02        31.96        28.60        17.03 
TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 
       25.41        27.12        23.24        19.43        21.04        23.87 
TCGA-E2-A158 TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G 
       14.79        22.82        17.29        20.71        21.63        18.21 
TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M 
       12.92        17.42        19.40         9.04        20.58         7.73 
TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 
       13.02        19.56        17.06        14.07        14.99        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE 
       53.03        29.95        32.35        16.47        17.10        38.30 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK 
       37.41        32.78        33.73        33.70        28.44        22.65 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L8 
        3.88        22.19        20.98        11.08        54.18        39.62 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH 
       19.66        24.59        40.47        28.90        18.87       106.75 
TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A574 
       16.93         5.52        15.72         7.20        18.05        19.89 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA 
       19.20        36.82        13.48        12.00        13.12        36.56 
TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       35.77        21.57         9.86        11.90        14.30         0.62 
TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA 
        2.10         6.12         1.38         2.76        21.21        32.09 
TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG 
       20.81        40.24         0.66        34.65         6.58        21.27 
TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
       34.59        35.64        34.13         0.79        12.53        13.32 
TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A245 
       39.09        22.75        12.89        24.10        17.06         0.85 
TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS 
       27.22         1.94         0.95        12.56         0.72        17.75 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FK 
        0.76        26.07        18.41        15.72         0.23         0.39 
TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
        0.26         0.23        15.39        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 
       18.21        18.90        13.25        16.57        15.68        28.77 
TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 
       25.94        29.95        40.41        39.78        52.96        29.82 
TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC 
       23.11        18.48        30.08        18.90        19.99         6.15 
TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR 
       13.94        10.52        14.43        34.55        19.96        55.00 
TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 
       52.73        22.09        21.27        17.49        10.16        10.59 
TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC 
        7.40       109.87        59.57       194.27        53.13        53.52 
TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       42.28        61.91        62.33        90.84        76.64        77.33 
TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 
       53.36       110.50        38.20        32.28        53.95        57.63 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 
       13.55        18.12        11.57         8.28         6.67         4.60 
TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN 
        0.66         3.58         6.90         5.56         4.70         3.65 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z 
        3.19         3.25         2.63         3.88         4.14         4.50 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-MS-A51U 
        4.50         5.59         3.22         6.21        15.91         2.79 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
        2.10        12.66         7.53        44.61        27.65        24.10 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66K 
       16.87        14.10        10.29         9.80        14.76        33.90 
TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-S3-A6ZG TCGA-W8-A86G 
       31.07        18.21         7.23         4.44         6.81         5.29 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.03              0.03 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           146.50            234.28 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            24.95             20.81 
[1] "0.0 - 146.5 (25.0)" "0.0 - 234.3 (20.8)"
[1] "hr=" "1.3"
D49V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5P LOSS MUTATED         9        7        0        0        50        31
  5P LOSS WILD-TYPE      71       70        9        9       285       193
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5P LOSS MUTATED           0         19          2          9        2
  5P LOSS WILD-TYPE         2        119         25         50       15
                   vv
clus                STAGE TIS STAGE X
  5P LOSS MUTATED           0       1
  5P LOSS WILD-TYPE         1      15
D49V3, multiclass
            clus
vv           5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                  9                71
  STAGE IA                 7                70
  STAGE IB                 0                 9
  STAGE II                 0                 9
  STAGE IIA               50               285
  STAGE IIB               31               193
  STAGE III                0                 2
  STAGE IIIA              19               119
  STAGE IIIB               2                25
  STAGE IIIC               9                50
  STAGE IV                 2                15
  STAGE TIS                0                 1
  STAGE X                  1                15
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  5P LOSS MUTATED    27  90   9   4
  5P LOSS WILD-TYPE 231 491 108  32
D49V4, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1              27               231
  T2              90               491
  T3               9               108
  T4               4                32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  5P LOSS MUTATED    62  42  16  10
  5P LOSS WILD-TYPE 406 288  95  60
D49V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0              62               406
  N1              42               288
  N2              16                95
  N3              10                60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  5P LOSS MUTATED          0 109   2  19
  5P LOSS WILD-TYPE        2 736  15 112
D49V6, multiclass
          clus
vv         5P LOSS MUTATED 5P LOSS WILD-TYPE
  CM0 (I+)               0                 2
  M0                   109               736
  M1                     2                15
  MX                    19               112
[1] 4 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   129   1
  5P LOSS WILD-TYPE 855  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED    129    1
  5P LOSS WILD-TYPE  855   10
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE             129               855
  MALE                 1                10
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  5P LOSS MUTATED                            0                           114
  5P LOSS WILD-TYPE                          1                           621
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  5P LOSS MUTATED                                2                   3
  5P LOSS WILD-TYPE                            164                   2
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  5P LOSS MUTATED                                  4                  0
  5P LOSS WILD-TYPE                               25                 14
                   vv
clus                OTHER  SPECIFY
  5P LOSS MUTATED                6
  5P LOSS WILD-TYPE             38
D49V8, multiclass
                                  clus
vv                                 5P LOSS MUTATED 5P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                114               621
  INFILTRATING LOBULAR CARCINOMA                 2               164
  MEDULLARY CARCINOMA                            3                 2
  MIXED HISTOLOGY (PLEASE SPECIFY)               4                25
  MUCINOUS CARCINOMA                             0                14
  OTHER  SPECIFY                                 6                38
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V9, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    44  86
  5P LOSS WILD-TYPE 238 627
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     44   86
  5P LOSS WILD-TYPE  238  627
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO               44               238
  YES              86               627
[1] 2 2
[1] FALSE
D49V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P LOSS MUTATED                                  0    11
  5P LOSS WILD-TYPE                                1    45
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED                          25    86
  5P LOSS WILD-TYPE                       112   622
D49V11, multiclass
                                  clus
vv                                 5P LOSS MUTATED 5P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         11                45
  BLACK OR AFRICAN AMERICAN                     25               112
  WHITE                                         86               622
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V12, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     3 109
  5P LOSS WILD-TYPE  33 687
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      3  109
  5P LOSS WILD-TYPE   33  687
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                33
  NOT HISPANIC OR LATINO             109               687
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5Q LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED   179  29
  5Q LOSS WILD-TYPE 681  85
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              208               766 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               29                85 
$`5Q LOSS MUTATED`
TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04T 
       31.79        28.01        19.20        18.02        41.95        73.84 
TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A0CM TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0EQ 
       22.06        64.04        24.79        21.14        34.55        79.76 
TCGA-A2-A0EY TCGA-A2-A0SX TCGA-A2-A0YH TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A1G1 
       24.16        50.43        21.67        18.61        31.73        19.20 
TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A4RW TCGA-A2-A4S3 
       33.93        83.01        38.40        34.98         7.30         3.42 
TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A26G TCGA-A7-A26I 
       30.61        35.67        31.73        10.72        23.74        21.73 
TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A6VY TCGA-A8-A06X 
       21.17        17.92        14.73        12.10         8.75        31.00 
TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A084 
       17.03        53.98         9.99         8.98         9.96        15.06 
TCGA-A8-A08F TCGA-A8-A08X TCGA-A8-A09A TCGA-A8-A09K TCGA-AC-A2BK TCGA-AC-A62X 
       18.05        33.99         9.99        29.98        38.53         1.12 
TCGA-AC-A6IW TCGA-AN-A041 TCGA-AN-A04C TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR 
        0.69         0.23         1.78         7.36         6.51         0.33 
TCGA-AN-A0AT TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FY 
        0.33         7.96         7.59         6.02         0.33         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XN TCGA-AN-A0XU TCGA-AO-A03M TCGA-AO-A0J4 TCGA-AO-A0J5 
        0.33         0.33         0.33        47.84        17.65        24.16 
TCGA-AO-A0JB TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A129 TCGA-AO-A12F TCGA-AO-A1KR 
       50.70        55.33       102.58        96.10        48.36        70.39 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A54N TCGA-AR-A0TP TCGA-AR-A0TT TCGA-AR-A0TV 
       26.93       130.09         2.56        82.88        56.88        29.75 
TCGA-AR-A0U0 TCGA-AR-A0U2 TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AQ TCGA-AR-A1AR 
       65.36        83.87        75.55        52.77        43.07        17.23 
TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24U TCGA-AR-A24Z 
       20.22        50.89        66.05        62.07        53.36        51.75 
TCGA-AR-A250 TCGA-AR-A251 TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IO 
       56.15        45.17       129.57        65.72       146.50       110.14 
TCGA-B6-A0RE TCGA-B6-A0RP TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WX TCGA-B6-A1KF 
      211.56       102.77       100.70       131.21        21.47       101.52 
TCGA-B6-A402 TCGA-BH-A0AV TCGA-BH-A0B3 TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BL 
       54.28        38.79        39.55        25.71        24.85        44.05 
TCGA-BH-A0BP TCGA-BH-A0BT TCGA-BH-A0BW TCGA-BH-A0C0 TCGA-BH-A0E0 TCGA-BH-A0E6 
       48.69        45.57        11.67        41.75         4.41         9.63 
TCGA-BH-A0HA TCGA-BH-A0WA TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EV TCGA-BH-A1F2 
       52.96        23.05         7.36        51.16        12.00        31.53 
TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FN TCGA-BH-A1FU TCGA-BH-A208 TCGA-BH-A209 
      114.15        74.73        72.07        72.07        57.83       130.16 
TCGA-C8-A12L TCGA-C8-A12O TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A138 
       11.93        12.66         3.12         1.78         0.69         3.75 
TCGA-C8-A1HF TCGA-C8-A1HJ TCGA-C8-A1HM TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A278 
       10.92         0.16         2.30         0.23         0.36         0.03 
TCGA-C8-A27A TCGA-C8-A27B TCGA-D8-A142 TCGA-D8-A147 TCGA-D8-A1JB TCGA-D8-A1JF 
       12.20         0.99        13.97        19.20        18.71        12.03 
TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1XF TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XQ 
       20.12        20.09        15.22        14.50        19.92        16.41 
TCGA-D8-A1XT TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y3 TCGA-D8-A27F TCGA-D8-A27H 
        6.35        12.66        15.32        14.14        16.04        13.05 
TCGA-D8-A27M TCGA-D8-A27R TCGA-E2-A10C TCGA-E2-A14N TCGA-E2-A150 TCGA-E2-A155 
       13.48        10.09        40.11        47.15        25.41        21.04 
TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B6 
       14.79        25.05        23.34        60.53        53.62        28.50 
TCGA-E2-A1II TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A1LA TCGA-E2-A1LI TCGA-E2-A1LK 
       33.70        20.98        27.42        24.59       102.61         8.75 
TCGA-E2-A1LL TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N8 TCGA-E9-A1NC TCGA-E9-A1ND 
       43.04        22.26        19.89        12.00        39.55        12.59 
TCGA-E9-A1RB TCGA-E9-A1RH TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A3QA TCGA-EW-A1OW 
       20.81        34.59        23.51         0.69         0.62        22.82 
TCGA-EW-A1P0 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PH TCGA-EW-A2FV TCGA-GI-A2C9 
       41.13         7.86        18.90        19.96        25.91       109.87 
TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A3XL TCGA-JL-A3YW TCGA-LL-A441 
       43.04        42.71        42.28        69.30        11.84         2.99 
TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YP TCGA-LL-A6FR TCGA-OL-A5D7 TCGA-OL-A5RW 
        4.70         3.65         3.25         3.88        46.55        26.20 
TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66I TCGA-OL-A66J 
       10.29         9.80        23.70        54.51 

$`5Q LOSS WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SQ TCGA-A2-A04N 
       20.88        13.68         7.96        39.32        18.21       104.81 
TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL 
       82.16        63.12        55.43        36.13       125.59        64.57 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT 
      112.08        92.48        88.60       107.93        75.55        75.25 
TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D2 TCGA-A2-A0D3 
        5.19        63.45        64.04        56.81        33.76        28.77 
TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER 
       25.22       101.72        89.36        80.28       107.61        74.40 
TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
       37.05        35.05        34.29        31.82        29.75        24.72 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 
       99.19        54.64        27.12        44.88        44.28        17.52 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.13         8.38        18.71        20.52        17.46        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG 
       20.75        32.55        25.28        18.21        15.42        21.90 
TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW 
       14.50        19.33        14.63        23.77        23.47        17.36 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       36.79        22.45        20.25        19.56        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
      107.70        16.31        17.19        18.15        91.92        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XZ 
       20.88        39.65        29.98        14.07        49.48        31.99 
TCGA-A2-A3Y0 TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 
       38.37         9.01         8.81         8.91        12.00         6.74 
TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB 
       38.30        35.31        34.29        35.47        37.45        33.11 
TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H 
       12.72        23.61        29.56        31.36        24.26        23.80 
TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       20.61        22.32        11.34        10.59        10.29        11.28 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD 
       13.41        14.70        11.97        14.93        13.74        14.50 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A8-A06O 
       10.72        11.05        10.29         9.37        10.42        13.02 
TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Y 
       13.02         1.02        17.98        41.06        29.03        26.01 
TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G 
        1.02         9.01        33.01        19.99        18.97        18.97 
TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07W 
       14.01        12.00        17.03        10.98         7.99         9.99 
TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B 
       28.04        18.05        36.95        13.02         0.99        23.08 
TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O 
       19.99        19.96        12.00        37.05         9.99        31.00 
TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 
       31.00         0.99        19.07        93.04        40.01        19.07 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09B 
       16.01        17.95        41.98        12.00         9.99        12.00 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09N 
        1.02        13.02        31.00        33.07        15.02         1.02 
TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X 
       25.02         8.98        19.04        15.02         0.99        14.01 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 
       12.00        19.04        13.02        21.04         0.99        13.02 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H 
       17.03        38.04         0.95         2.37        10.85         2.66 
TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
        1.48        38.20        40.57        55.43        36.99        38.79 
TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB 
       26.04        50.70         1.02         0.92         2.27         0.99 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 
        0.69        14.83         9.40         1.12         1.81         1.68 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV 
        1.55         1.32         1.55         0.07         1.81         1.18 
TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A046 TCGA-AN-A049 
        0.43         1.74         0.33         0.33         0.33         0.62 
TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FD 
        2.96         1.71         8.02         0.16         0.33         6.44 
TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FW TCGA-AN-A0FX 
        4.64         7.00         7.17         6.28         0.36         0.33 
TCGA-AN-A0XL TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT 
        0.33        12.33         0.30         0.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P 
        5.33         5.59        80.28        66.77        81.63        84.69 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 
       68.75        47.87        59.05        29.13        32.78        21.40 
TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JC 
       37.48        20.32        22.36        53.03        21.53        50.86 
TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ 
       72.00        76.77        21.37        26.24        38.53        62.04 
TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B 
       71.80        99.25        93.70        94.59        90.58        77.56 
TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       64.04        57.30        41.62        28.37        14.73        82.62 
TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A0Y5 TCGA-AQ-A1H2 
       61.87         0.53        17.79        24.79         5.65        15.62 
TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS 
       13.22        21.86         9.99        49.32         5.26        37.41 
TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U3 
       24.30        64.83        55.86        76.14        70.16        76.18 
TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
       55.36        61.84        51.25        48.82        62.56        43.73 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       43.56        39.98        40.83        46.32        42.58        35.24 
TCGA-AR-A1AX TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       36.26       109.58        73.02        65.46        68.19        65.69 
TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X 
        0.85        57.40        53.26        54.18        50.96        48.16 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH 
       40.64        39.85        34.82        93.83       128.65        20.25 
TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       42.87         7.36        40.04        17.10        20.81        16.96 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       20.38        54.74        16.04        20.45        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IH 
      143.38       149.59        12.13       220.90        50.70       112.37 
TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ 
      176.98        18.77       126.12        84.59       110.93       140.88 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN 
       68.45       189.01       234.28        81.17        78.02       172.96 
TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT 
      162.05       140.48        89.46       157.41        97.48       188.68 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 
       79.63        17.98       113.79       129.57       129.70       186.48 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A1KN 
       28.27        68.94        58.88        43.59        73.51       139.17 
TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
      170.17        85.35        49.94        82.88        55.00        24.53 
TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 
       20.45        25.55        28.50        46.95        40.83        39.16 
TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC 
       48.36        56.94        56.98        51.68        37.22        32.02 
TCGA-BH-A0BD TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR 
       18.21        21.70        61.68        35.67        27.19        53.69 
TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 
       53.95        49.94        49.05        44.02        48.13        42.90 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       45.83        31.17        23.44        38.01        22.13        13.91 
TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT 
       48.23        17.26        15.65         3.22         2.56        38.47 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 
       45.17        47.41        16.27        15.68        14.30        44.81 
TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY 
       46.19        32.65        24.49        31.00        24.43        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 
       10.78        15.16        37.78        35.51        24.56        23.08 
TCGA-BH-A0H9 TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       41.00        26.50        20.38         5.85         2.50        13.61 
TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX 
       36.85        12.89        51.32        27.25        50.79         5.59 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18F TCGA-BH-A18G 
       23.93        24.95        42.35        44.81         8.81         2.01 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N 
        7.23        20.12        90.84        26.66        72.56        37.74 
TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A1EN 
       30.28        55.63        37.55        66.05        51.39        69.93 
TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EX 
       91.99       113.82        82.85        42.28        55.69        49.58 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB 
       17.69        25.81        89.16        97.48        24.66       120.62 
TCGA-BH-A1FD TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM 
       33.17       122.89        36.92        63.35        55.00        45.63 
TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A28O 
      144.59         6.90         0.72        38.60        83.31        10.65 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12M 
        6.44        20.12         0.99       109.28         8.94        11.77 
TCGA-C8-A12N TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W 
       11.77        11.77         0.07        12.66        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A132 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HG 
       12.66         1.45         0.62         3.85        12.33        11.34 
TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26Y 
       11.34        12.03        10.42         3.25         0.30         0.43 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A3M7 TCGA-C8-A3M8 
        8.28         9.67         0.03         0.03         0.03         0.23 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A145 
       11.90        20.88        13.25        20.58        14.17        13.48 
TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JC TCGA-D8-A1JD 
       21.14        14.17        17.49        16.50        15.78        18.15 
TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JM 
       18.90        12.03        14.01        18.97        20.09        19.40 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 
       20.38        21.01        12.20        13.32        14.70        18.58 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB 
       17.79        16.73        25.74        23.90        27.58        18.15 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XM TCGA-D8-A1XO 
        2.66        17.16        14.73        21.83        17.69         7.96 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1Y0 
       15.85        16.31        12.99        15.16        16.54        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27I TCGA-D8-A27K 
        3.81        14.24        17.42        13.45        14.43         9.44 
TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W 
       16.41         4.80         0.76        13.08        12.53        12.26 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 
       14.50        18.51         7.33        43.00        34.42        27.52 
TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14O 
       46.59        40.41        37.51        28.44        28.87        44.68 
TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U 
       40.96        38.24        38.60        33.17        33.30        43.33 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A152 
       34.26        32.02        31.96        28.60        17.03        27.12 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A156 TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E 
       23.24        19.43        23.87        22.82        17.29        20.71 
TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       21.63        18.21        12.92        17.42        19.40         9.04 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
       20.58         7.73        13.02        19.56        17.06        14.07 
TCGA-E2-A15T TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1BC TCGA-E2-A1BD 
       14.99        53.03        29.95        32.35        16.47        17.10 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK 
       38.30        37.41        32.78        33.73        28.44        22.65 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L8 TCGA-E2-A1L9 
        3.88        22.19        11.08        54.18        39.62        19.66 
TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A2P5 TCGA-E2-A2P6 
       40.47        28.90        18.87       106.75        16.93         5.52 
TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 
       15.72         7.20        18.05        19.20        36.82        13.48 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI 
       13.12        36.56        35.77        20.05        21.57         9.86 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 
       11.90        14.30         0.62         2.10         6.12         1.38 
TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE 
        2.76        21.21        32.09        40.24         0.66        34.65 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 
        6.58        21.27        35.64        34.13         0.79        12.53 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 
       13.32        39.09        22.75        12.89        24.10        17.06 
TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
        0.85        27.22         1.94         0.95        12.56         0.72 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A54Y 
       17.75         0.76        26.07        18.41        15.72         0.23 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
        0.39         0.26         0.23        15.39        12.20        39.72 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
        8.48        18.21        18.90        13.25        16.57        15.68 
TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P1 
       28.77        25.94        29.95        29.85        40.41        39.78 
TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PB 
       52.96        29.82        23.11        18.48        30.08        19.99 
TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FR 
        6.15        13.94        10.52        14.43        34.55        55.00 
TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 
       52.73        22.09        21.27        17.49        10.16        10.59 
TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DI 
        7.40        59.57       194.27        53.13        53.52        61.91 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
       62.33        90.84        76.64        77.33        53.36       110.50 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX 
       38.20        32.28        53.95        57.63        13.55        18.12 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A442 
       11.57         8.28         6.67         4.60         0.66         3.58 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YO TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A73Z 
        6.90         5.56         3.19         2.63         4.14         4.50 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-MS-A51U 
        4.50         5.59         3.22         6.21        15.91         2.79 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
        2.10        12.66         7.53        44.61        27.65        24.10 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A66H TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       16.87        14.10        14.76        33.90        31.07        18.21 
TCGA-OL-A66O TCGA-OL-A66P TCGA-S3-A6ZG TCGA-W8-A86G 
        7.23         4.44         6.81         5.29 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.03              0.03 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           211.56            234.28 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           22.935            21.090 
[1] "0.0 - 211.6 (22.9)" "0.0 - 234.3 (21.1)"
[1] "hr=" "1.2"
D50V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5Q LOSS MUTATED        16       12        1        0        89        47
  5Q LOSS WILD-TYPE      64       65        8        9       246       177
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5Q LOSS MUTATED           0         25          4         11        3
  5Q LOSS WILD-TYPE         2        113         23         48       14
                   vv
clus                STAGE TIS STAGE X
  5Q LOSS MUTATED           1       3
  5Q LOSS WILD-TYPE         0      13
D50V3, multiclass
            clus
vv           5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                 16                64
  STAGE IA                12                65
  STAGE IB                 1                 8
  STAGE II                 0                 9
  STAGE IIA               89               246
  STAGE IIB               47               177
  STAGE III                0                 2
  STAGE IIIA              25               113
  STAGE IIIB               4                23
  STAGE IIIC              11                48
  STAGE IV                 3                14
  STAGE TIS                1                 0
  STAGE X                  3                13
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  5Q LOSS MUTATED    46 144  14   6
  5Q LOSS WILD-TYPE 212 437 103  30
D50V4, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1              46               212
  T2             144               437
  T3              14               103
  T4               6                30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  5Q LOSS MUTATED   113  62  23  12
  5Q LOSS WILD-TYPE 355 268  88  58
D50V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0             113               355
  N1              62               268
  N2              23                88
  N3              12                58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  5Q LOSS MUTATED          0 187   3  22
  5Q LOSS WILD-TYPE        2 658  14 109
D50V6, multiclass
          clus
vv         5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CM0 (I+)               0                 2
  M0                   187               658
  M1                     3                14
  MX                    22               109
[1] 4 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   212   0
  5Q LOSS WILD-TYPE 772  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED    212    0
  5Q LOSS WILD-TYPE  772   11
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE             212               772
  MALE                 0                11
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  5Q LOSS MUTATED                            1                           192
  5Q LOSS WILD-TYPE                          0                           543
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  5Q LOSS MUTATED                                3                   3
  5Q LOSS WILD-TYPE                            163                   2
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  5Q LOSS MUTATED                                  4                  0
  5Q LOSS WILD-TYPE                               25                 14
                   vv
clus                OTHER  SPECIFY
  5Q LOSS MUTATED                8
  5Q LOSS WILD-TYPE             36
D50V8, multiclass
                                  clus
vv                                 5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                192               543
  INFILTRATING LOBULAR CARCINOMA                 3               163
  MEDULLARY CARCINOMA                            3                 2
  MIXED HISTOLOGY (PLEASE SPECIFY)               4                25
  MUCINOUS CARCINOMA                             0                14
  OTHER  SPECIFY                                 8                36
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V9, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    64 148
  5Q LOSS WILD-TYPE 218 565
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     64  148
  5Q LOSS WILD-TYPE  218  565
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO               64               218
  YES             148               565
[1] 2 2
[1] FALSE
D50V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q LOSS MUTATED                                  0    17
  5Q LOSS WILD-TYPE                                1    39
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED                          48   131
  5Q LOSS WILD-TYPE                        89   577
D50V11, multiclass
                                  clus
vv                                 5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         17                39
  BLACK OR AFRICAN AMERICAN                     48                89
  WHITE                                        131               577
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V12, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     5 176
  5Q LOSS WILD-TYPE  31 620
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      5  176
  5Q LOSS WILD-TYPE   31  620
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                31
  NOT HISPANIC OR LATINO             176               620
[1] 2 2
[1] FALSE

Clustering(51) Variable = 6P LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED   149  18
  6P LOSS WILD-TYPE 711  96
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              167               807 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               18                96 
$`6P LOSS MUTATED`
TCGA-A1-A0SP TCGA-A2-A04R TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A0CQ TCGA-A2-A0CR 
       19.20        82.16        22.06        64.04        88.60       107.93 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0D4 TCGA-A2-A0EO 
       75.55        75.25         5.19        63.45        25.22        80.28 
TCGA-A2-A0SV TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T7 TCGA-A2-A1FW TCGA-A2-A3KD 
       27.12        18.71        20.52        20.75        17.36        39.65 
TCGA-A2-A3XW TCGA-A2-A4RY TCGA-A7-A13D TCGA-A7-A2KD TCGA-A8-A06O TCGA-A8-A06Y 
       49.48         8.81        31.73        22.32        13.02        26.01 
TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07J TCGA-A8-A07S TCGA-A8-A08F TCGA-A8-A08G 
        1.02         9.01        12.00         7.99        18.05        19.96 
TCGA-A8-A08I TCGA-A8-A08O TCGA-A8-A097 TCGA-A8-A09C TCGA-A8-A09K TCGA-A8-A09M 
       12.00        31.00        12.00         1.02        29.98        15.02 
TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A9 
        1.02         8.98        19.04        13.02        21.04        13.02 
TCGA-A8-A0AB TCGA-AC-A23G TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FM TCGA-AC-A3BB 
       17.03        10.85        38.53        38.20        26.04         0.99 
TCGA-AC-A62Y TCGA-AC-A8OP TCGA-AN-A04C TCGA-AN-A0FF TCGA-AN-A0FV TCGA-AN-A0FX 
        1.81         1.74         1.78         4.64         0.33         0.33 
TCGA-AN-A0XW TCGA-AO-A03T TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0JG 
        5.59        47.87        37.48        20.32        22.36        26.24 
TCGA-AO-A0JJ TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0TQ 
       62.04        70.39        17.79         2.56        21.86        49.32 
TCGA-AR-A1AP TCGA-AR-A1AU TCGA-AR-A24K TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24V 
       39.98        46.32        50.89         0.85        57.40        54.18 
TCGA-AR-A252 TCGA-B6-A0IA TCGA-B6-A0IJ TCGA-B6-A0RO TCGA-B6-A0WV TCGA-B6-A401 
       40.64       220.90       176.98       162.05        79.63        85.35 
TCGA-BH-A0AU TCGA-BH-A0B0 TCGA-BH-A0B5 TCGA-BH-A0BP TCGA-BH-A0C0 TCGA-BH-A0C3 
       24.53        46.95        48.36        48.69        41.75        48.13 
TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0E2 TCGA-BH-A0EI TCGA-BH-A0H7 TCGA-BH-A0HA 
       48.23        15.65        14.30        24.43        23.08        52.96 
TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0W3 TCGA-BH-A18I TCGA-BH-A18L TCGA-BH-A18S 
       51.32        27.25        23.93         7.23        26.66        66.05 
TCGA-BH-A1ES TCGA-BH-A1EU TCGA-BH-A1EY TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1FE 
      113.82        42.28        17.69        31.53        89.16        74.73 
TCGA-BH-A1FJ TCGA-BH-A1FM TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12W TCGA-C8-A137 
       63.35        45.63        12.66        11.77        12.66         3.85 
TCGA-C8-A1HG TCGA-C8-A274 TCGA-C8-A27A TCGA-D8-A145 TCGA-D8-A1JC TCGA-D8-A1JE 
       11.34         0.03        12.20        13.48        15.78        18.90 
TCGA-D8-A1JG TCGA-D8-A1JM TCGA-D8-A1XA TCGA-D8-A1XF TCGA-D8-A1XU TCGA-D8-A1Y1 
       12.03        19.40        27.58        15.22        12.99         3.81 
TCGA-D8-A27W TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A14V TCGA-E2-A152 TCGA-E2-A153 
       12.26        34.42        46.59        34.26        27.12        23.24 
TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15R TCGA-E2-A1AZ TCGA-E2-A1BD 
       20.71        21.63        12.92        17.06        60.53        17.10 
TCGA-E2-A1IE TCGA-E2-A1L8 TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LL TCGA-E9-A1N6 
       38.30        39.62        28.90        18.87        43.04        13.48 
TCGA-E9-A1N8 TCGA-E9-A1NA TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1QZ TCGA-E9-A1R4 
       12.00        36.56        35.77        20.05        11.90         6.12 
TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A229 
        2.76        32.09        20.81        21.27        35.64        13.32 
TCGA-E9-A22A TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A2JS TCGA-E9-A3X8 TCGA-EW-A1J1 
       39.09         1.94         0.95        17.75        15.72        18.90 
TCGA-EW-A1J6 TCGA-EW-A1P5 TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A3XL 
       28.77        23.11        53.13        53.52        43.04        69.30 
TCGA-LL-A5YM TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-MS-A51U TCGA-S3-A6ZG 
        4.70         5.59         6.21         2.79         6.81 

$`6P LOSS WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
       20.88        13.68        31.79         7.96        39.32        28.01 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04T TCGA-A2-A04V 
       18.21       104.81        18.02        41.95        73.84        63.12 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO 
       55.43        36.13       125.59        64.57        24.79       112.08 
TCGA-A2-A0CP TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 
       92.48        64.04        56.81        21.14        34.55        33.76 
TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER 
       28.77       101.72        89.36       107.61        79.76        74.40 
TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
       37.05        35.05        34.29        31.82        29.75        24.72 
TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY 
       24.16        99.19        54.64        44.88        50.43        44.28 
TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC 
       17.52        17.13         8.38        17.46        18.90        32.55 
TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI 
       25.28        18.21        15.42        21.90        21.67        14.50 
TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV 
       18.61        19.33        14.63        31.73        23.77        23.47 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 
       36.79        22.45        20.25        19.20        19.56        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       52.47       107.70        16.31        17.19        18.15        91.92 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV 
       10.59        20.88        33.93        83.01        29.98        14.07 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX 
       38.40        34.98        31.99        38.37         7.30         9.01 
TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE 
        8.91        12.00         6.74         3.42        38.30        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB 
       34.29        35.47        30.61        37.45        35.67        33.11 
TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F 
       10.72        12.72        23.61        29.56        31.36        24.26 
TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ 
       23.74        23.80        21.73        20.61        11.34        10.59 
TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA 
       10.29        11.28        13.41        14.70        11.97        14.93 
TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV 
       13.74        14.50        21.17        17.92        14.73        12.10 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY 
       10.72        11.05        10.29         9.37        10.42         8.75 
TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X 
       13.02         1.02        17.98        41.06        29.03        31.00 
TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G 
       17.03        53.98        33.01        19.99        18.97        18.97 
TCGA-A8-A07I TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07U 
       14.01        17.03         9.99        10.98         8.98         9.96 
TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 
        9.99        28.04        18.05        15.06        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08P 
        0.99        23.08        19.99        37.05         9.99        31.00 
TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 
        0.99        19.07        93.04        33.99        40.01        19.07 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B 
       16.01        17.95        41.98         9.99         9.99        12.00 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09Q TCGA-A8-A09V TCGA-A8-A09W 
       13.02        31.00        33.07        25.02        15.02         0.99 
TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A7 TCGA-A8-A0AD TCGA-AC-A23C 
       14.01        12.00        19.04         0.99        38.04         0.95 
TCGA-AC-A23E TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG 
        2.37         2.66         1.48        40.57        55.43        36.99 
TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3HN 
       38.79        50.70         1.02         0.92         2.27         0.69 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI 
       14.83         9.40         1.12         1.81         1.68         1.55 
TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IW 
        1.32         1.55         0.07         1.12         1.18         0.69 
TCGA-AC-A6IX TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 
        0.43         0.33         0.33         0.23         0.33         0.62 
TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM 
        2.96         1.71         8.02         7.36         6.51         0.16 
TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FJ TCGA-AN-A0FK 
        0.33         0.33         0.33         6.44         7.96         7.00 
TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FY 
        7.59         7.17         6.28         6.02         0.36         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR 
        0.33         0.33         0.33        12.33         0.30         0.33 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AO-A03L TCGA-AO-A03M 
        0.33         0.33         0.33         5.33        80.28        47.84 
TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03U TCGA-AO-A03V 
       66.77        81.63        84.69        68.75        59.05        29.13 
TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J9 TCGA-AO-A0JA 
       32.78        21.40        17.65        24.16        53.03        21.53 
TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JI 
       50.70        50.86        72.00        76.77        21.37        38.53 
TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 
       55.33        71.80       102.58        99.25        93.70        94.59 
TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F 
       96.10        90.58        77.56        64.04        57.30        48.36 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS 
       41.62        28.37        14.73        82.62        61.87         0.53 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       24.79        26.93       130.09         5.65        15.62        13.22 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV 
        9.99        82.88         5.26        37.41        56.88        29.75 
TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 
       24.30        64.83        55.86        76.14        65.36        70.16 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ 
       83.87        76.18        55.36        75.55        61.84        52.77 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AQ 
       51.25        48.82        62.56        43.73        43.56        43.07 
TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY 
       17.23        40.83        42.58        35.24        36.26        20.22 
TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24Q 
      109.58        73.02        65.46        68.19        65.69        66.05 
TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
       62.07        53.26        53.36        50.96        48.16        51.75 
TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE 
       56.15        45.17        39.85        34.82        93.83       128.65 
TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       20.25        42.87         7.36        40.04        17.10        20.81 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       16.96        20.38        54.74        16.04        20.45        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IB TCGA-B6-A0IC 
       77.62       143.38       149.59        12.13       129.57        50.70 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
       65.72       146.50       112.37        18.77       126.12        84.59 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH 
      110.14       110.93       140.88       211.56        68.45       189.01 
TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RQ 
      234.28        81.17        78.02       172.96       102.77       140.48 
TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT 
      100.70        89.46       131.21       157.41        97.48       188.68 
TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 
       17.98        21.47       113.79       129.57       129.70       186.48 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI 
       28.27        68.94        58.88        43.59       101.52        73.51 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C 
      139.17       170.17        54.28        49.94        82.88        55.00 
TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B2 TCGA-BH-A0B3 
       38.79        20.45        25.55        28.50        40.83        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC 
       39.16        56.94        56.98        51.68        37.22        32.02 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM 
       18.21        25.71        24.85        21.70        44.05        61.68 
TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV 
       35.67        27.19        53.69        53.95        45.57        49.94 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE 
       11.67        49.05        44.02        42.90        45.83        31.17 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DQ 
       23.44        38.01        22.13        13.91        17.26         3.22 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
        2.56        38.47        45.17        47.41        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB 
       15.68         9.63        44.81        46.19        32.65        24.49 
TCGA-BH-A0EE TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       31.00        30.35        10.78        15.16        37.78        35.51 
TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       24.56        41.00        26.50        20.38         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W4 
       13.61        36.85        12.89        50.79         5.59        24.95 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18J 
       42.35        44.81        23.05         8.81         2.01        20.12 
TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R 
       90.84        72.56        37.74        30.28        55.63        37.55 
TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ET 
        7.36        51.39        51.16        69.93        91.99        82.85 
TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1F6 TCGA-BH-A1F8 
       12.00        55.69        49.58        25.81        97.48        24.66 
TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FL 
      120.62       114.15        33.17       122.89        36.92        55.00 
TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 
       72.07       144.59        72.07         6.90         0.72        38.60 
TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
       83.31        57.83       130.16        10.65         6.44        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N 
        0.99       109.28         8.94        11.93        11.77        11.77 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A131 
        0.07        12.66        12.66        12.66         3.12         1.78 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF 
        1.45         0.69         0.62         3.75        12.33        10.92 
TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN 
       11.34         0.16        12.03        10.42         2.30         3.25 
TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 
        0.30         0.23         0.36         0.43         8.28         9.67 
TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y 
        0.03         0.03         0.99         0.03         0.23        11.90 
TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A146 
       20.88        13.25        20.58        13.97        14.17        21.14 
TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JD 
       19.20        14.17        17.49        16.50        18.71        18.15 
TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL 
       12.03        14.01        18.97        20.09        20.12        20.09 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 
       20.38        21.01        12.20        13.32        14.70        18.58 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XB TCGA-D8-A1XC 
       17.79        16.73        25.74        23.90        18.15         2.66 
TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM 
       17.16        14.73        21.83        14.50        19.92        17.69 
TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV 
        7.96        16.41        15.85        16.31         6.35        15.16 
TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A1Y3 
       12.66        16.54        15.32        15.52        14.24        14.14 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K 
       17.42        16.04        13.45        13.05        14.43         9.44 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T 
       16.41        13.48         4.80         0.76        10.09        13.08 
TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A108 
       12.53        14.50        18.51         7.33        43.00        27.52 
TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N 
       40.41        37.51        40.11        28.44        28.87        47.15 
TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T 
       44.68        40.96        38.24        38.60        33.17        33.30 
TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 
       43.33        32.02        31.96        28.60        17.03        25.41 
TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A 
       19.43        21.04        23.87        14.79        25.05        23.34 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       22.82        17.29        18.21        17.42        19.40         9.04 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15S TCGA-E2-A15T 
       20.58         7.73        13.02        19.56        14.07        14.99 
TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC 
       53.62        53.03        29.95        32.35        28.50        16.47 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK 
       37.41        32.78        33.73        33.70        28.44        22.65 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 
        3.88        22.19        20.98        11.08        54.18        27.42 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK 
       19.66        24.59        40.47       106.75       102.61         8.75 
TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 
       16.93         5.52        15.72         7.20        18.05        22.26 
TCGA-E2-A574 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N9 TCGA-E9-A1NC TCGA-E9-A1ND 
       19.89        19.20        36.82        13.12        39.55        12.59 
TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R5 
       21.57         9.86        14.30         0.62         2.10         1.38 
TCGA-E9-A1R7 TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RH 
       21.21        40.24         0.66        34.65         6.58        34.59 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G 
       34.13         0.79        12.53        22.75        12.89        23.51 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A24A 
       24.10        17.06         0.69         0.85        27.22        12.56 
TCGA-E9-A295 TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54Y 
        0.72         0.76        26.07        18.41         0.62         0.23 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
        0.39         0.26         0.23        15.39        12.20        39.72 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV 
        8.48        18.21        13.25        16.57        15.68        25.94 
TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 
       22.82        29.95        29.85        40.41        41.13        39.78 
TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA 
       52.96        29.82        18.48        30.08         7.86        18.90 
TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
       19.99         6.15        13.94        10.52        14.43        34.55 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 
       19.96        55.00        52.73        25.91        22.09        21.27 
TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 
       17.49        10.16        10.59         7.40       109.87        59.57 
TCGA-GM-A2DA TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
      194.27        42.71        42.28        61.91        62.33        90.84 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
       76.64        77.33        53.36       110.50        38.20        32.28 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX 
       53.95        57.63        13.55        18.12        11.84        11.57 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
        8.28         6.67         4.60         0.66         2.99         3.58 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FQ 
        6.90         5.56         3.65         3.19         3.25         2.63 
TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7T0 TCGA-LQ-A4E4 
        3.88         4.14         4.50         4.50         3.22        15.91 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.10        12.66        46.55         7.53        44.61        27.65 
TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 
       24.10        26.20        16.87        14.10        10.29         9.80 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       14.76        23.70        54.51        33.90        31.07        18.21 
TCGA-OL-A66O TCGA-OL-A66P TCGA-W8-A86G 
        7.23         4.44         5.29 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.03              0.03 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           220.90            234.28 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            21.86             21.37 
[1] "0.0 - 220.9 (21.9)" "0.0 - 234.3 (21.4)"
[1] "hr=" "1.1"
D51V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6P LOSS MUTATED        14       11        1        0        64        41
  6P LOSS WILD-TYPE      66       66        8        9       271       183
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6P LOSS MUTATED           0         22          6          6        3
  6P LOSS WILD-TYPE         2        116         21         53       14
                   vv
clus                STAGE TIS STAGE X
  6P LOSS MUTATED           0       2
  6P LOSS WILD-TYPE         1      14
D51V3, multiclass
            clus
vv           6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                 14                66
  STAGE IA                11                66
  STAGE IB                 1                 8
  STAGE II                 0                 9
  STAGE IIA               64               271
  STAGE IIB               41               183
  STAGE III                0                 2
  STAGE IIIA              22               116
  STAGE IIIB               6                21
  STAGE IIIC               6                53
  STAGE IV                 3                14
  STAGE TIS                0                 1
  STAGE X                  2                14
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  6P LOSS MUTATED    47 102  14   7
  6P LOSS WILD-TYPE 211 479 103  29
D51V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1              47               211
  T2             102               479
  T3              14               103
  T4               7                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                 N0  N1  N2  N3
  6P LOSS MUTATED    80  62  18   9
  6P LOSS WILD-TYPE 388 268  93  61
D51V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0              80               388
  N1              62               268
  N2              18                93
  N3               9                61
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  6P LOSS MUTATED          1 153   3  13
  6P LOSS WILD-TYPE        1 692  14 118
D51V6, multiclass
          clus
vv         6P LOSS MUTATED 6P LOSS WILD-TYPE
  CM0 (I+)               1                 1
  M0                   153               692
  M1                     3                14
  MX                    13               118
[1] 4 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   169   1
  6P LOSS WILD-TYPE 815  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED    169    1
  6P LOSS WILD-TYPE  815   10
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE             169               815
  MALE                 1                10
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  6P LOSS MUTATED                            0                           135
  6P LOSS WILD-TYPE                          1                           600
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  6P LOSS MUTATED                               21                   0
  6P LOSS WILD-TYPE                            145                   5
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  6P LOSS MUTATED                                  5                  3
  6P LOSS WILD-TYPE                               24                 11
                   vv
clus                OTHER  SPECIFY
  6P LOSS MUTATED                6
  6P LOSS WILD-TYPE             38
D51V8, multiclass
                                  clus
vv                                 6P LOSS MUTATED 6P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                135               600
  INFILTRATING LOBULAR CARCINOMA                21               145
  MEDULLARY CARCINOMA                            0                 5
  MIXED HISTOLOGY (PLEASE SPECIFY)               5                24
  MUCINOUS CARCINOMA                             3                11
  OTHER  SPECIFY                                 6                38
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V9, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    56 114
  6P LOSS WILD-TYPE 226 599
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     56  114
  6P LOSS WILD-TYPE  226  599
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO               56               226
  YES             114               599
[1] 2 2
[1] FALSE
D51V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P LOSS MUTATED                                  0    11
  6P LOSS WILD-TYPE                                1    45
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED                          24   112
  6P LOSS WILD-TYPE                       113   596
D51V11, multiclass
                                  clus
vv                                 6P LOSS MUTATED 6P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         11                45
  BLACK OR AFRICAN AMERICAN                     24               113
  WHITE                                        112               596
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V12, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     4 132
  6P LOSS WILD-TYPE  32 664
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      4  132
  6P LOSS WILD-TYPE   32  664
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                32
  NOT HISPANIC OR LATINO             132               664
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6Q LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED   220  26
  6Q LOSS WILD-TYPE 640  88
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              246               728 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               26                88 
$`6Q LOSS MUTATED`
TCGA-A1-A0SE TCGA-A1-A0SN TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W 
       43.43        39.32        82.16        73.84        22.06        64.04 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV 
       88.60       107.93        75.55        75.25         5.19        63.45 
TCGA-A2-A0D4 TCGA-A2-A0EO TCGA-A2-A0ET TCGA-A2-A0SV TCGA-A2-A0T3 TCGA-A2-A0T4 
       25.22        80.28        35.05        27.12        18.71        20.52 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A25A TCGA-A2-A25B 
       18.90        20.75        23.77        17.36       107.70        16.31 
TCGA-A2-A25E TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A4RY 
       91.92        39.65        33.93        14.07        49.48         8.81 
TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3J1 TCGA-A7-A426 
       31.73        12.72        20.61        11.34        11.28        11.97 
TCGA-A8-A06O TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07J 
       13.02        26.01         1.02        53.98         9.01        12.00 
TCGA-A8-A07S TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08O 
        7.99        18.05        19.96        12.00        37.05        31.00 
TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K 
       12.00         9.99         1.02        31.00        33.07        29.98 
TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A0A4 TCGA-A8-A0A6 
       15.02         1.02         8.98        19.04        13.02        21.04 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-AC-A23G TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FM 
       13.02        17.03        10.85        38.53        38.20        26.04 
TCGA-AC-A3BB TCGA-AC-A3W5 TCGA-AC-A62Y TCGA-AC-A8OP TCGA-AN-A041 TCGA-AN-A04C 
        0.99         1.81         1.81         1.74         0.23         1.78 
TCGA-AN-A0AS TCGA-AN-A0FF TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0XW TCGA-AO-A03N 
        0.33         4.64         0.33         0.33         5.59        66.77 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A0J3 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 
       68.75        47.87        21.40        37.48        20.32        22.36 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A1KR TCGA-AO-A1KT 
       26.24        38.53        62.04        55.33        70.39        17.79 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TZ TCGA-AR-A0U2 
        2.56        21.86        49.32         5.26        76.14        83.87 
TCGA-AR-A1AU TCGA-AR-A24K TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24V TCGA-AR-A252 
       46.32        50.89         0.85        57.40        54.18        40.64 
TCGA-AR-A255 TCGA-B6-A0IA TCGA-B6-A0IJ TCGA-B6-A0RG TCGA-B6-A0RO TCGA-B6-A0RU 
       34.82       220.90       176.98        68.45       162.05       131.21 
TCGA-B6-A0WV TCGA-B6-A0WY TCGA-B6-A1KC TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 
       79.63       113.79        43.59       139.17       170.17        85.35 
TCGA-B6-A408 TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0B0 TCGA-BH-A0B5 TCGA-BH-A0BJ 
       49.94        55.00        24.53        46.95        48.36        21.70 
TCGA-BH-A0BM TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BW TCGA-BH-A0C0 TCGA-BH-A0C3 
       61.68        48.69        27.19        11.67        41.75        48.13 
TCGA-BH-A0DE TCGA-BH-A0DH TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0E2 TCGA-BH-A0EI 
       31.17        38.01        48.23        15.65        14.30        24.43 
TCGA-BH-A0H0 TCGA-BH-A0H7 TCGA-BH-A0HA TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0W3 
       15.16        23.08        52.96        51.32        27.25        23.93 
TCGA-BH-A18F TCGA-BH-A18I TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18S TCGA-BH-A1EN 
        8.81         7.23        90.84        26.66        66.05        69.93 
TCGA-BH-A1ES TCGA-BH-A1EU TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1FC TCGA-BH-A1FE 
      113.82        42.28        31.53        89.16       114.15        74.73 
TCGA-BH-A1FJ TCGA-BH-A1FM TCGA-BH-A201 TCGA-C8-A12M TCGA-C8-A12O TCGA-C8-A12P 
       63.35        45.63         6.90        11.77        12.66        11.77 
TCGA-C8-A12W TCGA-C8-A137 TCGA-C8-A1HG TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A27A 
       12.66         3.85        11.34         0.43         9.67        12.20 
TCGA-D8-A145 TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JI 
       13.48        18.71        18.15        18.90        12.03        18.97 
TCGA-D8-A1JM TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XF TCGA-D8-A1XL TCGA-D8-A1XM 
       19.40        27.58        18.15        15.22        19.92        17.69 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A27R TCGA-D8-A27T 
        6.35        12.99        15.52         3.81        10.09        13.08 
TCGA-D8-A27W TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10F TCGA-E2-A14V TCGA-E2-A152 
       12.26        34.42        46.59        28.87        34.26        27.12 
TCGA-E2-A153 TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15P TCGA-E2-A15R 
       23.24        20.71        21.63        12.92        19.56        17.06 
TCGA-E2-A1AZ TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IL TCGA-E2-A1L8 
       60.53        16.47        17.10        38.30         3.88        39.62 
TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LL TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 
       28.90        18.87        43.04        19.20        36.82        13.48 
TCGA-E9-A1N8 TCGA-E9-A1NA TCGA-E9-A1NE TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R4 
       12.00        36.56        35.77        11.90        14.30         6.12 
TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI 
        2.76        32.09        20.81        21.27        34.59        35.64 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A2JS TCGA-E9-A3X8 
       13.32        39.09         1.94         0.95        17.75        15.72 
TCGA-E9-A5UO TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OY 
        0.23        18.90        13.25        15.68        28.77        29.85 
TCGA-EW-A1P0 TCGA-EW-A1P5 TCGA-EW-A3E8 TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD 
       41.13        23.11        21.27        53.13        53.52        43.04 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-LD-A66U TCGA-LD-A7W6 TCGA-LL-A5YM TCGA-LL-A740 
       69.30        53.95         8.28         4.60         4.70         4.50 
TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-MS-A51U TCGA-OL-A66L TCGA-OL-A66O TCGA-S3-A6ZG 
        5.59         6.21         2.79        31.07         7.23         6.81 

$`6Q LOSS WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI 
        8.52        14.37        48.10        14.27        47.24        20.88 
TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ 
       13.68        31.79         7.96        28.01        19.20        18.21 
TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04V TCGA-A2-A04X TCGA-A2-A04Y 
      104.81        18.02        41.95        63.12        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CW 
      125.59        64.57        24.79       112.08        92.48        64.04 
TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM 
       56.81        21.14        34.55        33.76        28.77       101.72 
TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EU 
       89.36       107.61        79.76        74.40        37.05        34.29 
TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU 
       31.82        29.75        24.72        24.16        99.19        54.64 
TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 
       44.88        50.43        44.28        17.52        17.13         8.38 
TCGA-A2-A0T5 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG 
       17.46        32.55        25.28        18.21        15.42        21.90 
TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       21.67        14.50        18.61        19.33        14.63        31.73 
TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 
       23.47        36.79        22.45        20.25        19.20        19.56 
TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25F TCGA-A2-A3KC 
       16.47        52.47        17.19        18.15        10.59        20.88 
TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 
       83.01        29.98        38.40        34.98        31.99        38.37 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 
        7.30         9.01         8.91        12.00         6.74         3.42 
TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 
       38.30        35.31        34.29        35.47        30.61        37.45 
TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       35.67        33.11        10.72        23.61        29.56        31.36 
TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3IZ 
       24.26        23.74        23.80        21.73        22.32        10.59 
TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD 
       10.29        13.41        14.70        14.93        13.74        14.50 
TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX 
       21.17        17.92        14.73        12.10        10.72        11.05 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q 
       10.29         9.37        10.42         8.75        13.02         1.02 
TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A07B 
       17.98        41.06        29.03        31.00        17.03        33.01 
TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07L TCGA-A8-A07O 
       19.99        18.97        18.97        14.01        17.03         9.99 
TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 
       10.98         8.98         9.96         9.99        28.04        18.05 
TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C 
       15.06        36.95        13.02         0.99        23.08        19.99 
TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X 
        9.99        31.00         0.99        19.07        93.04        33.99 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 
       40.01        19.07        16.01        17.95        41.98         9.99 
TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09Q TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X 
       12.00        13.02        25.02        15.02         0.99        14.01 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A7 TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E 
       12.00        19.04         0.99        38.04         0.95         2.37 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
        2.66         1.48        40.57        55.43        36.99        38.79 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3HN TCGA-AC-A3OD 
       50.70         1.02         0.92         2.27         0.69        14.83 
TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS 
        9.40         1.12         1.68         1.55         1.32         1.55 
TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AN-A03X 
        0.07         1.12         1.18         0.69         0.43         0.33 
TCGA-AN-A03Y TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ 
        0.33         0.33         0.62         2.96         1.71         8.02 
TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD 
        7.36         6.51         0.16         0.33         0.33         6.44 
TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT 
        7.96         7.00         7.59         7.17         6.28         6.02 
TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO 
        0.36         0.33         0.33         0.33         0.33        12.33 
TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV 
        0.30         0.33         0.33         0.33         0.33         5.33 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03U TCGA-AO-A03V 
       80.28        47.84        81.63        84.69        59.05        29.13 
TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB 
       32.78        17.65        24.16        53.03        21.53        50.70 
TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JM TCGA-AO-A124 
       50.86        72.00        76.77        21.37        71.80       102.58 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B 
       99.25        93.70        94.59        96.10        90.58        77.56 
TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
       64.04        57.30        48.36        41.62        28.37        14.73 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       82.62        61.87         0.53        24.79        26.93       130.09 
TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TS 
        5.65        15.62        13.22         9.99        82.88        37.41 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0U0 
       56.88        29.75        24.30        64.83        55.86        65.36 
TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ 
       70.16        76.18        55.36        75.55        61.84        52.77 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP 
       51.25        48.82        62.56        43.73        43.56        39.98 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX 
       43.07        17.23        40.83        42.58        35.24        36.26 
TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       20.22       109.58        73.02        65.46        68.19        65.69 
TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24W TCGA-AR-A24X 
       66.05        62.07        53.26        53.36        50.96        48.16 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LE 
       51.75        56.15        45.17        39.85        93.83       128.65 
TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       20.25        42.87         7.36        40.04        17.10        20.81 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       16.96        20.38        54.74        16.04        20.45        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IB TCGA-B6-A0IC 
       77.62       143.38       149.59        12.13       129.57        50.70 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
       65.72       146.50       112.37        18.77       126.12        84.59 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RI 
      110.14       110.93       140.88       211.56       189.01       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS 
       81.17        78.02       172.96       102.77       140.48       100.70 
TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX 
       89.46       157.41        97.48       188.68        17.98        21.47 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      129.57       129.70       186.48        28.27        68.94        58.88 
TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A402 TCGA-B6-A40B TCGA-BH-A0AV TCGA-BH-A0AW 
      101.52        73.51        54.28        82.88        38.79        20.45 
TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B6 
       25.55        28.50        40.83        39.55        39.16        56.94 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       56.98        51.68        37.22        32.02        18.21        25.71 
TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BO TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT 
       24.85        44.05        35.67        53.69        53.95        45.57 
TCGA-BH-A0BV TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DG 
       49.94        49.05        44.02        42.90        45.83        23.44 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT 
       22.13        13.91        17.26         3.22         2.56        38.47 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E6 
       45.17        47.41        16.27         4.41        15.68         9.63 
TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0GY 
       44.81        46.19        32.65        24.49        31.00        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HB 
       10.78        37.78        35.51        24.56        41.00        26.50 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU 
       20.38         5.85         2.50        13.61        36.85        12.89 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA 
       50.79         5.59        24.95        42.35        44.81        23.05 
TCGA-BH-A18G TCGA-BH-A18J TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q 
        2.01        20.12        72.56        37.74        30.28        55.63 
TCGA-BH-A18R TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ET 
       37.55         7.36        51.39        51.16        91.99        82.85 
TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F6 
       12.00        55.69        49.58        17.69        25.81        97.48 
TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FL 
       24.66       120.62        33.17       122.89        36.92        55.00 
TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 
       72.07       144.59        72.07         0.72        38.60        83.31 
TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T 
       57.83       130.16        10.65         6.44        20.12         0.99 
TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12L TCGA-C8-A12N TCGA-C8-A12Q TCGA-C8-A12U 
      109.28         8.94        11.93        11.77         0.07        12.66 
TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 
       12.66        12.66         3.12         1.78         1.45         0.69 
TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HI TCGA-C8-A1HJ 
        0.62         3.75        12.33        10.92        11.34         0.16 
TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W 
       12.03        10.42         2.30         3.25         0.30         0.23 
TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B 
        0.36         8.28         0.03         0.03         0.03         0.99 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 
        0.03         0.23        11.90        20.88        13.25        20.58 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 
       13.97        14.17        21.14        19.20        14.17        17.49 
TCGA-D8-A1JA TCGA-D8-A1JC TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JJ TCGA-D8-A1JK 
       16.50        15.78        12.03        14.01        20.09        20.12 
TCGA-D8-A1JL TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU 
       20.09        20.38        21.01        12.20        13.32        14.70 
TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XC 
       18.58        17.79        16.73        25.74        23.90         2.66 
TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XO TCGA-D8-A1XQ 
       17.16        14.73        21.83        14.50         7.96        16.41 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ 
       15.85        16.31        15.16        12.66        16.54        15.32 
TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H 
       14.24        14.14        17.42        16.04        13.45        13.05 
TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P 
       14.43         9.44        16.41        13.48         4.80         0.76 
TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A108 
       12.53        14.50        18.51         7.33        43.00        27.52 
TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A14N TCGA-E2-A14O 
       40.41        37.51        40.11        28.44        47.15        44.68 
TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U 
       40.96        38.24        38.60        33.17        33.30        43.33 
TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A154 
       32.02        31.96        28.60        17.03        25.41        19.43 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C 
       21.04        23.87        14.79        25.05        23.34        22.82 
TCGA-E2-A15D TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       17.29        18.21        17.42        19.40         9.04        20.58 
TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 
        7.73        13.02        14.07        14.99        53.62        53.03 
TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       29.95        32.35        28.50        37.41        32.78        33.73 
TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       33.70        28.44        22.65        22.19        20.98        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LH 
       54.18        27.42        19.66        24.59        40.47       106.75 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z 
      102.61         8.75        16.93         5.52        15.72         7.20 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N9 TCGA-E9-A1NC TCGA-E9-A1ND 
       18.05        22.26        19.89        13.12        39.55        12.59 
TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R5 
       20.05        21.57         9.86         0.62         2.10         1.38 
TCGA-E9-A1R7 TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A226 
       21.21        40.24         0.66        34.65         6.58        34.13 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H 
        0.79        12.53        22.75        12.89        23.51        24.10 
TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A24A TCGA-E9-A295 
       17.06         0.69         0.85        27.22        12.56         0.72 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54Y TCGA-E9-A5FK 
        0.76        26.07        18.41         0.62         0.23         0.39 
TCGA-E9-A5FL TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
        0.26        15.39        12.20        39.72         8.48        18.21 
TCGA-EW-A1J3 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1P1 
       16.57        25.94        22.82        29.95        40.41        39.78 
TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA 
       52.96        29.82        18.48        30.08         7.86        18.90 
TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
       19.99         6.15        13.94        10.52        14.43        34.55 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3U0 
       19.96        55.00        52.73        25.91        22.09        17.49 
TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       10.16        10.59         7.40       109.87        59.57       194.27 
TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       42.71        42.28        61.91        62.33        90.84        76.64 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A4E0 
       77.33        53.36       110.50        38.20        32.28        57.63 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A74U TCGA-LL-A440 
       13.55        18.12        11.84        11.57         6.67         0.66 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO 
        2.99         3.58         6.90         5.56         3.65         3.19 
TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A7T0 
        3.25         2.63         3.88         4.14         4.50         3.22 
TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA 
       15.91         2.10        12.66        46.55         7.53        44.61 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       27.65        24.10        26.20        16.87        14.10        10.29 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66N 
        9.80        14.76        23.70        54.51        33.90        18.21 
TCGA-OL-A66P TCGA-W8-A86G 
        4.44         5.29 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.23              0.03 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           220.90            234.28 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            21.78             21.19 
[1] "0.2 - 220.9 (21.8)" "0.0 - 234.3 (21.2)"
[1] "hr=" "1.1"
D52V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6Q LOSS MUTATED        19       20        1        0        85        66
  6Q LOSS WILD-TYPE      61       57        8        9       250       158
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6Q LOSS MUTATED           0         32          9         11        4
  6Q LOSS WILD-TYPE         2        106         18         48       13
                   vv
clus                STAGE TIS STAGE X
  6Q LOSS MUTATED           0       3
  6Q LOSS WILD-TYPE         1      13
D52V3, multiclass
            clus
vv           6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                 19                61
  STAGE IA                20                57
  STAGE IB                 1                 8
  STAGE II                 0                 9
  STAGE IIA               85               250
  STAGE IIB               66               158
  STAGE III                0                 2
  STAGE IIIA              32               106
  STAGE IIIB               9                18
  STAGE IIIC              11                48
  STAGE IV                 4                13
  STAGE TIS                0                 1
  STAGE X                  3                13
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  6Q LOSS MUTATED    72 144  23  11
  6Q LOSS WILD-TYPE 186 437  94  25
D52V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1              72               186
  T2             144               437
  T3              23                94
  T4              11                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                 N0  N1  N2  N3
  6Q LOSS MUTATED   111  94  27  15
  6Q LOSS WILD-TYPE 357 236  84  55
D52V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0             111               357
  N1              94               236
  N2              27                84
  N3              15                55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  6Q LOSS MUTATED          1 218   4  27
  6Q LOSS WILD-TYPE        1 627  13 104
D52V6, multiclass
          clus
vv         6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CM0 (I+)               1                 1
  M0                   218               627
  M1                     4                13
  MX                    27               104
[1] 4 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   249   1
  6Q LOSS WILD-TYPE 735  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED    249    1
  6Q LOSS WILD-TYPE  735   10
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE             249               735
  MALE                 1                10
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  6Q LOSS MUTATED                            0                           190
  6Q LOSS WILD-TYPE                          1                           545
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  6Q LOSS MUTATED                               37                   1
  6Q LOSS WILD-TYPE                            129                   4
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  6Q LOSS MUTATED                                  9                  5
  6Q LOSS WILD-TYPE                               20                  9
                   vv
clus                OTHER  SPECIFY
  6Q LOSS MUTATED                8
  6Q LOSS WILD-TYPE             36
D52V8, multiclass
                                  clus
vv                                 6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                190               545
  INFILTRATING LOBULAR CARCINOMA                37               129
  MEDULLARY CARCINOMA                            1                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               9                20
  MUCINOUS CARCINOMA                             5                 9
  OTHER  SPECIFY                                 8                36
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V9, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    86 164
  6Q LOSS WILD-TYPE 196 549
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     86  164
  6Q LOSS WILD-TYPE  196  549
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               86               196
  YES             164               549
[1] 2 2
[1] FALSE
D52V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q LOSS MUTATED                                  0    14
  6Q LOSS WILD-TYPE                                1    42
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED                          35   173
  6Q LOSS WILD-TYPE                       102   535
D52V11, multiclass
                                  clus
vv                                 6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         14                42
  BLACK OR AFRICAN AMERICAN                     35               102
  WHITE                                        173               535
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V12, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     7 198
  6Q LOSS WILD-TYPE  29 598
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      7  198
  6Q LOSS WILD-TYPE   29  598
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   7                29
  NOT HISPANIC OR LATINO             198               598
[1] 2 2
[1] FALSE

Clustering(53) Variable = 7P LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED    91  11
  7P LOSS WILD-TYPE 769 103
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
              102               872 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               11               103 
$`7P LOSS MUTATED`
TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A2-A04T TCGA-A2-A0CT TCGA-A2-A0D4 TCGA-A2-A0EQ 
       31.79        28.01        73.84        75.25        25.22        79.76 
TCGA-A2-A0ET TCGA-A2-A0SX TCGA-A2-A0T3 TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FW 
       35.05        50.43        18.71        31.73        23.77        17.36 
TCGA-A2-A1G1 TCGA-A2-A4RX TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A26I 
       19.20         9.01         3.42        38.30        30.61        21.73 
TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A06U TCGA-A8-A075 TCGA-A8-A079 TCGA-A8-A07B 
       10.42        13.02        29.03        17.03         9.01        33.01 
TCGA-A8-A07G TCGA-A8-A08B TCGA-A8-A08F TCGA-A8-A08L TCGA-A8-A08S TCGA-A8-A091 
       18.97        23.08        18.05         9.99        19.07        19.07 
TCGA-A8-A092 TCGA-A8-A09Q TCGA-A8-A0A2 TCGA-A8-A0A9 TCGA-AC-A23E TCGA-AC-A2QH 
       16.01        25.02        19.04        13.02         2.37         1.02 
TCGA-AC-A62X TCGA-AN-A04C TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FZ TCGA-AN-A0XS 
        1.12         1.78         0.16         0.33         0.33         0.33 
TCGA-AN-A0XT TCGA-AO-A03L TCGA-AO-A0J7 TCGA-AO-A12F TCGA-AO-A1KS TCGA-AQ-A54N 
        0.33        80.28        20.32        48.36         0.53         2.56 
TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AQ TCGA-AR-A255 TCGA-AR-A2LK TCGA-B6-A0IJ 
       55.36        61.84        43.07        34.82        42.87       176.98 
TCGA-B6-A0IO TCGA-B6-A0RG TCGA-B6-A0RS TCGA-B6-A0WY TCGA-B6-A402 TCGA-B6-A408 
      110.14        68.45       100.70       113.79        54.28        49.94 
TCGA-BH-A0BG TCGA-BH-A0C0 TCGA-BH-A0HI TCGA-BH-A18F TCGA-BH-A18L TCGA-BH-A18Q 
       24.85        41.75        20.38         8.81        26.66        55.63 
TCGA-BH-A18U TCGA-BH-A1F8 TCGA-BH-A42T TCGA-C8-A1HF TCGA-C8-A1HM TCGA-C8-A274 
       51.39        24.66         0.99        10.92         2.30         0.03 
TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JE TCGA-D8-A1JM TCGA-D8-A1JU TCGA-D8-A1X5 
       19.20        17.49        18.90        19.40        14.70        18.58 
TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XK TCGA-D8-A1XQ TCGA-D8-A27M TCGA-E2-A14Z 
       27.58        18.15        14.50        16.41        13.48        17.03 
TCGA-E2-A15H TCGA-E2-A15S TCGA-E2-A1L7 TCGA-E9-A1N6 TCGA-E9-A1RF TCGA-E9-A22B 
       12.92        14.07        27.42        13.48         6.58        22.75 
TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A54Y TCGA-EW-A1PC TCGA-GI-A2C9 
       23.51         0.69         1.94         0.23         6.15       109.87 
TCGA-GM-A2DI TCGA-GM-A3XL TCGA-LL-A5YP TCGA-LL-A7T0 TCGA-OL-A5RY TCGA-S3-A6ZG 
       61.91        69.30         3.25         3.22        14.10         6.81 

$`7P LOSS WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A1-A0SQ 
       20.88        13.68         7.96        39.32        19.20        18.21 
TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04U TCGA-A2-A04V 
      104.81        18.02        41.95        82.16        22.06        63.12 
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM 
       64.04        55.43        36.13       125.59        64.57        24.79 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CU 
      112.08        92.48        88.60       107.93        75.55         5.19 
TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 
       63.45        64.04        56.81        21.14        34.55        33.76 
TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER 
       28.77       101.72        89.36        80.28       107.61        74.40 
TCGA-A2-A0ES TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY 
       37.05        34.29        31.82        29.75        24.72        24.16 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 
       99.19        54.64        27.12        44.88        44.28        17.52 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 
       17.13         8.38        20.52        17.46        18.90        20.75 
TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH 
       32.55        25.28        18.21        15.42        21.90        21.67 
TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A1FV TCGA-A2-A1FX 
       14.50        18.61        19.33        14.63        23.47        36.79 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A 
       22.45        20.25        19.56        16.47        52.47       107.70 
TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
       16.31        17.19        18.15        91.92        10.59        20.88 
TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW 
       39.65        33.93        83.01        29.98        14.07        49.48 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RY 
       38.40        34.98        31.99        38.37         7.30         8.81 
TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH 
        8.91        12.00         6.74        35.31        34.29        35.47 
TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F 
       37.45        35.67        33.11        31.73        10.72        12.72 
TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H 
       23.61        29.56        31.36        24.26        23.74        23.80 
TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       20.61        22.32        11.34        10.59        10.29        11.28 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD 
       13.41        14.70        11.97        14.93        13.74        14.50 
TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX 
       21.17        17.92        14.73        12.10        10.72        11.05 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R 
       10.29         9.37         8.75        13.02         1.02        17.98 
TCGA-A8-A06T TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A07E 
       41.06        31.00        26.01         1.02        53.98        19.99 
TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P 
       18.97        14.01        12.00        17.03         9.99        10.98 
TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 
        8.98         7.99         9.96         9.99        28.04        18.05 
TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08G 
       15.06        36.95        13.02         0.99        19.99        19.96 
TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T 
       12.00        37.05        31.00        31.00         0.99        93.04 
TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 
       33.99        40.01        17.95        41.98        12.00         9.99 
TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I 
        9.99        12.00         1.02        13.02        31.00        33.07 
TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       29.98        15.02         1.02         8.98        19.04        15.02 
TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 
        0.99        14.01        12.00        13.02        21.04         0.99 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 
       17.03        38.04         0.95        10.85         2.66         1.48 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
       38.53        38.20        40.57        55.43        36.99        38.79 
TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN 
       26.04        50.70         0.92         2.27         0.99         0.69 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI 
       14.83         9.40         1.12         1.81         1.68         1.55 
TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW 
        1.32         1.55         0.07         1.81         1.18         0.69 
TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 
        0.43         1.74         0.33         0.33         0.23         0.33 
TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL 
        0.62         2.96         1.71         8.02         7.36         6.51 
TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK 
        0.33         0.33         6.44         4.64         7.96         7.00 
TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW 
        7.59         7.17         6.28         6.02         0.33         0.36 
TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP 
        0.33         0.33         0.33         0.33        12.33         0.30 
TCGA-AN-A0XR TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03N 
        0.33         0.33         5.33         5.59        47.84        66.77 
TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V 
       81.63        84.69        68.75        47.87        59.05        29.13 
TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 
       32.78        21.40        17.65        24.16        37.48        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE 
       53.03        21.53        50.70        50.86        72.00        76.77 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM 
       21.37        26.24        38.53        62.04        55.33        71.80 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A 
      102.58        99.25        93.70        94.59        96.10        90.58 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
       77.56        64.04        57.30        41.62        28.37        14.73 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J 
       82.62        61.87        70.39        17.79        24.79        26.93 
TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AQ-A7U7 
      130.09         5.65        15.62        13.22        21.86         9.99 
TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV 
       82.88        49.32         5.26        37.41        56.88        29.75 
TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 
       24.30        64.83        55.86        76.14        65.36        70.16 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL 
       83.87        76.18        75.55        52.77        51.25        48.82 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AR TCGA-AR-A1AS 
       62.56        43.73        43.56        39.98        17.23        40.83 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H 
       46.32        42.58        35.24        36.26        20.22       109.58 
TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
       50.89        73.02        65.46        68.19        65.69         0.85 
TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V 
       66.05        57.40        62.07        53.26        53.36        54.18 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 
       50.96        48.16        51.75        56.15        45.17        40.64 
TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LL TCGA-AR-A2LM 
       39.85        93.83       128.65        20.25         7.36        40.04 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN 
       17.10        20.81        16.96        20.38        54.74        16.04 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 
       20.45        10.59        77.62       143.38       149.59        12.13 
TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH 
      220.90       129.57        50.70        65.72       146.50       112.37 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE 
       18.77       126.12        84.59       110.93       140.88       211.56 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
      189.01       234.28        81.17        78.02       172.96       162.05 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS 
      102.77       140.48        89.46       131.21       157.41        97.48 
TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 
      188.68        79.63        17.98        21.47       129.57       129.70 
TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF 
      186.48        28.27        68.94        58.88        43.59       101.52 
TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A40B TCGA-B6-A40C 
       73.51       139.17       170.17        85.35        82.88        55.00 
TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 
       24.53        38.79        20.45        25.55        28.50        46.95 
TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 
       40.83        39.55        39.16        48.36        56.94        56.98 
TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ 
       51.68        37.22        32.02        18.21        25.71        21.70 
TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR 
       44.05        61.68        35.67        48.69        27.19        53.69 
TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 
       53.95        45.57        49.94        11.67        49.05        44.02 
TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH 
       48.13        42.90        45.83        31.17        23.44        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ 
       22.13        13.91        48.23        17.26        15.65         3.22 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
        2.56        38.47        45.17        47.41        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA 
       15.68        14.30         9.63        44.81        46.19        32.65 
TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 
       24.49        31.00        24.43        30.35        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA 
       37.78        35.51        24.56        23.08        41.00        52.96 
TCGA-BH-A0HB TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU 
       26.50         5.85         2.50        13.61        36.85        12.89 
TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 
       51.32        27.25        50.79         5.59        23.93        24.95 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J 
       42.35        44.81        23.05         2.01         7.23        20.12 
TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S 
       90.84        72.56        37.74        30.28        37.55        66.05 
TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET 
        7.36        51.16        69.93        91.99       113.82        82.85 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 
       42.28        12.00        55.69        49.58        17.69        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD 
       31.53        89.16        97.48       120.62       114.15        33.17 
TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM 
       74.73       122.89        36.92        63.35        55.00        45.63 
TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 
       72.07       144.59        72.07         6.90         0.72        38.60 
TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
       83.31        57.83       130.16        10.65         6.44        20.12 
TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O 
      109.28         8.94        11.93        11.77        11.77        12.66 
TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X 
       11.77         0.07        12.66        12.66        12.66        12.66 
TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 
        3.12         1.78         1.45         0.69         0.62         3.85 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK 
        3.75        12.33        11.34        11.34         0.16        12.03 
TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y 
       10.42         3.25         0.30         0.23         0.36         0.43 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B 
        8.28         9.67         0.03         0.03        12.20         0.99 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 
        0.03         0.23        11.90        20.88        13.25        20.58 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1JA 
       13.97        14.17        13.48        21.14        14.17        16.50 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH 
       18.71        15.78        18.15        12.03        12.03        14.01 
TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JN TCGA-D8-A1JP 
       18.97        20.09        20.12        20.09        20.38        21.01 
TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 
       12.20        13.32        17.79        16.73        25.74        23.90 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XL 
        2.66        17.16        15.22        14.73        21.83        19.92 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU 
       17.69         7.96        15.85        16.31         6.35        12.99 
TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       15.16        12.66        16.54        15.32        15.52         3.81 
TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H 
       14.24        14.14        17.42        16.04        13.45        13.05 
TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R 
       14.43         9.44        16.41         4.80         0.76        10.09 
TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 
       13.08        12.53        12.26        14.50        18.51         7.33 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B 
       43.00        34.42        27.52        46.59        40.41        37.51 
TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P 
       40.11        28.44        28.87        47.15        44.68        40.96 
TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V 
       38.24        38.60        33.17        33.30        43.33        34.26 
TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 
       32.02        31.96        28.60        25.41        27.12        23.24 
TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A 
       19.43        21.04        23.87        14.79        25.05        23.34 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15I 
       22.82        17.29        20.71        21.63        18.21        17.42 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P 
       19.40         9.04        20.58         7.73        13.02        19.56 
TCGA-E2-A15R TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 
       17.06        14.99        60.53        53.62        53.03        29.95 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF 
       32.35        28.50        16.47        17.10        38.30        37.41 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       32.78        33.73        33.70        28.44        22.65         3.88 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L8 TCGA-E2-A1L9 
       22.19        20.98        11.08        54.18        39.62        19.66 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI 
       24.59        40.47        28.90        18.87       106.75       102.61 
TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z 
        8.75        43.04        16.93         5.52        15.72         7.20 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 
       18.05        22.26        19.89        19.20        36.82        12.00 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF 
       13.12        36.56        39.55        12.59        35.77        20.05 
TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 
       21.57         9.86        11.90        14.30         0.62         2.10 
TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB 
        6.12         1.38         2.76        21.21        32.09        20.81 
TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI 
       40.24         0.66        34.65        21.27        34.59        35.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22E 
       34.13         0.79        12.53        13.32        39.09        12.89 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A24A 
       24.10        17.06         0.85        27.22         0.95        12.56 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA 
        0.72        17.75         0.76        26.07        18.41         0.62 
TCGA-E9-A3X8 TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW 
       15.72         0.39         0.26         0.23        15.39        12.20 
TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 
       39.72         8.48        18.21        18.90        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY 
       15.68        28.77        25.94        22.82        29.95        29.85 
TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 
       40.41        41.13        39.78        52.96        29.82        23.11 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PD 
       18.48        30.08         7.86        18.90        19.99        13.94 
TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS 
       10.52        14.43        34.55        19.96        55.00        52.73 
TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 
       25.91        22.09        21.27        17.49        10.16        10.59 
TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD 
        7.40        59.57       194.27        53.13        53.52        43.04 
TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       42.71        42.28        62.33        90.84        76.64        77.33 
TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 
       53.36       110.50        38.20        32.28        53.95        57.63 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U 
       13.55        18.12        11.84        11.57         8.28         6.67 
TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL 
        4.60         0.66         2.99         3.58         6.90         5.56 
TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y 
        4.70         3.65         3.19         2.63         3.88         4.14 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-MS-A51U 
        4.50         4.50         5.59         6.21        15.91         2.79 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.10        12.66        46.55         7.53        44.61        27.65 
TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H 
       24.10        26.20        16.87        10.29         9.80        14.76 
TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O 
       23.70        54.51        33.90        31.07        18.21         7.23 
TCGA-OL-A66P TCGA-W8-A86G 
        4.44         5.29 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             0.03              0.03 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           176.98            234.28 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           19.055            21.845 
[1] "0.0 - 177.0 (19.1)" "0.0 - 234.3 (21.8)"
[1] "hr=" "1.2"
D53V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7P LOSS MUTATED         7        7        2        0        41        23
  7P LOSS WILD-TYPE      73       70        7        9       294       201
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7P LOSS MUTATED           1         15          4          3        0
  7P LOSS WILD-TYPE         1        123         23         56       17
                   vv
clus                STAGE TIS STAGE X
  7P LOSS MUTATED           0       1
  7P LOSS WILD-TYPE         1      15
D53V3, multiclass
            clus
vv           7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                  7                73
  STAGE IA                 7                70
  STAGE IB                 2                 7
  STAGE II                 0                 9
  STAGE IIA               41               294
  STAGE IIB               23               201
  STAGE III                1                 1
  STAGE IIIA              15               123
  STAGE IIIB               4                23
  STAGE IIIC               3                56
  STAGE IV                 0                17
  STAGE TIS                0                 1
  STAGE X                  1                15
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  7P LOSS MUTATED    21  68  11   4
  7P LOSS WILD-TYPE 237 513 106  32
D53V4, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  T1              21               237
  T2              68               513
  T3              11               106
  T4               4                32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  7P LOSS MUTATED    56  27  17   4
  7P LOSS WILD-TYPE 412 303  94  66
D53V5, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0              56               412
  N1              27               303
  N2              17                94
  N3               4                66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  7P LOSS MUTATED          0  96   0   8
  7P LOSS WILD-TYPE        2 749  17 123
D53V6, multiclass
          clus
vv         7P LOSS MUTATED 7P LOSS WILD-TYPE
  CM0 (I+)               0                 2
  M0                    96               749
  M1                     0                17
  MX                     8               123
[1] 4 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   104   0
  7P LOSS WILD-TYPE 880  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED    104    0
  7P LOSS WILD-TYPE  880   11
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE             104               880
  MALE                 0                11
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  7P LOSS MUTATED                            0                            91
  7P LOSS WILD-TYPE                          1                           644
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  7P LOSS MUTATED                                5                   1
  7P LOSS WILD-TYPE                            161                   4
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  7P LOSS MUTATED                                  2                  0
  7P LOSS WILD-TYPE                               27                 14
                   vv
clus                OTHER  SPECIFY
  7P LOSS MUTATED                5
  7P LOSS WILD-TYPE             39
D53V8, multiclass
                                  clus
vv                                 7P LOSS MUTATED 7P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                 91               644
  INFILTRATING LOBULAR CARCINOMA                 5               161
  MEDULLARY CARCINOMA                            1                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               2                27
  MUCINOUS CARCINOMA                             0                14
  OTHER  SPECIFY                                 5                39
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V9, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    33  71
  7P LOSS WILD-TYPE 249 642
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     33   71
  7P LOSS WILD-TYPE  249  642
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO               33               249
  YES              71               642
[1] 2 2
[1] FALSE
D53V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P LOSS MUTATED                                  0     6
  7P LOSS WILD-TYPE                                1    50
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED                          18    65
  7P LOSS WILD-TYPE                       119   643
D53V11, multiclass
                                  clus
vv                                 7P LOSS MUTATED 7P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          6                50
  BLACK OR AFRICAN AMERICAN                     18               119
  WHITE                                         65               643
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V12, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     1  83
  7P LOSS WILD-TYPE  35 713
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      1   83
  7P LOSS WILD-TYPE   35  713
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                35
  NOT HISPANIC OR LATINO              83               713
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7Q LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED    96  14
  7Q LOSS WILD-TYPE 764 100
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
              110               864 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               14               100 
$`7Q LOSS MUTATED`
TCGA-A1-A0SO TCGA-A2-A0CT TCGA-A2-A0D4 TCGA-A2-A0EQ TCGA-A2-A0ET TCGA-A2-A0SX 
       28.01        75.25        25.22        79.76        35.05        50.43 
TCGA-A2-A0T3 TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1G1 TCGA-A2-A4RX 
       18.71        31.73        23.77        17.36        19.20         9.01 
TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A26I TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A06U 
       38.30        30.61        21.73        10.42        13.02        29.03 
TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A08B 
       17.03        53.98         9.01        18.97        14.01        23.08 
TCGA-A8-A08S TCGA-A8-A092 TCGA-A8-A099 TCGA-A8-A09I TCGA-A8-A09W TCGA-A8-A0A1 
       19.07        16.01         9.99        33.07         0.99        12.00 
TCGA-A8-A0A2 TCGA-A8-A0A9 TCGA-AC-A23E TCGA-AC-A2QH TCGA-AC-A62V TCGA-AN-A049 
       19.04        13.02         2.37         1.02         0.07         0.62 
TCGA-AN-A04C TCGA-AN-A0AJ TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FT TCGA-AN-A0FZ 
        1.78         8.02         0.16         0.33         6.02         0.33 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AO-A03L TCGA-AO-A0J7 TCGA-AO-A0JE TCGA-AO-A1KS 
        0.33         0.33        80.28        20.32        76.77         0.53 
TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A24H TCGA-AR-A24W TCGA-AR-A255 TCGA-AR-A2LK 
       83.87        55.36       109.58        50.96        34.82        42.87 
TCGA-B6-A0IC TCGA-B6-A0IO TCGA-B6-A0RS TCGA-B6-A0WY TCGA-B6-A408 TCGA-BH-A0AZ 
       50.70       110.14       100.70       113.79        49.94        28.50 
TCGA-BH-A0BG TCGA-BH-A0DZ TCGA-BH-A0HI TCGA-BH-A0W7 TCGA-BH-A18F TCGA-BH-A18L 
       24.85        16.27        20.38        44.81         8.81        26.66 
TCGA-BH-A18Q TCGA-BH-A18U TCGA-BH-A1EV TCGA-BH-A1FN TCGA-BH-A42T TCGA-C8-A12W 
       55.63        51.39        12.00        72.07         0.99        12.66 
TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HM TCGA-D8-A1JE TCGA-D8-A1JJ TCGA-D8-A1JU 
        3.75        10.92         2.30        18.90        20.09        14.70 
TCGA-D8-A1X5 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XK TCGA-D8-A1XQ TCGA-D8-A1XU 
       18.58        27.58        18.15        14.50        16.41        12.99 
TCGA-D8-A27M TCGA-E2-A14Z TCGA-E2-A15H TCGA-E2-A15M TCGA-E2-A1BC TCGA-E2-A1L7 
       13.48        17.03        12.92         7.73        16.47        27.42 
TCGA-E2-A1L8 TCGA-E2-A1LB TCGA-E9-A1N6 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R7 
       39.62        40.47        13.48         2.10         6.12        21.21 
TCGA-E9-A1RF TCGA-E9-A22B TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A3HO 
        6.58        22.75         0.69         1.94        12.56        26.07 
TCGA-E9-A54Y TCGA-EW-A1PC TCGA-GI-A2C9 TCGA-GM-A2DI TCGA-LL-A5YP TCGA-LL-A7SZ 
        0.23         6.15       109.87        61.91         3.25         5.59 
TCGA-OL-A5RY TCGA-S3-A6ZG 
       14.10         6.81 

$`7Q LOSS WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP 
       20.88        13.68        31.79         7.96        39.32        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T 
       18.21       104.81        18.02        41.95        82.16        73.84 
TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK 
       22.06        63.12        64.04        55.43        36.13       125.59 
TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
       64.57        24.79       112.08        92.48        88.60       107.93 
TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 
       75.55         5.19        63.45        64.04        56.81        21.14 
TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO 
       34.55        33.76        28.77       101.72        89.36        80.28 
TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW 
      107.61        74.40        37.05        34.29        31.82        29.75 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW 
       24.72        24.16        99.19        54.64        27.12        44.88 
TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T4 TCGA-A2-A0T5 
       44.28        17.52        17.13         8.38        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF 
       18.90        20.75        32.55        25.28        18.21        15.42 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL 
       21.90        21.67        14.50        18.61        19.33        14.63 
TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 
       23.47        36.79        22.45        20.25        19.56        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       52.47       107.70        16.31        17.19        18.15        91.92 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU 
       10.59        20.88        39.65        33.93        83.01        29.98 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 
       14.07        49.48        38.40        34.98        31.99        38.37 
TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 
        7.30         8.81         8.91        12.00         6.74         3.42 
TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB 
       35.31        34.29        35.47        37.45        35.67        33.11 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       31.73        10.72        12.72        23.61        29.56        31.36 
TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY 
       24.26        23.74        23.80        20.61        22.32        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 
       10.59        10.29        11.28        13.41        14.70        11.97 
TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D 
       14.93        13.74        14.50        21.17        17.92        14.73 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY 
       12.10        10.72        11.05        10.29         9.37         8.75 
TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06X TCGA-A8-A06Y 
       13.02         1.02        17.98        41.06        31.00        26.01 
TCGA-A8-A06Z TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07J TCGA-A8-A07L 
        1.02        33.01        19.99        18.97        12.00        17.03 
TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W 
        9.99        10.98         8.98         7.99         9.96         9.99 
TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A 
       28.04        18.05        15.06        36.95        13.02         0.99 
TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L 
       19.99        18.05        19.96        12.00        37.05         9.99 
TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z 
       31.00        31.00         0.99        93.04        33.99        40.01 
TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09B 
       19.07        17.95        41.98        12.00         9.99        12.00 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N 
        1.02        13.02        31.00        29.98        15.02         1.02 
TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09X TCGA-A8-A0A4 
       25.02         8.98        19.04        15.02        14.01        13.02 
TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G 
       21.04         0.99        17.03        38.04         0.95        10.85 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF 
        2.66         1.48        38.53        38.20        40.57        55.43 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ 
       36.99        38.79        26.04        50.70         0.92         2.27 
TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 
        0.99         0.69        14.83         9.40         1.12         1.81 
TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62X TCGA-AC-A62Y 
        1.68         1.55         1.32         1.55         1.12         1.81 
TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A03Y 
        1.18         0.69         0.43         1.74         0.33         0.33 
TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL 
        0.23         0.33         2.96         1.71         7.36         6.51 
TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK 
        0.33         0.33         6.44         4.64         7.96         7.00 
TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX 
        7.59         7.17         6.28         0.33         0.36         0.33 
TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR 
        0.33         0.33         0.33        12.33         0.30         0.33 
TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O 
        0.33         5.33         5.59        47.84        66.77        81.63 
TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 
       84.69        68.75        47.87        59.05        29.13        32.78 
TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 
       21.40        17.65        24.16        37.48        22.36        53.03 
TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JG 
       21.53        50.70        50.86        72.00        21.37        26.24 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 
       38.53        62.04        55.33        71.80       102.58        99.25 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D 
       93.70        94.59        96.10        90.58        77.56        64.04 
TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       57.30        48.36        41.62        28.37        14.73        82.62 
TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       61.87        70.39        17.79        24.79        26.93       130.09 
TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 
        5.65        15.62        13.22         2.56        21.86         9.99 
TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV 
       82.88        49.32         5.26        37.41        56.88        29.75 
TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 
       24.30        64.83        55.86        76.14        65.36        70.16 
TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL 
       76.18        75.55        61.84        52.77        51.25        48.82 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR 
       62.56        43.73        43.56        39.98        43.07        17.23 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY 
       40.83        46.32        42.58        35.24        36.26        20.22 
TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
       50.89        73.02        65.46        68.19        65.69         0.85 
TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V 
       66.05        57.40        62.07        53.26        53.36        54.18 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 
       48.16        51.75        56.15        45.17        40.64        39.85 
TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN 
       93.83       128.65        20.25         7.36        40.04        17.10 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP 
       20.81        16.96        20.38        54.74        16.04        20.45 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA 
       10.59        77.62       143.38       149.59        12.13       220.90 
TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK 
      129.57        65.72       146.50       112.37       176.98        18.77 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG 
      126.12        84.59       110.93       140.88       211.56        68.45 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
      189.01       234.28        81.17        78.02       172.96       162.05 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS 
      102.77       140.48        89.46       131.21       157.41        97.48 
TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 
      188.68        79.63        17.98        21.47       129.57       129.70 
TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF 
      186.48        28.27        68.94        58.88        43.59       101.52 
TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A40B 
       73.51       139.17       170.17        85.35        54.28        82.88 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0B0 
       55.00        24.53        38.79        20.45        25.55        46.95 
TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 
       40.83        39.55        39.16        48.36        56.94        56.98 
TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ 
       51.68        37.22        32.02        18.21        25.71        21.70 
TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR 
       44.05        61.68        35.67        48.69        27.19        53.69 
TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 
       53.95        45.57        49.94        11.67        49.05        41.75 
TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG 
       44.02        48.13        42.90        45.83        31.17        23.44 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP 
       38.01        22.13        13.91        48.23        17.26        15.65 
TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0E0 
        3.22         2.56        38.47        45.17        47.41         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA 
       15.68        14.30         9.63        44.81        46.19        32.65 
TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 
       24.49        31.00        24.43        30.35        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA 
       37.78        35.51        24.56        23.08        41.00        52.96 
TCGA-BH-A0HB TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU 
       26.50         5.85         2.50        13.61        36.85        12.89 
TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 
       51.32        27.25        50.79         5.59        23.93        24.95 
TCGA-BH-A0W5 TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K 
       42.35        23.05         2.01         7.23        20.12        90.84 
TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T 
       72.56        37.74        30.28        37.55        66.05         7.36 
TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU 
       51.16        69.93        91.99       113.82        82.85        42.28 
TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 
       55.69        49.58        17.69        25.81        31.53        89.16 
TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE 
       97.48        24.66       120.62       114.15        33.17        74.73 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR 
      122.89        36.92        63.35        55.00        45.63       144.59 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 
       72.07         6.90         0.72        38.60        83.31        57.83 
TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V 
      130.16        10.65         6.44        20.12       109.28         8.94 
TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q 
       11.93        11.77        11.77        12.66        11.77         0.07 
TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 
       12.66        12.66        12.66         3.12         1.78         1.45 
TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HG TCGA-C8-A1HI 
        0.69         0.62         3.85        12.33        11.34        11.34 
TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W 
        0.16        12.03        10.42         3.25         0.30         0.23 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
        0.36         0.43         8.28         9.67         0.03         0.03 
TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y 
        0.03        12.20         0.99         0.03         0.23        11.90 
TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 
       20.88        13.25        20.58        13.97        14.17        13.48 
TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
       21.14        19.20        14.17        17.49        16.50        18.71 
TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI 
       15.78        18.15        12.03        12.03        14.01        18.97 
TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS 
       20.12        20.09        19.40        20.38        21.01        12.20 
TCGA-D8-A1JT TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XC 
       13.32        17.79        16.73        25.74        23.90         2.66 
TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XL TCGA-D8-A1XM 
       17.16        15.22        14.73        21.83        19.92        17.69 
TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW 
        7.96        15.85        16.31         6.35        15.16        12.66 
TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 
       16.54        15.32        15.52         3.81        14.24        14.14 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K 
       17.42        16.04        13.45        13.05        14.43         9.44 
TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V 
       16.41         4.80         0.76        10.09        13.08        12.53 
TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A107 
       12.26        14.50        18.51         7.33        43.00        34.42 
TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E 
       27.52        46.59        40.41        37.51        40.11        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R 
       28.87        47.15        44.68        40.96        38.24        38.60 
TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X 
       33.17        33.30        43.33        34.26        32.02        31.96 
TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 
       28.60        25.41        27.12        23.24        19.43        21.04 
TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D 
       23.87        14.79        25.05        23.34        22.82        17.29 
TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       20.71        21.63        18.21        17.42        19.40         9.04 
TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
       20.58        13.02        19.56        17.06        14.07        14.99 
TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       60.53        53.62        53.03        29.95        32.35        28.50 
TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II 
       17.10        38.30        37.41        32.78        33.73        33.70 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       28.44        22.65         3.88        22.19        20.98        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH 
       54.18        19.66        24.59        28.90        18.87       106.75 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX 
      102.61         8.75        43.04        16.93         5.52        15.72 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N4 TCGA-E9-A1N5 
        7.20        18.05        22.26        19.89        19.20        36.82 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE 
       12.00        13.12        36.56        39.55        12.59        35.77 
TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       20.05        21.57         9.86        11.90        14.30         0.62 
TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD 
        1.38         2.76        32.09        20.81        40.24         0.66 
TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
       34.65        21.27        34.59        35.64        34.13         0.79 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H 
       12.53        13.32        39.09        12.89        23.51        24.10 
TCGA-E9-A243 TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A295 TCGA-E9-A2JS 
       17.06         0.85        27.22         0.95         0.72        17.75 
TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A5FK TCGA-E9-A5FL 
        0.76        18.41         0.62        15.72         0.39         0.26 
TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
        0.23        15.39        12.20        39.72         8.48        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV 
       18.90        13.25        16.57        15.68        28.77        25.94 
TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 
       22.82        29.95        29.85        40.41        41.13        39.78 
TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 
       52.96        29.82        23.11        18.48        30.08         7.86 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
       18.90        19.99        13.94        10.52        14.43        34.55 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 
       19.96        55.00        52.73        25.91        22.09        21.27 
TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA 
       17.49        10.16        10.59         7.40        59.57       194.27 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DK 
       53.13        53.52        43.04        42.71        42.28        62.33 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY 
       90.84        76.64        77.33        53.36       110.50        38.20 
TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX 
       32.28        69.30        53.95        57.63        13.55        18.12 
TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 
       11.84        11.57         8.28         6.67         4.60         0.66 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN 
        2.99         3.58         6.90         5.56         4.70         3.65 
TCGA-LL-A5YO TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 
        3.19         2.63         3.88         4.14         4.50         4.50 
TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
        3.22         6.21        15.91         2.79         2.10        12.66 
TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW 
       46.55         7.53        44.61        27.65        24.10        26.20 
TCGA-OL-A5RX TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J 
       16.87        10.29         9.80        14.76        23.70        54.51 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-W8-A86G 
       33.90        31.07        18.21         7.23         4.44         5.29 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             0.07              0.03 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           113.79            234.28 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           17.755            22.160 
[1] "0.1 - 113.8 (17.8)" "0.0 - 234.3 (22.2)"
[1] "hr=" "1.6"
D54V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7Q LOSS MUTATED         7        9        2        1        40        23
  7Q LOSS WILD-TYPE      73       68        7        8       295       201
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7Q LOSS MUTATED           1         20          4          3        1
  7Q LOSS WILD-TYPE         1        118         23         56       16
                   vv
clus                STAGE TIS STAGE X
  7Q LOSS MUTATED           0       2
  7Q LOSS WILD-TYPE         1      14
D54V3, multiclass
            clus
vv           7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                  7                73
  STAGE IA                 9                68
  STAGE IB                 2                 7
  STAGE II                 1                 8
  STAGE IIA               40               295
  STAGE IIB               23               201
  STAGE III                1                 1
  STAGE IIIA              20               118
  STAGE IIIB               4                23
  STAGE IIIC               3                56
  STAGE IV                 1                16
  STAGE TIS                0                 1
  STAGE X                  2                14
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  7Q LOSS MUTATED    23  74  12   4
  7Q LOSS WILD-TYPE 235 507 105  32
D54V4, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1              23               235
  T2              74               507
  T3              12               105
  T4               4                32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  7Q LOSS MUTATED    55  33  18   6
  7Q LOSS WILD-TYPE 413 297  93  64
D54V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0              55               413
  N1              33               297
  N2              18                93
  N3               6                64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  7Q LOSS MUTATED          1 101   1  10
  7Q LOSS WILD-TYPE        1 744  16 121
D54V6, multiclass
          clus
vv         7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CM0 (I+)               1                 1
  M0                   101               744
  M1                     1                16
  MX                    10               121
[1] 4 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   112   1
  7Q LOSS WILD-TYPE 872  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED    112    1
  7Q LOSS WILD-TYPE  872   10
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE             112               872
  MALE                 1                10
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  7Q LOSS MUTATED                            0                            95
  7Q LOSS WILD-TYPE                          1                           640
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  7Q LOSS MUTATED                               11                   0
  7Q LOSS WILD-TYPE                            155                   5
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  7Q LOSS MUTATED                                  2                  0
  7Q LOSS WILD-TYPE                               27                 14
                   vv
clus                OTHER  SPECIFY
  7Q LOSS MUTATED                5
  7Q LOSS WILD-TYPE             39
D54V8, multiclass
                                  clus
vv                                 7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                 95               640
  INFILTRATING LOBULAR CARCINOMA                11               155
  MEDULLARY CARCINOMA                            0                 5
  MIXED HISTOLOGY (PLEASE SPECIFY)               2                27
  MUCINOUS CARCINOMA                             0                14
  OTHER  SPECIFY                                 5                39
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V9, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    36  77
  7Q LOSS WILD-TYPE 246 636
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     36   77
  7Q LOSS WILD-TYPE  246  636
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO               36               246
  YES              77               636
[1] 2 2
[1] FALSE
D54V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q LOSS MUTATED                                  0     6
  7Q LOSS WILD-TYPE                                1    50
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED                          16    73
  7Q LOSS WILD-TYPE                       121   635
D54V11, multiclass
                                  clus
vv                                 7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          6                50
  BLACK OR AFRICAN AMERICAN                     16               121
  WHITE                                         73               635
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V12, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     0  90
  7Q LOSS WILD-TYPE  36 706
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0   90
  7Q LOSS WILD-TYPE   36  706
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                36
  NOT HISPANIC OR LATINO              90               706
[1] 2 2
[1] FALSE

Clustering(55) Variable = 8P LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED   301  54
  8P LOSS WILD-TYPE 559  60
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              355               619 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               54                60 
$`8P LOSS MUTATED`
TCGA-A1-A0SK TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A04P TCGA-A2-A04Q 
       31.79        39.32        28.01        19.20        18.02        41.95 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CL TCGA-A2-A0CO 
       73.84        22.06        63.12        36.13        64.57       112.08 
TCGA-A2-A0CP TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0D1 TCGA-A2-A0D4 TCGA-A2-A0EU 
       92.48         5.19        64.04        34.55        25.22        34.29 
TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0SX TCGA-A2-A0T0 TCGA-A2-A0T1 
       31.82        29.75        24.72        50.43        17.52        17.13 
TCGA-A2-A0T3 TCGA-A2-A0YH TCGA-A2-A0YK TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX 
       18.71        21.67        19.33        23.77        17.36        36.79 
TCGA-A2-A1G4 TCGA-A2-A25D TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XZ TCGA-A2-A4RW 
       19.56        18.15        83.01        29.98        31.99         7.30 
TCGA-A2-A4S3 TCGA-A7-A0D9 TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A26J TCGA-A7-A3IZ 
        3.42        37.45        31.73        10.72        20.61        10.59 
TCGA-A7-A3J1 TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A8-A06O 
       11.28        21.17        17.92        14.73        12.10        13.02 
TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A075 TCGA-A8-A07E TCGA-A8-A07L TCGA-A8-A07O 
       17.98        41.06        17.03        19.99        17.03         9.99 
TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07W TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A08G 
       10.98         7.99         9.99        15.06        36.95        19.96 
TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08X TCGA-A8-A091 TCGA-A8-A097 
       37.05        31.00        19.07        33.99        19.07        12.00 
TCGA-A8-A09D TCGA-A8-A09K TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T 
       13.02        29.98         1.02        25.02         8.98        19.04 
TCGA-A8-A0A7 TCGA-AC-A23H TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A3TN TCGA-AC-A3W5 
        0.99         2.66        50.70         1.02         1.12         1.81 
TCGA-AC-A8OP TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C 
        1.74         0.33         0.23         0.62         2.96         1.78 
TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FS TCGA-AN-A0FV 
        0.16         0.33         0.33         6.44         6.28         0.33 
TCGA-AN-A0FX TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU 
        0.33         0.33         0.33         0.33         0.33         0.33 
TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 
       66.77        81.63        84.69        29.13        32.78        21.40 
TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB 
       17.65        24.16        37.48        53.03        21.53        50.70 
TCGA-AO-A0JE TCGA-AO-A0JG TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A126 
       76.77        26.24        55.33        71.80       102.58        93.70 
TCGA-AO-A12D TCGA-AO-A12G TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04L TCGA-AQ-A0Y5 
       64.04        41.62        70.39        17.79       130.09         5.65 
TCGA-AQ-A1H2 TCGA-AR-A0TP TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW 
       15.62        82.88        37.41        56.88        29.75        24.30 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AJ 
       64.83        55.86        70.16        83.87        76.18        52.77 
TCGA-AR-A1AK TCGA-AR-A1AM TCGA-AR-A1AP TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AW 
       51.25        62.56        39.98        17.23        40.83        35.24 
TCGA-AR-A1AX TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24U TCGA-AR-A24V 
       36.26       109.58        50.89        73.02        53.36        54.18 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A2LE TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 
       51.75        56.15       128.65        10.59        77.62       143.38 
TCGA-B6-A0I9 TCGA-B6-A0IG TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IQ 
       12.13       146.50       176.98        18.77       126.12       140.88 
TCGA-B6-A0RG TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW 
       68.45       100.70       131.21        97.48       188.68        17.98 
TCGA-B6-A0WY TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KN TCGA-B6-A408 TCGA-B6-A40C 
      113.79        68.94        58.88       139.17        49.94        55.00 
TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0B2 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0BL 
       38.79        25.55        40.83        56.94        56.98        44.05 
TCGA-BH-A0BP TCGA-BH-A0BR TCGA-BH-A0BV TCGA-BH-A0C0 TCGA-BH-A0C7 TCGA-BH-A0DG 
       48.69        53.69        49.94        41.75        42.90        23.44 
TCGA-BH-A0DL TCGA-BH-A0E6 TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0H7 
       48.23         9.63        24.49        31.00        24.43        23.08 
TCGA-BH-A0HK TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0W3 TCGA-BH-A0WA 
        5.85        51.32        27.25        50.79        23.93        23.05 
TCGA-BH-A18F TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18N TCGA-BH-A18S 
        8.81         7.23        20.12        90.84        37.74        66.05 
TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EW TCGA-BH-A1EY 
        7.36        51.39        51.16        69.93        55.69        17.69 
TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FH 
       25.81        31.53        24.66       120.62        33.17        36.92 
TCGA-BH-A1FN TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A209 
       72.07        72.07         6.90        38.60        57.83       130.16 
TCGA-BH-A42V TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12P TCGA-C8-A131 TCGA-C8-A132 
        8.94        11.77        11.77        11.77         1.78         1.45 
TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK 
        0.69         3.85         3.75        11.34        11.34        12.03 
TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26W TCGA-C8-A278 TCGA-C8-A27A 
       10.42         2.30         3.25         0.23         0.03        12.20 
TCGA-C8-A27B TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A143 
        0.99         0.23        11.90        20.88        13.25        14.17 
TCGA-D8-A145 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JG 
       13.48        14.17        17.49        15.78        18.15        12.03 
TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JT TCGA-D8-A1X8 TCGA-D8-A1XD TCGA-D8-A1XJ 
       20.09        20.12        13.32        25.74        17.16        21.83 
TCGA-D8-A1XM TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A27F 
       17.69        16.41        16.31        15.52        14.24        16.04 
TCGA-D8-A27H TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27R TCGA-D8-A3Z6 TCGA-E2-A105 
       13.05        16.41        13.48        10.09        18.51        43.00 
TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A14N TCGA-E2-A14S TCGA-E2-A14T 
       27.52        40.41        40.11        47.15        33.17        33.30 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A15A 
       34.26        32.02        31.96        17.03        25.41        23.34 
TCGA-E2-A15C TCGA-E2-A15H TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15R TCGA-E2-A1B0 
       22.82        12.92        19.40         9.04        17.06        53.62 
TCGA-E2-A1B5 TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II 
       32.35        38.30        37.41        32.78        33.73        33.70 
TCGA-E2-A1IO TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LE TCGA-E2-A1LG 
       20.98        54.18        27.42        39.62        28.90        18.87 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A56Z TCGA-E2-A574 TCGA-E9-A1N8 
      102.61         8.75        43.04         7.20        19.89        12.00 
TCGA-E9-A1N9 TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1R5 TCGA-E9-A1R7 
       13.12        12.59        20.05         9.86         1.38        21.21 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A229 TCGA-E9-A22A 
       34.65         6.58        34.59        34.13        13.32        39.09 
TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A3QA TCGA-E9-A54Y 
       22.75        12.89         0.69         1.94         0.62         0.23 
TCGA-EW-A1IX TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P8 
       39.72        25.94        22.82        29.85        40.41         7.86 
TCGA-EW-A1PA TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FV 
       18.90        10.52        14.43        19.96        55.00        25.91 
TCGA-EW-A3U0 TCGA-EW-A424 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A3NW 
       17.49        10.59       109.87        59.57       194.27       110.50 
TCGA-GM-A3XL TCGA-GM-A5PV TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A7W6 TCGA-LL-A440 
       69.30        13.55        11.84        11.57         4.60         0.66 
TCGA-LL-A441 TCGA-LL-A50Y TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A6FR TCGA-LL-A7T0 
        2.99         6.90         4.70         3.65         3.88         3.22 
TCGA-LL-A8F5 TCGA-OL-A5RW TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66J 
        6.21        26.20        14.10        10.29         9.80        54.51 
TCGA-OL-A66P 
        4.44 

$`8P LOSS WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04R 
       20.88        13.68         7.96        18.21       104.81        82.16 
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CM TCGA-A2-A0CQ TCGA-A2-A0CR 
       64.04        55.43       125.59        24.79        88.60       107.93 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D2 
       75.55        75.25        63.45        56.81        21.14        33.76 
TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ 
       28.77       101.72        89.36        80.28       107.61        79.76 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU 
       74.40        37.05        35.05        24.16        99.19        54.64 
TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T2 TCGA-A2-A0T4 TCGA-A2-A0T5 
       27.12        44.88        44.28         8.38        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF 
       18.90        20.75        32.55        25.28        18.21        15.42 
TCGA-A2-A0YG TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV 
       21.90        14.50        18.61        14.63        31.73        23.47 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A 
       22.45        20.25        19.20        16.47        52.47       107.70 
TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD 
       16.31        17.19        91.92        10.59        20.88        39.65 
TCGA-A2-A3XS TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 
       33.93        14.07        49.48        38.40        34.98        38.37 
TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CD 
        9.01         8.81         8.91        12.00         6.74        38.30 
TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A0DB 
       35.31        34.29        35.47        30.61        35.67        33.11 
TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G 
       12.72        23.61        29.56        31.36        24.26        23.74 
TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3J0 TCGA-A7-A3RF 
       23.80        21.73        22.32        11.34        10.29        13.41 
TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A5ZW 
       14.70        11.97        14.93        13.74        14.50        10.72 
TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P 
       11.05        10.29         9.37        10.42         8.75        13.02 
TCGA-A8-A06Q TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 
        1.02        29.03        31.00        26.01         1.02        53.98 
TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J 
        9.01        33.01        18.97        18.97        14.01        12.00 
TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A086 TCGA-A8-A08A 
        8.98         9.96        28.04        18.05        13.02         0.99 
TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O 
       23.08        19.99        18.05        12.00         9.99        31.00 
TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 
        0.99        93.04        40.01        16.01        17.95        41.98 
TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I 
        9.99         9.99        12.00         1.02        31.00        33.07 
TCGA-A8-A09M TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 
       15.02        15.02         0.99        14.01        12.00        19.04 
TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C 
       13.02        21.04        13.02        17.03        38.04         0.95 
TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB 
        2.37        10.85         1.48        38.53        38.20        40.57 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2QI TCGA-AC-A2QJ 
       55.43        36.99        38.79        26.04         0.92         2.27 
TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3W6 TCGA-AC-A3YI 
        0.99         0.69        14.83         9.40         1.68         1.55 
TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV 
        1.32         1.55         0.07         1.12         1.81         1.18 
TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AN-A03X TCGA-AN-A046 TCGA-AN-A04D TCGA-AN-A0AJ 
        0.69         0.43         0.33         0.33         1.71         8.02 
TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK 
        7.36         6.51         0.33         4.64         7.96         7.00 
TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ 
        7.59         7.17         6.02         0.36         0.33         0.33 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L 
       12.33         0.30         0.33         5.33         5.59        80.28 
TCGA-AO-A03M TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A0J7 TCGA-AO-A0J8 
       47.84        68.75        47.87        59.05        20.32        22.36 
TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A125 
       50.86        72.00        21.37        38.53        62.04        99.25 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12F 
       94.59        96.10        90.58        77.56        57.30        48.36 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AQ-A04H 
       28.37        14.73        82.62        61.87         0.53        24.79 
TCGA-AQ-A04J TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TQ 
       26.93        13.22         2.56        21.86         9.99        49.32 
TCGA-AR-A0TR TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
        5.26        76.14        65.36        55.36        75.55        61.84 
TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AQ TCGA-AR-A1AU TCGA-AR-A1AV 
       48.82        43.73        43.56        43.07        46.32        42.58 
TCGA-AR-A1AY TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q 
       20.22        65.46        68.19        65.69         0.85        66.05 
TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A251 
       57.40        62.07        53.26        50.96        48.16        45.17 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LH TCGA-AR-A2LK 
       40.64        39.85        34.82        93.83        20.25        42.87 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
        7.36        40.04        17.10        20.81        16.96        20.38 
TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IB 
       54.74        16.04        20.45       149.59       220.90       129.57 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP 
       50.70        65.72       112.37        84.59       110.14       110.93 
TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN 
      211.56       189.01       234.28        81.17        78.02       172.96 
TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WV 
      162.05       102.77       140.48        89.46       157.41        79.63 
TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A1KC 
       21.47       129.57       129.70       186.48        28.27        43.59 
TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A40B 
      101.52        73.51       170.17        85.35        54.28        82.88 
TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 
       24.53        20.45        28.50        46.95        39.55        39.16 
TCGA-BH-A0B5 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       48.36        51.68        37.22        32.02        18.21        25.71 
TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BS 
       24.85        21.70        61.68        35.67        27.19        53.95 
TCGA-BH-A0BT TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0DD 
       45.57        11.67        49.05        44.02        48.13        45.83 
TCGA-BH-A0DE TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DP 
       31.17        38.01        22.13        13.91        17.26        15.65 
TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ 
        3.22         2.56        38.47        45.17        47.41        16.27 
TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA 
        4.41        15.68        14.30        44.81        46.19        32.65 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       30.35        10.78        15.16        37.78        35.51        24.56 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HO TCGA-BH-A0HP 
       41.00        52.96        26.50        20.38         2.50        13.61 
TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       36.85        12.89         5.59        24.95        42.35        44.81 
TCGA-BH-A18G TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R 
        2.01        26.66        72.56        30.28        55.63        37.55 
TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EX 
       91.99       113.82        82.85        42.28        12.00        49.58 
TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FJ 
       89.16        97.48       114.15        74.73       122.89        63.35 
TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A202 TCGA-BH-A204 TCGA-BH-A28O 
       55.00        45.63       144.59         0.72        83.31        10.65 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-C8-A12L TCGA-C8-A12O 
        6.44        20.12         0.99       109.28        11.93        12.66 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 
        0.07        12.66        12.66        12.66        12.66         3.12 
TCGA-C8-A135 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HJ TCGA-C8-A26V TCGA-C8-A26X 
        0.62        12.33        10.92         0.16         0.30         0.36 
TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A3M7 
        0.43         8.28         9.67         0.03         0.03         0.03 
TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1JA TCGA-D8-A1JB 
       20.58        13.97        21.14        19.20        16.50        18.71 
TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JL TCGA-D8-A1JM 
       18.90        12.03        14.01        18.97        20.09        19.40 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 
       20.38        21.01        12.20        14.70        18.58        17.79 
TCGA-D8-A1X7 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XF 
       16.73        23.90        27.58        18.15         2.66        15.22 
TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XT 
       14.73        14.50        19.92         7.96        15.85         6.35 
TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y1 
       12.99        15.16        12.66        16.54        15.32         3.81 
TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27N 
       14.14        17.42        13.45        14.43         9.44         4.80 
TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A4Z1 
        0.76        13.08        12.53        12.26        14.50         7.33 
TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14O 
       34.42        46.59        37.51        28.44        28.87        44.68 
TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14U TCGA-E2-A14Y TCGA-E2-A152 
       40.96        38.24        38.60        43.33        28.60        27.12 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 
       23.24        19.43        21.04        23.87        14.79        25.05 
TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15L 
       17.29        20.71        21.63        18.21        17.42        20.58 
TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ 
        7.73        13.02        19.56        14.07        14.99        60.53 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IJ 
       53.03        29.95        28.50        16.47        17.10        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L9 TCGA-E2-A1LA 
       22.65         3.88        22.19        11.08        19.66        24.59 
TCGA-E2-A1LB TCGA-E2-A1LH TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 
       40.47       106.75        16.93         5.52        15.72        18.05 
TCGA-E2-A573 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1NA TCGA-E9-A1NC 
       22.26        19.20        36.82        13.48        36.56        39.55 
TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 
       35.77        21.57        11.90        14.30         0.62         2.10 
TCGA-E9-A1R4 TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD 
        6.12         2.76        32.09        20.81        40.24         0.66 
TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A22G TCGA-E9-A22H 
       21.27        35.64         0.79        12.53        23.51        24.10 
TCGA-E9-A243 TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
       17.06         0.85        27.22         0.95        12.56         0.72 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A5FK 
       17.75         0.76        26.07        18.41        15.72         0.39 
TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IY TCGA-EW-A1IZ 
        0.26         0.23        15.39        12.20         8.48        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OX 
       18.90        13.25        16.57        15.68        28.77        29.95 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 
       41.13        39.78        52.96        29.82        23.11        18.48 
TCGA-EW-A1P7 TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PG TCGA-EW-A2FS 
       30.08        19.99         6.15        13.94        34.55        52.73 
TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A423 TCGA-GI-A2C8 TCGA-GM-A2DB TCGA-GM-A2DC 
       22.09        21.27        10.16         7.40        53.13        53.52 
TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       43.04        42.71        42.28        61.91        62.33        90.84 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN 
       76.64        77.33        53.36        38.20        32.28        53.95 
TCGA-GM-A4E0 TCGA-GM-A5PX TCGA-LD-A66U TCGA-LD-A74U TCGA-LL-A442 TCGA-LL-A5YL 
       57.63        18.12         8.28         6.67         3.58         5.56 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 
        3.19         3.25         2.63         4.14         4.50         4.50 
TCGA-LL-A7SZ TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 
        5.59        15.91         2.79         2.10        12.66        46.55 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A66H 
        7.53        44.61        27.65        24.10        16.87        14.76 
TCGA-OL-A66I TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-S3-A6ZG 
       23.70        33.90        31.07        18.21         7.23         6.81 
TCGA-W8-A86G 
        5.29 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.03              0.03 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           194.27            234.28 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            22.82             21.04 
[1] "0.0 - 194.3 (22.8)" "0.0 - 234.3 (21.0)"
[1] "hr=" "1.5"
D55V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8P LOSS MUTATED        28       31        4        1       126        82
  8P LOSS WILD-TYPE      52       46        5        8       209       142
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8P LOSS MUTATED           0         50          8         20        6
  8P LOSS WILD-TYPE         2         88         19         39       11
                   vv
clus                STAGE TIS STAGE X
  8P LOSS MUTATED           0       6
  8P LOSS WILD-TYPE         1      10
D55V3, multiclass
            clus
vv           8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                 28                52
  STAGE IA                31                46
  STAGE IB                 4                 5
  STAGE II                 1                 8
  STAGE IIA              126               209
  STAGE IIB               82               142
  STAGE III                0                 2
  STAGE IIIA              50                88
  STAGE IIIB               8                19
  STAGE IIIC              20                39
  STAGE IV                 6                11
  STAGE TIS                0                 1
  STAGE X                  6                10
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  8P LOSS MUTATED    95 220  33  14
  8P LOSS WILD-TYPE 163 361  84  22
D55V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1              95               163
  T2             220               361
  T3              33                84
  T4              14                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                 N0  N1  N2  N3
  8P LOSS MUTATED   173 116  44  22
  8P LOSS WILD-TYPE 295 214  67  48
D55V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0             173               295
  N1             116               214
  N2              44                67
  N3              22                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  8P LOSS MUTATED          1 316   6  39
  8P LOSS WILD-TYPE        1 529  11  92
D55V6, multiclass
          clus
vv         8P LOSS MUTATED 8P LOSS WILD-TYPE
  CM0 (I+)               1                 1
  M0                   316               529
  M1                     6                11
  MX                    39                92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   359   3
  8P LOSS WILD-TYPE 625   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    359    3
  8P LOSS WILD-TYPE  625    8
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE             359               625
  MALE                 3                 8
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  8P LOSS MUTATED                            1                           297
  8P LOSS WILD-TYPE                          0                           438
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  8P LOSS MUTATED                               35                   2
  8P LOSS WILD-TYPE                            131                   3
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  8P LOSS MUTATED                                  8                  1
  8P LOSS WILD-TYPE                               21                 13
                   vv
clus                OTHER  SPECIFY
  8P LOSS MUTATED               17
  8P LOSS WILD-TYPE             27
D55V8, multiclass
                                  clus
vv                                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                297               438
  INFILTRATING LOBULAR CARCINOMA                35               131
  MEDULLARY CARCINOMA                            2                 3
  MIXED HISTOLOGY (PLEASE SPECIFY)               8                21
  MUCINOUS CARCINOMA                             1                13
  OTHER  SPECIFY                                17                27
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V9, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   107 255
  8P LOSS WILD-TYPE 175 458
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    107  255
  8P LOSS WILD-TYPE  175  458
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO              107               175
  YES             255               458
[1] 2 2
[1] FALSE
D55V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P LOSS MUTATED                                  1    28
  8P LOSS WILD-TYPE                                0    28
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED                          55   246
  8P LOSS WILD-TYPE                        82   462
D55V11, multiclass
                                  clus
vv                                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         28                28
  BLACK OR AFRICAN AMERICAN                     55                82
  WHITE                                        246               462
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V12, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    11 298
  8P LOSS WILD-TYPE  25 498
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     11  298
  8P LOSS WILD-TYPE   25  498
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                  11                25
  NOT HISPANIC OR LATINO             298               498
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8Q LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    65  14
  8Q LOSS WILD-TYPE 795 100
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               79               895 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               14               100 
$`8Q LOSS MUTATED`
TCGA-A1-A0SO TCGA-A2-A0CU TCGA-A2-A3XZ TCGA-A7-A0D9 TCGA-A7-A13E TCGA-A7-A4SF 
       28.01         5.19        31.99        37.45        10.72        17.92 
TCGA-A8-A07L TCGA-A8-A097 TCGA-A8-A09D TCGA-AC-A2FO TCGA-AC-A3W5 TCGA-AN-A041 
       17.03        12.00        13.02        50.70         1.81         0.23 
TCGA-AN-A04A TCGA-AN-A0FD TCGA-AO-A03P TCGA-AO-A0J2 TCGA-AO-A0J9 TCGA-AO-A0JA 
        2.96         6.44        84.69        32.78        53.03        21.53 
TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AQ-A0Y5 TCGA-AR-A0TY TCGA-AR-A0U3 
       55.33        71.80       102.58         5.65        55.86        76.18 
TCGA-AR-A24H TCGA-AR-A24K TCGA-B6-A0IK TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RS 
      109.58        50.89        18.77       140.88        68.45       100.70 
TCGA-B6-A0WS TCGA-B6-A0X5 TCGA-B6-A408 TCGA-BH-A0B7 TCGA-BH-A0BR TCGA-BH-A0C7 
       97.48        68.94        49.94        56.98        53.69        42.90 
TCGA-BH-A0DG TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0W3 TCGA-BH-A18S TCGA-BH-A18T 
       23.44        24.49        31.00        23.93        66.05         7.36 
TCGA-BH-A1EN TCGA-BH-A1F8 TCGA-BH-A1FD TCGA-C8-A12P TCGA-C8-A132 TCGA-C8-A134 
       69.93        24.66        33.17        11.77         1.45         0.69 
TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HI TCGA-C8-A1HL TCGA-C8-A26W TCGA-D8-A140 
        3.85         3.75        11.34        10.42         0.23        13.25 
TCGA-D8-A145 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A3Z6 TCGA-E2-A14V TCGA-E2-A15K 
       13.48        14.17        17.49        18.51        34.26         9.04 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-E2-A1LL TCGA-E9-A1N8 
       32.78        33.73        39.62        18.87        43.04        12.00 
TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A244 TCGA-EW-A1PE TCGA-EW-A3U0 TCGA-EW-A424 
        1.38        21.21         0.69        10.52        17.49        10.59 
TCGA-JL-A3YX TCGA-LL-A440 TCGA-LL-A8F5 TCGA-OL-A5RW TCGA-OL-A5RZ TCGA-OL-A5S0 
       11.57         0.66         6.21        26.20        10.29         9.80 
TCGA-OL-A66P 
        4.44 

$`8Q LOSS WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP 
       20.88        13.68        31.79         7.96        39.32        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T 
       18.21       104.81        18.02        41.95        82.16        73.84 
TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK 
       22.06        63.12        64.04        55.43        36.13       125.59 
TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
       64.57        24.79       112.08        92.48        88.60       107.93 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 
       75.55        75.25        63.45        64.04        56.81        21.14 
TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN 
       34.55        33.76        28.77        25.22       101.72        89.36 
TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET 
       80.28       107.61        79.76        74.40        37.05        35.05 
TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST 
       34.29        31.82        29.75        24.72        24.16        99.19 
TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 
       54.64        27.12        44.88        50.43        44.28        17.52 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.13         8.38        18.71        20.52        17.46        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG 
       20.75        32.55        25.28        18.21        15.42        21.90 
TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       21.67        14.50        18.61        19.33        14.63        31.73 
TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 
       23.77        23.47        17.36        36.79        22.45        20.25 
TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B 
       19.20        19.56        16.47        52.47       107.70        16.31 
TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD 
       17.19        18.15        91.92        10.59        20.88        39.65 
TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX 
       33.93        83.01        29.98        14.07        49.48        38.40 
TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       34.98        38.37         7.30         9.01         8.81         8.91 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG 
       12.00         6.74         3.42        38.30        35.31        34.29 
TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13F 
       35.47        30.61        35.67        33.11        31.73        12.72 
TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H 
       23.61        29.56        31.36        24.26        23.74        23.80 
TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 
       21.73        20.61        22.32        11.34        10.59        10.29 
TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB 
       11.28        13.41        14.70        11.97        14.93        13.74 
TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX 
       14.50        21.17        14.73        12.10        10.72        11.05 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P 
       10.29         9.37        10.42         8.75        13.02        13.02 
TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y 
        1.02        17.98        41.06        29.03        31.00        26.01 
TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E 
        1.02        17.03        53.98         9.01        33.01        19.99 
TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07O TCGA-A8-A07P 
       18.97        18.97        14.01        12.00         9.99        10.98 
TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 
        8.98         7.99         9.96         9.99        28.04        18.05 
TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C 
       15.06        36.95        13.02         0.99        23.08        19.99 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O 
       18.05        19.96        12.00        37.05         9.99        31.00 
TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z 
       31.00         0.99        19.07        93.04        33.99        40.01 
TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A 
       19.07        16.01        17.95        41.98         9.99         9.99 
TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M 
       12.00         1.02        31.00        33.07        29.98        15.02 
TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
        1.02        25.02         8.98        19.04        15.02         0.99 
TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 
       14.01        12.00        19.04        13.02        21.04         0.99 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G 
       13.02        17.03        38.04         0.95         2.37        10.85 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF 
        2.66         1.48        38.53        38.20        40.57        55.43 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ 
       36.99        38.79        26.04         1.02         0.92         2.27 
TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W6 
        0.99         0.69        14.83         9.40         1.12         1.68 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y 
        1.55         1.32         1.55         0.07         1.12         1.81 
TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A03Y 
        1.18         0.69         0.43         1.74         0.33         0.33 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK 
        0.33         0.62         1.78         1.71         8.02         7.36 
TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FF 
        6.51         0.16         0.33         0.33         0.33         4.64 
TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT 
        7.96         7.00         7.59         7.17         6.28         6.02 
TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL 
        0.33         0.36         0.33         0.33         0.33         0.33 
TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT 
        0.33        12.33         0.30         0.33         0.33         0.33 
TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N 
        0.33         5.33         5.59        80.28        47.84        66.77 
TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J3 
       81.63        68.75        47.87        59.05        29.13        21.40 
TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0JB 
       17.65        24.16        37.48        20.32        22.36        50.70 
TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI 
       50.86        72.00        76.77        21.37        26.24        38.53 
TCGA-AO-A0JJ TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A 
       62.04        99.25        93.70        94.59        96.10        90.58 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
       77.56        64.04        57.30        48.36        41.62        28.37 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT 
       14.73        82.62        61.87        70.39         0.53        17.79 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N 
       24.79        26.93       130.09        15.62        13.22         2.56 
TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS 
       21.86         9.99        82.88        49.32         5.26        37.41 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TZ TCGA-AR-A0U0 
       56.88        29.75        24.30        64.83        76.14        65.36 
TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ 
       70.16        83.87        55.36        75.55        61.84        52.77 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP 
       51.25        48.82        62.56        43.73        43.56        39.98 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       43.07        17.23        40.83        46.32        42.58        35.24 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       36.26        20.22        73.02        65.46        68.19        65.69 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U 
        0.85        66.05        57.40        62.07        53.26        53.36 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 
       54.18        50.96        48.16        51.75        56.15        45.17 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH 
       40.64        39.85        34.82        93.83       128.65        20.25 
TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       42.87         7.36        40.04        17.10        20.81        16.96 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       20.38        54.74        16.04        20.45        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC 
      143.38       149.59        12.13       220.90       129.57        50.70 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IM TCGA-B6-A0IN 
       65.72       146.50       112.37       176.98       126.12        84.59 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL 
      110.14       110.93       211.56       189.01       234.28        81.17 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT 
       78.02       172.96       162.05       102.77       140.48        89.46 
TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX 
      131.21       157.41       188.68        79.63        17.98        21.47 
TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X7 
      113.79       129.57       129.70       186.48        28.27        58.88 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 
       43.59       101.52        73.51       139.17       170.17        85.35 
TCGA-B6-A402 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW 
       54.28        82.88        55.00        24.53        38.79        20.45 
TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 
       25.55        28.50        46.95        40.83        39.55        39.16 
TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
       48.36        56.94        51.68        37.22        32.02        18.21 
TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO 
       25.71        24.85        21.70        44.05        61.68        35.67 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW 
       48.69        27.19        53.95        45.57        49.94        11.67 
TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE 
       49.05        41.75        44.02        48.13        45.83        31.17 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP 
       38.01        22.13        13.91        48.23        17.26        15.65 
TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ 
        3.22         2.56        38.47        45.17        47.41        16.27 
TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 
        4.41        15.68        14.30         9.63        44.81        46.19 
TCGA-BH-A0EA TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       32.65        24.43        30.35        10.78        15.16        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB 
       35.51        24.56        23.08        41.00        52.96        26.50 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU 
       20.38         5.85         2.50        13.61        36.85        12.89 
TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A0W5 
       51.32        27.25        50.79         5.59        24.95        42.35 
TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J 
       44.81        23.05         8.81         2.01         7.23        20.12 
TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q 
       90.84        26.66        72.56        37.74        30.28        55.63 
TCGA-BH-A18R TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET 
       37.55        51.39        51.16        91.99       113.82        82.85 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 
       42.28        12.00        55.69        49.58        17.69        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FE 
       31.53        89.16        97.48       120.62       114.15        74.73 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN 
      122.89        36.92        63.35        55.00        45.63        72.07 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 
      144.59        72.07         6.90         0.72        38.60        83.31 
TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T 
       57.83       130.16        10.65         6.44        20.12         0.99 
TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O 
      109.28         8.94        11.93        11.77        11.77        12.66 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 
        0.07        12.66        12.66        12.66        12.66         3.12 
TCGA-C8-A131 TCGA-C8-A135 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ 
        1.78         0.62        12.33        10.92        11.34         0.16 
TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26X TCGA-C8-A26Y 
       12.03         2.30         3.25         0.30         0.36         0.43 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A 
        8.28         9.67         0.03         0.03         0.03        12.20 
TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A141 
        0.99         0.03         0.23        11.90        20.88        20.58 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1JA TCGA-D8-A1JB 
       13.97        14.17        21.14        19.20        16.50        18.71 
TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH 
       15.78        18.15        18.90        12.03        12.03        14.01 
TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN 
       18.97        20.09        20.12        20.09        19.40        20.38 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 
       21.01        12.20        13.32        14.70        18.58        17.79 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC 
       16.73        25.74        23.90        27.58        18.15         2.66 
TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL 
       17.16        15.22        14.73        21.83        14.50        19.92 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT 
       17.69         7.96        16.41        15.85        16.31         6.35 
TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 
       12.99        15.16        12.66        16.54        15.32        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G 
        3.81        14.24        14.14        17.42        16.04        13.45 
TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N 
       13.05        14.43         9.44        16.41        13.48         4.80 
TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 
        0.76        10.09        13.08        12.53        12.26        14.50 
TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A 
        7.33        43.00        34.42        27.52        46.59        40.41 
TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O 
       37.51        40.11        28.44        28.87        47.15        44.68 
TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U 
       40.96        38.24        38.60        33.17        33.30        43.33 
TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 
       32.02        31.96        28.60        17.03        25.41        27.12 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 
       23.24        19.43        21.04        23.87        14.79        25.05 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G 
       23.34        22.82        17.29        20.71        21.63        18.21 
TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O 
       12.92        17.42        19.40        20.58         7.73        13.02 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 
       19.56        17.06        14.07        14.99        60.53        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD 
       53.03        29.95        32.35        28.50        16.47        17.10 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       38.30        37.41        33.70        28.44        22.65         3.88 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 
       22.19        20.98        11.08        54.18        27.42        19.66 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK 
       24.59        40.47        28.90       106.75       102.61         8.75 
TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 
       16.93         5.52        15.72         7.20        18.05        22.26 
TCGA-E2-A574 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA 
       19.89        19.20        36.82        13.48        13.12        36.56 
TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI 
       39.55        12.59        35.77        20.05        21.57         9.86 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R6 
       11.90        14.30         0.62         2.10         6.12         2.76 
TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF 
       32.09        20.81        40.24         0.66        34.65         6.58 
TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 
       21.27        34.59        35.64        34.13         0.79        12.53 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H 
       13.32        39.09        22.75        12.89        23.51        24.10 
TCGA-E9-A243 TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A 
       17.06         0.85        27.22         1.94         0.95        12.56 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA 
        0.72        17.75         0.76        26.07        18.41         0.62 
TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE 
       15.72         0.23         0.39         0.26         0.23        15.39 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 
       12.20        39.72         8.48        18.21        18.90        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX 
       16.57        15.68        28.77        25.94        22.82        29.95 
TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 
       29.85        40.41        41.13        39.78        52.96        29.82 
TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB 
       23.11        18.48        30.08         7.86        18.90        19.99 
TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR 
        6.15        13.94        14.43        34.55        19.96        55.00 
TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A423 TCGA-GI-A2C8 
       52.73        25.91        22.09        21.27        10.16         7.40 
TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD 
      109.87        59.57       194.27        53.13        53.52        43.04 
TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       42.71        42.28        61.91        62.33        90.84        76.64 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL 
       77.33        53.36       110.50        38.20        32.28        69.30 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-LD-A66U 
       53.95        57.63        13.55        18.12        11.84         8.28 
TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL 
        6.67         4.60         2.99         3.58         6.90         5.56 
TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A6FR 
        4.70         3.65         3.19         3.25         2.63         3.88 
TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LQ-A4E4 
        4.14         4.50         4.50         5.59         3.22        15.91 
TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA 
        2.79         2.10        12.66        46.55         7.53        44.61 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A66H TCGA-OL-A66I 
       27.65        24.10        16.87        14.10        14.76        23.70 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-S3-A6ZG 
       54.51        33.90        31.07        18.21         7.23         6.81 
TCGA-W8-A86G 
        5.29 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             0.23              0.03 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           140.88            234.28 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            18.87             21.57 
[1] "0.2 - 140.9 (18.9)" "0.0 - 234.3 (21.6)"
[1] "hr=" "1.8"
D56V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8Q LOSS MUTATED         4        7        0        0        29        24
  8Q LOSS WILD-TYPE      76       70        9        9       306       200
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8Q LOSS MUTATED           0         10          2          4        0
  8Q LOSS WILD-TYPE         2        128         25         55       17
                   vv
clus                STAGE TIS STAGE X
  8Q LOSS MUTATED           0       1
  8Q LOSS WILD-TYPE         1      15
D56V3, multiclass
            clus
vv           8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                  4                76
  STAGE IA                 7                70
  STAGE IB                 0                 9
  STAGE II                 0                 9
  STAGE IIA               29               306
  STAGE IIB               24               200
  STAGE III                0                 2
  STAGE IIIA              10               128
  STAGE IIIB               2                25
  STAGE IIIC               4                55
  STAGE IV                 0                17
  STAGE TIS                0                 1
  STAGE X                  1                15
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  8Q LOSS MUTATED    16  54   9   2
  8Q LOSS WILD-TYPE 242 527 108  34
D56V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1              16               242
  T2              54               527
  T3               9               108
  T4               2                34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  8Q LOSS MUTATED    34  34   7   4
  8Q LOSS WILD-TYPE 434 296 104  66
D56V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0              34               434
  N1              34               296
  N2               7               104
  N3               4                66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  8Q LOSS MUTATED          0  68   0  13
  8Q LOSS WILD-TYPE        2 777  17 118
D56V6, multiclass
          clus
vv         8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CM0 (I+)               0                 2
  M0                    68               777
  M1                     0                17
  MX                    13               118
[1] 4 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    81   0
  8Q LOSS WILD-TYPE 903  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     81    0
  8Q LOSS WILD-TYPE  903   11
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE              81               903
  MALE                 0                11
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  8Q LOSS MUTATED                            0                            66
  8Q LOSS WILD-TYPE                          1                           669
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  8Q LOSS MUTATED                               11                   0
  8Q LOSS WILD-TYPE                            155                   5
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  8Q LOSS MUTATED                                  1                  1
  8Q LOSS WILD-TYPE                               28                 13
                   vv
clus                OTHER  SPECIFY
  8Q LOSS MUTATED                2
  8Q LOSS WILD-TYPE             42
D56V8, multiclass
                                  clus
vv                                 8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                 66               669
  INFILTRATING LOBULAR CARCINOMA                11               155
  MEDULLARY CARCINOMA                            0                 5
  MIXED HISTOLOGY (PLEASE SPECIFY)               1                28
  MUCINOUS CARCINOMA                             1                13
  OTHER  SPECIFY                                 2                42
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V9, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    17  64
  8Q LOSS WILD-TYPE 265 649
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     17   64
  8Q LOSS WILD-TYPE  265  649
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO               17               265
  YES              64               649
[1] 2 2
[1] FALSE
D56V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q LOSS MUTATED                                  0     9
  8Q LOSS WILD-TYPE                                1    47
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED                          18    50
  8Q LOSS WILD-TYPE                       119   658
D56V11, multiclass
                                  clus
vv                                 8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          9                47
  BLACK OR AFRICAN AMERICAN                     18               119
  WHITE                                         50               658
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V12, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     4  68
  8Q LOSS WILD-TYPE  32 728
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      4   68
  8Q LOSS WILD-TYPE   32  728
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                32
  NOT HISPANIC OR LATINO              68               728
[1] 2 2
[1] FALSE

Clustering(57) Variable = 9P LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED   253  38
  9P LOSS WILD-TYPE 607  76
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              291               683 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               38                76 
$`9P LOSS MUTATED`
TCGA-A1-A0SJ TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A0CT TCGA-A2-A0D0 TCGA-A2-A0EO 
       13.68        28.01        18.02        75.25        21.14        80.28 
TCGA-A2-A0EQ TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0T0 
       79.76        35.05        34.29        27.12        44.88        17.52 
TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX 
       18.21        21.90        21.67        23.77        17.36        36.79 
TCGA-A2-A1G1 TCGA-A2-A25B TCGA-A2-A25E TCGA-A2-A3XS TCGA-A2-A3XV TCGA-A2-A3XX 
       19.20        16.31        91.92        33.93        14.07        38.40 
TCGA-A2-A3XY TCGA-A2-A4S1 TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A13D 
       34.98        12.00        30.61        37.45        35.67        31.73 
TCGA-A7-A13F TCGA-A7-A26G TCGA-A7-A2KD TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SF 
       12.72        23.74        22.32        14.93        13.74        17.92 
TCGA-A7-A6VV TCGA-A8-A06O TCGA-A8-A06R TCGA-A8-A06U TCGA-A8-A06Z TCGA-A8-A075 
       10.29        13.02        17.98        29.03         1.02        17.03 
TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07G TCGA-A8-A07W TCGA-A8-A08G TCGA-A8-A08I 
        9.01        33.01        18.97         9.99        19.96        12.00 
TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A097 TCGA-A8-A09A 
       37.05        31.00        31.00         0.99        12.00         9.99 
TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09N 
       12.00         1.02        31.00        33.07        15.02         1.02 
TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09W TCGA-A8-A0A2 TCGA-A8-A0A6 
       25.02         8.98        19.04         0.99        19.04        21.04 
TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-AC-A2BM TCGA-AC-A2FF TCGA-AC-A2QH 
        0.99        13.02        17.03        38.20        55.43         1.02 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A62V TCGA-AC-A6IW TCGA-AC-A8OP TCGA-AN-A03X 
        0.92         2.27         0.07         0.69         1.74         0.33 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A0AJ 
        0.33         0.23         0.62         2.96         1.78         8.02 
TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0FJ TCGA-AN-A0FW TCGA-AN-A0FZ 
        7.36         6.51         0.16         7.96         0.36         0.33 
TCGA-AN-A0XS TCGA-AN-A0XU TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03O 
        0.33         0.33         5.59        80.28        66.77        81.63 
TCGA-AO-A03V TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0JA TCGA-AO-A0JD TCGA-AO-A0JE 
       29.13        17.65        24.16        21.53        72.00        76.77 
TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04L TCGA-AQ-A0Y5 
       48.36        61.87         0.53        17.79       130.09         5.65 
TCGA-AQ-A1H2 TCGA-AQ-A54O TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TV 
       15.62        21.86        49.32         5.26        37.41        29.75 
TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 
       55.86        76.14        65.36        70.16        83.87        76.18 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AW TCGA-AR-A24K 
       75.55        61.84        39.98        43.07        35.24        50.89 
TCGA-AR-A24N TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24Z 
       68.19        57.40        62.07        54.18        50.96        51.75 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A2LK TCGA-AR-A2LL TCGA-B6-A0I9 
       45.17        40.64        34.82        42.87         7.36        12.13 
TCGA-B6-A0IB TCGA-B6-A0IK TCGA-B6-A0IO TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0WV 
      129.57        18.77       110.14       162.05       102.77        79.63 
TCGA-B6-A0WW TCGA-B6-A401 TCGA-B6-A408 TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AZ 
       17.98        85.35        49.94        24.53        20.45        28.50 
TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0BF TCGA-BH-A0BL TCGA-BH-A0BP 
       39.55        48.36        56.98        25.71        44.05        48.69 
TCGA-BH-A0BR TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DI 
       53.69        49.94        11.67        48.13        42.90        22.13 
TCGA-BH-A0DK TCGA-BH-A0DQ TCGA-BH-A0E6 TCGA-BH-A0EB TCGA-BH-A0GY TCGA-BH-A0GZ 
       13.91         3.22         9.63        24.49        30.35        10.78 
TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HY TCGA-BH-A0W3 TCGA-BH-A18K 
       23.08        41.00        52.96        50.79        23.93        90.84 
TCGA-BH-A18L TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1EY 
       26.66         7.36        51.39        69.93       113.82        17.69 
TCGA-BH-A1F2 TCGA-BH-A1F8 TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FU TCGA-BH-A208 
       31.53        24.66        45.63        72.07        72.07        57.83 
TCGA-BH-A209 TCGA-BH-A42T TCGA-C8-A12L TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12U 
      130.16         0.99        11.93        12.66        11.77        12.66 
TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A137 TCGA-C8-A1HG 
       12.66        12.66         3.12         1.78         3.85        11.34 
TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A26V TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A27B 
       10.42         2.30         0.30         0.43         9.67         0.99 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A1JC TCGA-D8-A1JG 
       11.90        20.88        14.17        13.48        15.78        12.03 
TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JM TCGA-D8-A1X5 TCGA-D8-A1X6 
       18.97        20.09        20.12        19.40        18.58        17.79 
TCGA-D8-A1XA TCGA-D8-A1XD TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XY 
       27.58        17.16        16.41        16.31         6.35        16.54 
TCGA-D8-A1Y3 TCGA-D8-A27F TCGA-D8-A27N TCGA-D8-A27R TCGA-D8-A27W TCGA-E2-A109 
       14.14        16.04         4.80        10.09        12.26        46.59 
TCGA-E2-A14O TCGA-E2-A14R TCGA-E2-A14T TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Z 
       44.68        38.60        33.30        32.02        31.96        17.03 
TCGA-E2-A152 TCGA-E2-A15A TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15S 
       27.12        23.34        20.71        21.63        12.92        14.07 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A573 
       24.59        40.47       106.75       102.61         8.75        22.26 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R2 
       13.12        36.56        20.05         9.86        11.90         0.62 
TCGA-E9-A1R4 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RE 
        6.12         2.76        21.21        20.81        40.24        34.65 
TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A5UO 
       21.27        34.59        39.09        22.75        12.89         0.23 
TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1P3 TCGA-EW-A1P4 
       28.77        25.94        22.82        29.85        52.96        29.82 
TCGA-EW-A1P5 TCGA-EW-A1PA TCGA-EW-A1PD TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV 
       23.11        18.90        13.94        55.00        52.73        25.91 
TCGA-EW-A3E8 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C9 TCGA-GM-A2DB TCGA-JL-A3YX 
       21.27        10.16        10.59       109.87        53.13        11.57 
TCGA-LL-A441 TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-OL-A5D6 
        2.99         3.25         2.63         5.59         3.22        12.66 
TCGA-OL-A5RZ TCGA-OL-A66N TCGA-OL-A66P 
       10.29        18.21         4.44 

$`9P LOSS WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A1-A0SQ 
       20.88        31.79         7.96        39.32        19.20        18.21 
TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V 
      104.81        41.95        82.16        73.84        22.06        63.12 
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM 
       64.04        55.43        36.13       125.59        64.57        24.79 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CU 
      112.08        92.48        88.60       107.93        75.55         5.19 
TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 
       63.45        64.04        56.81        34.55        33.76        28.77 
TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES 
       25.22       101.72        89.36       107.61        74.40        37.05 
TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU 
       31.82        29.75        24.72        24.16        99.19        54.64 
TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 
       50.43        44.28        17.13         8.38        18.71        20.52 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF 
       17.46        18.90        20.75        32.55        25.28        15.42 
TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV 
       14.50        18.61        19.33        14.63        31.73        23.47 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A 
       22.45        20.25        19.56        16.47        52.47       107.70 
TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XT 
       17.19        18.15        10.59        20.88        39.65        83.01 
TCGA-A2-A3XU TCGA-A2-A3XW TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX 
       29.98        49.48        31.99        38.37         7.30         9.01 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE 
        8.81         8.91         6.74         3.42        38.30        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0DB TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H 
       34.29        35.47        33.11        10.72        23.61        29.56 
TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A3IY 
       31.36        24.26        23.80        21.73        20.61        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 
       10.59        10.29        11.28        13.41        14.70        11.97 
TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX 
       14.50        21.17        14.73        12.10        10.72        11.05 
TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06T 
        9.37        10.42         8.75        13.02         1.02        41.06 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A076 TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07I 
       31.00        26.01        53.98        19.99        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S 
       12.00        17.03         9.99        10.98         8.98         7.99 
TCGA-A8-A07U TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 
        9.96        28.04        18.05        15.06        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08L TCGA-A8-A08S 
        0.99        23.08        19.99        18.05         9.99        19.07 
TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 
       93.04        33.99        40.01        19.07        16.01        17.95 
TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09D TCGA-A8-A09K TCGA-A8-A09V TCGA-A8-A09X 
       41.98         9.99        13.02        29.98        15.02        14.01 
TCGA-A8-A0A1 TCGA-A8-A0A4 TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G 
       12.00        13.02        38.04         0.95         2.37        10.85 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2FB TCGA-AC-A2FG TCGA-AC-A2FK 
        2.66         1.48        38.53        40.57        36.99        38.79 
TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
       26.04        50.70         0.99         0.69        14.83         9.40 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS 
        1.12         1.81         1.68         1.55         1.32         1.55 
TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AN-A046 TCGA-AN-A04D 
        1.12         1.81         1.18         0.43         0.33         1.71 
TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK 
        0.33         0.33         0.33         6.44         4.64         7.00 
TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FX 
        7.59         7.17         6.28         6.02         0.33         0.33 
TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR 
        0.33         0.33         0.33        12.33         0.30         0.33 
TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AO-A03M TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T 
        0.33         5.33        47.84        84.69        68.75        47.87 
TCGA-AO-A03U TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 
       59.05        32.78        21.40        37.48        20.32        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI 
       53.03        50.70        50.86        21.37        26.24        38.53 
TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 
       62.04        55.33        71.80       102.58        99.25        93.70 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
       94.59        96.10        90.58        77.56        64.04        57.30 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AQ-A04H 
       41.62        28.37        14.73        82.62        70.39        24.79 
TCGA-AQ-A04J TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TT 
       26.93        13.22         2.56         9.99        82.88        56.88 
TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0U4 TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL 
       24.30        64.83        55.36        52.77        51.25        48.82 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU 
       62.56        43.73        43.56        17.23        40.83        46.32 
TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M 
       42.58        36.26        20.22       109.58        73.02        65.46 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X 
       65.69         0.85        66.05        53.26        53.36        48.16 
TCGA-AR-A250 TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LM 
       56.15        39.85        93.83       128.65        20.25        40.04 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN 
       17.10        20.81        16.96        20.38        54.74        16.04 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IA 
       20.45        10.59        77.62       143.38       149.59       220.90 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IM 
       50.70        65.72       146.50       112.37       176.98       126.12 
TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH 
       84.59       110.93       140.88       211.56        68.45       189.01 
TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RQ TCGA-B6-A0RS 
      234.28        81.17        78.02       172.96       140.48       100.70 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WX 
       89.46       131.21       157.41        97.48       188.68        21.47 
TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
      113.79       129.57       129.70       186.48        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU 
       58.88        43.59       101.52        73.51       139.17       170.17 
TCGA-B6-A402 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0B0 
       54.28        82.88        55.00        38.79        25.55        46.95 
TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC 
       40.83        39.16        56.94        51.68        37.22        32.02 
TCGA-BH-A0BD TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ 
       18.21        24.85        21.70        61.68        35.67        27.19 
TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0DD 
       53.95        45.57        49.05        41.75        44.02        45.83 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP 
       31.17        23.44        38.01        48.23        17.26        15.65 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
        2.56        38.47        45.17        47.41        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EE 
       15.68        14.30        44.81        46.19        32.65        31.00 
TCGA-BH-A0EI TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0HB 
       24.43        15.16        37.78        35.51        24.56        26.50 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU 
       20.38         5.85         2.50        13.61        36.85        12.89 
TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       51.32        27.25         5.59        24.95        42.35        44.81 
TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18M 
       23.05         8.81         2.01         7.23        20.12        72.56 
TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18V 
       37.74        30.28        55.63        37.55        66.05        51.16 
TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX 
       91.99        82.85        42.28        12.00        55.69        49.58 
TCGA-BH-A1F0 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD 
       25.81        89.16        97.48       120.62       114.15        33.17 
TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FR 
       74.73       122.89        36.92        63.35        55.00       144.59 
TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A28O TCGA-BH-A28Q 
        6.90         0.72        38.60        83.31        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12Q 
       20.12       109.28         8.94        11.77        11.77         0.07 
TCGA-C8-A12V TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HE 
       12.66         1.45         0.69         0.62         3.75        12.33 
TCGA-C8-A1HF TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HN TCGA-C8-A26W 
       10.92        11.34         0.16        12.03         3.25         0.23 
TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A 
        0.36         8.28         0.03         0.03         0.03        12.20 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A146 
        0.03         0.23        13.25        20.58        13.97        21.14 
TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JD 
       19.20        14.17        17.49        16.50        18.71        18.15 
TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JL TCGA-D8-A1JN TCGA-D8-A1JP 
       18.90        12.03        14.01        20.09        20.38        21.01 
TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 
       12.20        13.32        14.70        16.73        25.74        23.90 
TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK 
       18.15         2.66        15.22        14.73        21.83        14.50 
TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XU TCGA-D8-A1XV 
       19.92        17.69         7.96        15.85        12.99        15.16 
TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E 
       12.66        15.32        15.52         3.81        14.24        17.42 
TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M 
       13.45        13.05        14.43         9.44        16.41        13.48 
TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 
        0.76        13.08        12.53        14.50        18.51         7.33 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C 
       43.00        34.42        27.52        40.41        37.51        40.11 
TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14S 
       28.44        28.87        47.15        40.96        38.24        33.17 
TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 
       43.33        34.26        28.60        25.41        23.24        19.43 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15C TCGA-E2-A15D 
       21.04        23.87        14.79        25.05        22.82        17.29 
TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M 
       18.21        17.42        19.40         9.04        20.58         7.73 
TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 
       13.02        19.56        17.06        14.99        60.53        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD 
       53.03        29.95        32.35        28.50        16.47        17.10 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ 
       38.30        37.41        32.78        33.73        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       22.65         3.88        22.19        20.98        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LL 
       27.42        39.62        19.66        28.90        18.87        43.04 
TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A574 
       16.93         5.52        15.72         7.20        18.05        19.89 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1NC TCGA-E9-A1ND 
       19.20        36.82        13.48        12.00        39.55        12.59 
TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1R0 TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1RA 
       35.77        21.57        14.30         2.10         1.38        32.09 
TCGA-E9-A1RD TCGA-E9-A1RF TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 
        0.66         6.58        35.64        34.13         0.79        12.53 
TCGA-E9-A229 TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A245 
       13.32        23.51        24.10        17.06         0.69         0.85 
TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS 
       27.22         1.94         0.95        12.56         0.72        17.75 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54Y 
        0.76        26.07        18.41         0.62        15.72         0.23 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
        0.39         0.26        15.39        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OX 
       18.21        18.90        13.25        16.57        15.68        29.95 
TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 
       40.41        41.13        39.78        18.48        30.08         7.86 
TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH 
       19.99         6.15        10.52        14.43        34.55        19.96 
TCGA-EW-A2FW TCGA-EW-A3U0 TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DC 
       22.09        17.49         7.40        59.57       194.27        53.52 
TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       43.04        42.71        42.28        61.91        62.33        90.84 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
       76.64        77.33        53.36       110.50        38.20        32.28 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW 
       69.30        53.95        57.63        13.55        18.12        11.84 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y 
        8.28         6.67         4.60         0.66         3.58         6.90 
TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FR TCGA-LL-A73Y 
        5.56         4.70         3.65         3.19         3.88         4.14 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 
        4.50         4.50         6.21        15.91         2.79         2.10 
TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW 
       46.55         7.53        44.61        27.65        24.10        26.20 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J 
       16.87        14.10         9.80        14.76        23.70        54.51 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66O TCGA-S3-A6ZG TCGA-W8-A86G 
       33.90        31.07         7.23         6.81         5.29 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.07              0.03 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           162.05            234.28 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            21.04             21.83 
[1] "0.1 - 162.1 (21.0)" "0.0 - 234.3 (21.8)"
[1] "hr=" "1.6"
D57V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9P LOSS MUTATED        21       14        0        2       103        59
  9P LOSS WILD-TYPE      59       63        9        7       232       165
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9P LOSS MUTATED           1         48         16         17       10
  9P LOSS WILD-TYPE         1         90         11         42        7
                   vv
clus                STAGE TIS STAGE X
  9P LOSS MUTATED           0       5
  9P LOSS WILD-TYPE         1      11
D57V3, multiclass
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                 21                59
  STAGE IA                14                63
  STAGE IB                 0                 9
  STAGE II                 2                 7
  STAGE IIA              103               232
  STAGE IIB               59               165
  STAGE III                1                 1
  STAGE IIIA              48                90
  STAGE IIIB              16                11
  STAGE IIIC              17                42
  STAGE IV                10                 7
  STAGE TIS                0                 1
  STAGE X                  5                11
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  9P LOSS MUTATED    55 194  29  18
  9P LOSS WILD-TYPE 203 387  88  18
D57V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1              55               203
  T2             194               387
  T3              29                88
  T4              18                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  9P LOSS MUTATED   135  89  46  22
  9P LOSS WILD-TYPE 333 241  65  48
D57V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0             135               333
  N1              89               241
  N2              46                65
  N3              22                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  9P LOSS MUTATED          1 248  10  37
  9P LOSS WILD-TYPE        1 597   7  94
D57V6, multiclass
          clus
vv         9P LOSS MUTATED 9P LOSS WILD-TYPE
  CM0 (I+)               1                 1
  M0                   248               597
  M1                    10                 7
  MX                    37                94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED   290   6
  9P LOSS WILD-TYPE 694   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    290    6
  9P LOSS WILD-TYPE  694    5
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE             290               694
  MALE                 6                 5
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  9P LOSS MUTATED                            0                           252
  9P LOSS WILD-TYPE                          1                           483
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  9P LOSS MUTATED                               20                   3
  9P LOSS WILD-TYPE                            146                   2
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  9P LOSS MUTATED                                  9                  3
  9P LOSS WILD-TYPE                               20                 11
                   vv
clus                OTHER  SPECIFY
  9P LOSS MUTATED                9
  9P LOSS WILD-TYPE             35
D57V8, multiclass
                                  clus
vv                                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                252               483
  INFILTRATING LOBULAR CARCINOMA                20               146
  MEDULLARY CARCINOMA                            3                 2
  MIXED HISTOLOGY (PLEASE SPECIFY)               9                20
  MUCINOUS CARCINOMA                             3                11
  OTHER  SPECIFY                                 9                35
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V9, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    95 201
  9P LOSS WILD-TYPE 187 512
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     95  201
  9P LOSS WILD-TYPE  187  512
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               95               187
  YES             201               512
[1] 2 2
[1] FALSE
D57V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P LOSS MUTATED                                  0    20
  9P LOSS WILD-TYPE                                1    36
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED                          46   192
  9P LOSS WILD-TYPE                        91   516
D57V11, multiclass
                                  clus
vv                                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         20                36
  BLACK OR AFRICAN AMERICAN                     46                91
  WHITE                                        192               516
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V12, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    12 229
  9P LOSS WILD-TYPE  24 567
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     12  229
  9P LOSS WILD-TYPE   24  567
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                  12                24
  NOT HISPANIC OR LATINO             229               567
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9Q LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED   231  33
  9Q LOSS WILD-TYPE 629  81
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              264               710 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               33                81 
$`9Q LOSS MUTATED`
TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A04W TCGA-A2-A0CT 
       13.68         7.96        28.01        18.02        64.04        75.25 
TCGA-A2-A0D0 TCGA-A2-A0EO TCGA-A2-A0EQ TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0SX 
       21.14        80.28        79.76        35.05        34.29        50.43 
TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX 
       18.21        21.90        21.67        23.77        17.36        36.79 
TCGA-A2-A1G1 TCGA-A2-A3XS TCGA-A2-A3XV TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A4S1 
       19.20        33.93        14.07        38.40        34.98        12.00 
TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13F 
        3.42        35.31        37.45        35.67        31.73        12.72 
TCGA-A7-A26G TCGA-A7-A2KD TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A6VV 
       23.74        22.32        13.74        14.50        17.92        10.29 
TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06X TCGA-A8-A06Z 
       13.02         1.02        17.98        41.06        31.00         1.02 
TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07G TCGA-A8-A07R TCGA-A8-A08F TCGA-A8-A08I 
        9.01        33.01        18.97         8.98        18.05        12.00 
TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A097 
       37.05        31.00        31.00         0.99        33.99        12.00 
TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09T 
       12.00         1.02        33.07        15.02        25.02        19.04 
TCGA-A8-A0A2 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-AC-A2BM 
       19.04        21.04         0.99        13.02        17.03        38.20 
TCGA-AC-A2FF TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A62V TCGA-AC-A6IW 
       55.43         1.02         0.92         2.27         0.07         0.69 
TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A04A TCGA-AN-A04C 
        1.74         0.33         0.33         0.23         2.96         1.78 
TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0FJ TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XS 
        7.36         0.16         7.96         0.36         0.33         0.33 
TCGA-AN-A0XU TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03V 
        0.33         5.59        80.28        66.77        81.63        29.13 
TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0JD TCGA-AO-A0JL TCGA-AO-A12F 
       21.40        17.65        24.16        72.00        55.33        48.36 
TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04L TCGA-AQ-A0Y5 
       61.87        70.39         0.53        17.79       130.09         5.65 
TCGA-AQ-A1H2 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TY 
       15.62         2.56        21.86        49.32        37.41        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AI 
       76.14        65.36        70.16        76.18        75.55        61.84 
TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AW TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24N 
       39.98        43.07        35.24        20.22        50.89        68.19 
TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24V TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 
       57.40        62.07        54.18        51.75        45.17        40.64 
TCGA-AR-A2LK TCGA-AR-A2LL TCGA-B6-A0I9 TCGA-B6-A0IB TCGA-B6-A0IO TCGA-B6-A0RE 
       42.87         7.36        12.13       129.57       110.14       211.56 
TCGA-B6-A0RL TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX 
       81.17       162.05       102.77        79.63        17.98        21.47 
TCGA-B6-A1KC TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-BH-A0AU TCGA-BH-A0B3 
       43.59        85.35        54.28        49.94        24.53        39.55 
TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BF TCGA-BH-A0BL TCGA-BH-A0BT 
       48.36        56.98        51.68        25.71        44.05        45.57 
TCGA-BH-A0BV TCGA-BH-A0C3 TCGA-BH-A0DQ TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0EB 
       49.94        48.13         3.22         4.41         9.63        24.49 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0W3 
       30.35        10.78        23.08        41.00        52.96        23.93 
TCGA-BH-A18K TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1F8 
       90.84        55.63         7.36        69.93       113.82        24.66 
TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FU TCGA-BH-A208 
       33.17        74.73        45.63        72.07        72.07        57.83 
TCGA-BH-A209 TCGA-BH-A42T TCGA-C8-A12L TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12U 
      130.16         0.99        11.93        12.66        11.77        12.66 
TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A137 TCGA-C8-A1HJ 
       12.66        12.66         3.12         1.78         3.85         0.16 
TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A27B TCGA-D8-A13Z TCGA-D8-A143 TCGA-D8-A145 
        0.36         8.28         0.99        20.88        14.17        13.48 
TCGA-D8-A1JC TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1X5 TCGA-D8-A1X6 
       15.78        18.97        20.09        20.12        18.58        17.79 
TCGA-D8-A1XA TCGA-D8-A1XD TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1XY TCGA-D8-A1Y3 
       27.58        17.16        16.41        16.31        16.54        14.14 
TCGA-D8-A27F TCGA-D8-A27R TCGA-D8-A27W TCGA-E2-A109 TCGA-E2-A14O TCGA-E2-A14R 
       16.04        10.09        12.26        46.59        44.68        38.60 
TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A159 
       32.02        31.96        17.03        25.41        27.12        25.05 
TCGA-E2-A15A TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A1AZ TCGA-E2-A1LB TCGA-E2-A1LH 
       23.34        20.71        21.63        60.53        40.47       106.75 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A573 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC 
      102.61         8.75        22.26        13.12        36.56        39.55 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R4 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RC 
        9.86        11.90         6.12         2.76        21.21        40.24 
TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A22B TCGA-E9-A5UO TCGA-EW-A1J6 TCGA-EW-A1OV 
       21.27        34.59        22.75         0.23        28.77        25.94 
TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A2FR TCGA-EW-A2FS 
       22.82        29.85        52.96        23.11        55.00        52.73 
TCGA-EW-A2FV TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C9 
       25.91        21.27        17.49        10.16        10.59       109.87 
TCGA-GM-A2DB TCGA-JL-A3YX TCGA-LL-A441 TCGA-LL-A5YM TCGA-LL-A5YP TCGA-LL-A6FQ 
       53.13        11.57         2.99         4.70         3.25         2.63 
TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66N TCGA-OL-A66P 
        5.59         3.22        10.29         9.80        18.21         4.44 

$`9Q LOSS WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N 
       20.88        31.79        39.32        19.20        18.21       104.81 
TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04X 
       41.95        82.16        73.84        22.06        63.12        55.43 
TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
       36.13       125.59        64.57        24.79       112.08        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW 
       88.60       107.93        75.55         5.19        63.45        64.04 
TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM 
       56.81        34.55        33.76        28.77        25.22       101.72 
TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EV TCGA-A2-A0EW 
       89.36       107.61        74.40        37.05        31.82        29.75 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW 
       24.72        24.16        99.19        54.64        27.12        44.88 
TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 
       44.28        17.52        17.13         8.38        18.71        20.52 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF 
       17.46        18.90        20.75        32.55        25.28        15.42 
TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV 
       14.50        18.61        19.33        14.63        31.73        23.47 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A 
       22.45        20.25        19.56        16.47        52.47       107.70 
TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
       16.31        17.19        18.15        91.92        10.59        20.88 
TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XW TCGA-A2-A3XZ TCGA-A2-A3Y0 
       39.65        83.01        29.98        49.48        31.99        38.37 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A7-A0CD 
        7.30         9.01         8.81         8.91         6.74        38.30 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0DB TCGA-A7-A13E TCGA-A7-A13G 
       34.29        35.47        30.61        33.11        10.72        23.61 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J 
       29.56        31.36        24.26        23.80        21.73        20.61 
TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 
       11.34        10.59        10.29        11.28        13.41        14.70 
TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW 
       11.97        14.93        21.17        14.73        12.10        10.72 
TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06U 
       11.05         9.37        10.42         8.75        13.02        29.03 
TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07I 
       26.01        17.03        53.98        19.99        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U 
       12.00        17.03         9.99        10.98         7.99         9.96 
TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 
        9.99        28.04        18.05        15.06        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08L TCGA-A8-A08S 
        0.99        23.08        19.99        19.96         9.99        19.07 
TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 
       93.04        40.01        19.07        16.01        17.95        41.98 
TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09N 
        9.99         9.99        13.02        31.00        29.98         1.02 
TCGA-A8-A09R TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A4 
        8.98        15.02         0.99        14.01        12.00        13.02 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 
       38.04         0.95         2.37        10.85         2.66         1.48 
TCGA-AC-A2BK TCGA-AC-A2FB TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO 
       38.53        40.57        36.99        38.79        26.04        50.70 
TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 
        0.99         0.69        14.83         9.40         1.12         1.81 
TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62X TCGA-AC-A62Y 
        1.68         1.55         1.32         1.55         1.12         1.81 
TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04D TCGA-AN-A0AJ 
        1.18         0.43         0.33         0.62         1.71         8.02 
TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF 
        6.51         0.33         0.33         0.33         6.44         4.64 
TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV 
        7.00         7.59         7.17         6.28         6.02         0.33 
TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP 
        0.33         0.33         0.33         0.33        12.33         0.30 
TCGA-AN-A0XR TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AO-A03M TCGA-AO-A03P TCGA-AO-A03R 
        0.33         0.33         5.33        47.84        84.69        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A0J2 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 
       47.87        59.05        32.78        37.48        20.32        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF 
       53.03        21.53        50.70        50.86        76.77        21.37 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 
       26.24        38.53        62.04        71.80       102.58        99.25 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D 
       93.70        94.59        96.10        90.58        77.56        64.04 
TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AQ-A04H 
       57.30        41.62        28.37        14.73        82.62        24.79 
TCGA-AQ-A04J TCGA-AQ-A1H3 TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TT 
       26.93        13.22         9.99        82.88         5.26        56.88 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AJ 
       29.75        24.30        64.83        83.87        55.36        52.77 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AR 
       51.25        48.82        62.56        43.73        43.56        17.23 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A24H TCGA-AR-A24L 
       40.83        46.32        42.58        36.26       109.58        73.02 
TCGA-AR-A24M TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24T TCGA-AR-A24U 
       65.46        65.69         0.85        66.05        53.26        53.36 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
       50.96        48.16        56.15        39.85        34.82        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
      128.65        20.25        40.04        17.10        20.81        16.96 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       20.38        54.74        16.04        20.45        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG 
      143.38       149.59       220.90        50.70        65.72       146.50 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP 
      112.37       176.98        18.77       126.12        84.59       110.93 
TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN 
      140.88        68.45       189.01       234.28        78.02       172.96 
TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS 
      140.48       100.70        89.46       131.21       157.41        97.48 
TCGA-B6-A0WT TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
      188.68       113.79       129.57       129.70       186.48        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU 
       68.94        58.88       101.52        73.51       139.17       170.17 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ 
       82.88        55.00        38.79        20.45        25.55        28.50 
TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0BA TCGA-BH-A0BC 
       46.95        40.83        39.16        56.94        37.22        32.02 
TCGA-BH-A0BD TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP 
       18.21        24.85        21.70        61.68        35.67        48.69 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 
       27.19        53.69        53.95        11.67        49.05        41.75 
TCGA-BH-A0C1 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH 
       44.02        42.90        45.83        31.17        23.44        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DS 
       22.13        13.91        48.23        17.26        15.65         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 
       38.47        45.17        47.41        16.27        15.68        14.30 
TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0H0 
       44.81        46.19        32.65        31.00        24.43        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK 
       37.78        35.51        24.56        26.50        20.38         5.85 
TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX 
        2.50        13.61        36.85        12.89        51.32        27.25 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA 
       50.79         5.59        24.95        42.35        44.81        23.05 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18L TCGA-BH-A18M 
        8.81         2.01         7.23        20.12        26.66        72.56 
TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A18V 
       37.74        30.28        37.55        66.05        51.39        51.16 
TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX 
       91.99        82.85        42.28        12.00        55.69        49.58 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1FB 
       17.69        25.81        31.53        89.16        97.48       120.62 
TCGA-BH-A1FC TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FR 
      114.15       122.89        36.92        63.35        55.00       144.59 
TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A28O TCGA-BH-A28Q 
        6.90         0.72        38.60        83.31        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12Q 
       20.12       109.28         8.94        11.77        11.77         0.07 
TCGA-C8-A12V TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HE 
       12.66         1.45         0.69         0.62         3.75        12.33 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM 
       10.92        11.34        11.34        12.03        10.42         2.30 
TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A274 
        3.25         0.30         0.23         0.43         9.67         0.03 
TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y 
        0.03         0.03        12.20         0.03         0.23        11.90 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 
       13.25        20.58        13.97        21.14        19.20        14.17 
TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF 
       17.49        16.50        18.71        18.15        18.90        12.03 
TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP 
       12.03        14.01        20.09        19.40        20.38        21.01 
TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 
       12.20        13.32        14.70        16.73        25.74        23.90 
TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK 
       18.15         2.66        15.22        14.73        21.83        14.50 
TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XT TCGA-D8-A1XU 
       19.92        17.69         7.96        15.85         6.35        12.99 
TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 
       15.16        12.66        15.32        15.52         3.81        14.24 
TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       17.42        13.45        13.05        14.43         9.44        16.41 
TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 
       13.48         4.80         0.76        13.08        12.53        14.50 
TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10A 
       18.51         7.33        43.00        34.42        27.52        40.41 
TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P 
       37.51        40.11        28.44        28.87        47.15        40.96 
TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14Y 
       38.24        33.17        33.30        43.33        34.26        28.60 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15C 
       23.24        19.43        21.04        23.87        14.79        22.82 
TCGA-E2-A15D TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       17.29        18.21        12.92        17.42        19.40         9.04 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
       20.58         7.73        13.02        19.56        17.06        14.07 
TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       14.99        53.62        53.03        29.95        32.35        28.50 
TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       16.47        17.10        38.30        37.41        32.78        33.73 
TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO 
       33.70        28.44        22.65         3.88        22.19        20.98 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA 
       11.08        54.18        27.42        39.62        19.66        24.59 
TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX 
       28.90        18.87        43.04        16.93         5.52        15.72 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A574 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 
        7.20        18.05        19.89        19.20        36.82        13.48 
TCGA-E9-A1N8 TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1R0 
       12.00        12.59        35.77        20.05        21.57        14.30 
TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RD 
        0.62         2.10         1.38        32.09        20.81         0.66 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 
       34.65         6.58        35.64        34.13         0.79        12.53 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 
       13.32        39.09        12.89        23.51        24.10        17.06 
TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A 
        0.69         0.85        27.22         1.94         0.95        12.56 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA 
        0.72        17.75         0.76        26.07        18.41         0.62 
TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A6HE TCGA-EW-A1IW 
       15.72         0.23         0.39         0.26        15.39        12.20 
TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 
       39.72         8.48        18.21        18.90        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 
       15.68        29.95        40.41        41.13        39.78        29.82 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC 
       18.48        30.08         7.86        18.90        19.99         6.15 
TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FW 
       13.94        10.52        14.43        34.55        19.96        22.09 
TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF 
        7.40        59.57       194.27        53.52        43.04        42.71 
TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       42.28        61.91        62.33        90.84        76.64        77.33 
TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN 
       53.36       110.50        38.20        32.28        69.30        53.95 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-LD-A66U TCGA-LD-A74U 
       57.63        13.55        18.12        11.84         8.28         6.67 
TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN 
        4.60         0.66         3.58         6.90         5.56         3.65 
TCGA-LL-A5YO TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A8F5 
        3.19         3.88         4.14         4.50         4.50         6.21 
TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 
       15.91         2.79         2.10        12.66        46.55         7.53 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY 
       44.61        27.65        24.10        26.20        16.87        14.10 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66O 
       14.76        23.70        54.51        33.90        31.07         7.23 
TCGA-S3-A6ZG TCGA-W8-A86G 
        6.81         5.29 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.07              0.03 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           211.56            234.28 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           22.080            20.995 
[1] "0.1 - 211.6 (22.1)" "0.0 - 234.3 (21.0)"
[1] "hr=" "1.3"
D58V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9Q LOSS MUTATED        19       15        0        1        94        54
  9Q LOSS WILD-TYPE      61       62        9        8       241       170
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9Q LOSS MUTATED           1         42         12         18        7
  9Q LOSS WILD-TYPE         1         96         15         41       10
                   vv
clus                STAGE TIS STAGE X
  9Q LOSS MUTATED           0       5
  9Q LOSS WILD-TYPE         1      11
D58V3, multiclass
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                 19                61
  STAGE IA                15                62
  STAGE IB                 0                 9
  STAGE II                 1                 8
  STAGE IIA               94               241
  STAGE IIB               54               170
  STAGE III                1                 1
  STAGE IIIA              42                96
  STAGE IIIB              12                15
  STAGE IIIC              18                41
  STAGE IV                 7                10
  STAGE TIS                0                 1
  STAGE X                  5                11
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  9Q LOSS MUTATED    51 170  30  16
  9Q LOSS WILD-TYPE 207 411  87  20
D58V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1              51               207
  T2             170               411
  T3              30                87
  T4              16                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                 N0  N1  N2  N3
  9Q LOSS MUTATED   127  78  38  22
  9Q LOSS WILD-TYPE 341 252  73  48
D58V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0             127               341
  N1              78               252
  N2              38                73
  N3              22                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  9Q LOSS MUTATED          0 225   7  36
  9Q LOSS WILD-TYPE        2 620  10  95
D58V6, multiclass
          clus
vv         9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CM0 (I+)               0                 2
  M0                   225               620
  M1                     7                10
  MX                    36                95
[1] 4 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   262   6
  9Q LOSS WILD-TYPE 722   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED    262    6
  9Q LOSS WILD-TYPE  722    5
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE             262               722
  MALE                 6                 5
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  9Q LOSS MUTATED                            0                           225
  9Q LOSS WILD-TYPE                          1                           510
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  9Q LOSS MUTATED                               18                   2
  9Q LOSS WILD-TYPE                            148                   3
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  9Q LOSS MUTATED                                  9                  3
  9Q LOSS WILD-TYPE                               20                 11
                   vv
clus                OTHER  SPECIFY
  9Q LOSS MUTATED               11
  9Q LOSS WILD-TYPE             33
D58V8, multiclass
                                  clus
vv                                 9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                225               510
  INFILTRATING LOBULAR CARCINOMA                18               148
  MEDULLARY CARCINOMA                            2                 3
  MIXED HISTOLOGY (PLEASE SPECIFY)               9                20
  MUCINOUS CARCINOMA                             3                11
  OTHER  SPECIFY                                11                33
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V9, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    88 180
  9Q LOSS WILD-TYPE 194 533
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     88  180
  9Q LOSS WILD-TYPE  194  533
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO               88               194
  YES             180               533
[1] 2 2
[1] FALSE
D58V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q LOSS MUTATED                                  0    17
  9Q LOSS WILD-TYPE                                1    39
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED                          50   169
  9Q LOSS WILD-TYPE                        87   539
D58V11, multiclass
                                  clus
vv                                 9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         17                39
  BLACK OR AFRICAN AMERICAN                     50                87
  WHITE                                        169               539
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V12, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    11 207
  9Q LOSS WILD-TYPE  25 589
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     11  207
  9Q LOSS WILD-TYPE   25  589
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                  11                25
  NOT HISPANIC OR LATINO             207               589
[1] 2 2
[1] FALSE

Clustering(59) Variable = 10P LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED   135  22
  10P LOSS WILD-TYPE 725  92
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               157                817 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                22                 92 
$`10P LOSS MUTATED`
TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A2-A04T TCGA-A2-A0CS 
       13.68        31.79        39.32        19.20        73.84        75.55 
TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D4 TCGA-A2-A0YE 
       75.25         5.19        64.04        21.14        25.22        18.21 
TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A2-A4S3 
       17.36        36.79         7.30         9.01        12.00         3.42 
TCGA-A7-A0CJ TCGA-A7-A13F TCGA-A7-A26E TCGA-A7-A2KD TCGA-A7-A4SB TCGA-A7-A4SE 
       30.61        12.72        31.36        22.32        13.74        21.17 
TCGA-A8-A06R TCGA-A8-A076 TCGA-A8-A07I TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A08I 
       17.98        53.98        14.01        15.06        18.05        12.00 
TCGA-A8-A08L TCGA-A8-A097 TCGA-A8-A09B TCGA-A8-A09R TCGA-A8-A0A6 TCGA-A8-A0AB 
        9.99        12.00        12.00         8.98        21.04        17.03 
TCGA-A8-A0AD TCGA-AC-A23H TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A62Y 
       38.04         2.66         1.02         0.92         2.27         1.81 
TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AN-A049 TCGA-AN-A0AK TCGA-AN-A0AT TCGA-AN-A0FV 
        0.69         0.43         0.62         7.36         0.33         0.33 
TCGA-AN-A0FW TCGA-AN-A0XN TCGA-AN-A0XP TCGA-AN-A0XS TCGA-AN-A0XU TCGA-AO-A03M 
        0.36         0.33         0.30         0.33         0.33        47.84 
TCGA-AO-A03N TCGA-AO-A03U TCGA-AO-A0JD TCGA-AO-A12F TCGA-AR-A0TR TCGA-AR-A0TV 
       66.77        59.05        72.00        48.36         5.26        29.75 
TCGA-AR-A0U2 TCGA-AR-A1AN TCGA-AR-A24L TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24W 
       83.87        43.73        73.02        66.05        57.40        50.96 
TCGA-AR-A250 TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LK TCGA-AR-A2LO TCGA-AR-A2LR 
       56.15        39.85        93.83        42.87        20.81        20.38 
TCGA-AR-A5QQ TCGA-B6-A0IK TCGA-B6-A0RL TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A1KI 
       10.59        18.77        81.17       100.70       131.21        73.51 
TCGA-B6-A1KN TCGA-B6-A408 TCGA-BH-A0AU TCGA-BH-A0B3 TCGA-BH-A0B7 TCGA-BH-A0BA 
      139.17        49.94        24.53        39.55        56.98        37.22 
TCGA-BH-A0BJ TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C7 
       21.70        45.57        49.94        49.05        44.02        42.90 
TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HW TCGA-BH-A0WA 
       24.49        31.00        41.00        52.96        51.32        23.05 
TCGA-BH-A18I TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1EU TCGA-BH-A1F8 TCGA-BH-A1FH 
        7.23        51.16        91.99        42.28        24.66        36.92 
TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A202 TCGA-BH-A208 TCGA-C8-A12L TCGA-C8-A132 
       45.63        72.07         0.72        57.83        11.93         1.45 
TCGA-C8-A134 TCGA-C8-A138 TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HN TCGA-C8-A26V 
        0.69         3.75        11.34        12.03         3.25         0.30 
TCGA-C8-A26W TCGA-C8-A26Y TCGA-D8-A1J8 TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JK 
        0.23         0.43        14.17        18.90        12.03        20.12 
TCGA-D8-A1XB TCGA-D8-A1XQ TCGA-D8-A1XV TCGA-D8-A27F TCGA-D8-A27I TCGA-D8-A27T 
       18.15        16.41        15.16        16.04        14.43        13.08 
TCGA-E2-A10C TCGA-E2-A14T TCGA-E2-A14Z TCGA-E2-A15F TCGA-E2-A15R TCGA-E2-A15S 
       40.11        33.30        17.03        21.63        17.06        14.07 
TCGA-E2-A1IN TCGA-E2-A1L7 TCGA-E2-A1LG TCGA-E2-A56Z TCGA-E9-A1ND TCGA-E9-A1NF 
       22.19        27.42        18.87         7.20        12.59        20.05 
TCGA-E9-A1NI TCGA-E9-A1R3 TCGA-E9-A1RC TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A226 
        9.86         2.10        40.24         6.58        21.27        34.13 
TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A248 TCGA-E9-A54Y TCGA-E9-A5FK TCGA-EW-A1P5 
       22.75        12.89         1.94         0.23         0.39        23.11 
TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-GM-A3XL TCGA-LL-A7T0 TCGA-OL-A5RW TCGA-OL-A66I 
        7.86        18.90        69.30         3.22        26.20        23.70 
TCGA-S3-A6ZG 
        6.81 

$`10P LOSS WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P 
       20.88         7.96        28.01        18.21       104.81        18.02 
TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X 
       41.95        82.16        22.06        63.12        64.04        55.43 
TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
       36.13       125.59        64.57        24.79       112.08        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D2 
       88.60       107.93        63.45        56.81        34.55        33.76 
TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ 
       28.77       101.72        89.36        80.28       107.61        79.76 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW 
       74.40        37.05        35.05        34.29        31.82        29.75 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW 
       24.72        24.16        99.19        54.64        27.12        44.88 
TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 
       50.43        44.28        17.52        17.13         8.38        18.71 
TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD 
       20.52        17.46        18.90        20.75        32.55        25.28 
TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK 
       15.42        21.90        21.67        14.50        18.61        19.33 
TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FZ TCGA-A2-A1G0 
       14.63        31.73        23.77        23.47        22.45        20.25 
TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B 
       19.20        19.56        16.47        52.47       107.70        16.31 
TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD 
       17.19        18.15        91.92        10.59        20.88        39.65 
TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX 
       33.93        83.01        29.98        14.07        49.48        38.40 
TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 
       34.98        31.99        38.37         8.81         8.91         6.74 
TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DA 
       38.30        35.31        34.29        35.47        37.45        35.67 
TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26F 
       33.11        31.73        10.72        23.61        29.56        24.26 
TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ 
       23.74        23.80        21.73        20.61        11.34        10.59 
TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA 
       10.29        11.28        13.41        14.70        11.97        14.93 
TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX 
       14.50        17.92        14.73        12.10        10.72        11.05 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P 
       10.29         9.37        10.42         8.75        13.02        13.02 
TCGA-A8-A06Q TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z 
        1.02        41.06        29.03        31.00        26.01         1.02 
TCGA-A8-A075 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G 
       17.03         9.01        33.01        19.99        18.97        18.97 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S 
       12.00        17.03         9.99        10.98         8.98         7.99 
TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A086 
        9.96         9.99        28.04        18.05        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08O 
        0.99        23.08        19.99        19.96        37.05        31.00 
TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z 
       31.00         0.99        19.07        93.04        33.99        40.01 
TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A 
       19.07        16.01        17.95        41.98         9.99         9.99 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M 
        1.02        13.02        31.00        33.07        29.98        15.02 
TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X 
        1.02        25.02        19.04        15.02         0.99        14.01 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-AC-A23C 
       12.00        19.04        13.02         0.99        13.02         0.95 
TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB 
        2.37        10.85         1.48        38.53        38.20        40.57 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A3BB 
       55.43        36.99        38.79        26.04        50.70         0.99 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 
        0.69        14.83         9.40         1.12         1.81         1.68 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IV 
        1.55         1.32         1.55         0.07         1.12         1.18 
TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A04A 
        1.74         0.33         0.33         0.23         0.33         2.96 
TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR 
        1.78         1.71         8.02         6.51         0.16         0.33 
TCGA-AN-A0AS TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL 
        0.33         6.44         4.64         7.96         7.00         7.59 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ 
        7.17         6.28         6.02         0.33         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XO TCGA-AN-A0XR TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AN-A0XW 
        0.33        12.33         0.33         0.33         5.33         5.59 
TCGA-AO-A03L TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03V 
       80.28        81.63        84.69        68.75        47.87        29.13 
TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 
       32.78        21.40        17.65        24.16        37.48        20.32 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE 
       22.36        53.03        21.53        50.70        50.86        76.77 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM 
       21.37        26.24        38.53        62.04        55.33        71.80 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A 
      102.58        99.25        93.70        94.59        96.10        90.58 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
       77.56        64.04        57.30        41.62        28.37        14.73 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H 
       82.62        61.87        70.39         0.53        17.79        24.79 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N 
       26.93       130.09         5.65        15.62        13.22         2.56 
TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT 
       21.86         9.99        82.88        49.32        37.41        56.88 
TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 
       24.30        64.83        55.86        76.14        65.36        70.16 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK 
       76.18        55.36        75.55        61.84        52.77        51.25 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR 
       48.82        62.56        43.56        39.98        43.07        17.23 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY 
       40.83        46.32        42.58        35.24        36.26        20.22 
TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
      109.58        50.89        65.46        68.19        65.69         0.85 
TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24X TCGA-AR-A24Z 
       62.07        53.26        53.36        54.18        48.16        51.75 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LL 
       45.17        40.64        34.82       128.65        20.25         7.36 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP 
       40.04        17.10        16.96        54.74        16.04        20.45 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB 
       77.62       143.38       149.59        12.13       220.90       129.57 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IM 
       50.70        65.72       146.50       112.37       176.98       126.12 
TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG 
       84.59       110.14       110.93       140.88       211.56        68.45 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP 
      189.01       234.28        78.02       172.96       162.05       102.77 
TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV 
      140.48        89.46       157.41        97.48       188.68        79.63 
TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 
       17.98        21.47       113.79       129.57       129.70       186.48 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A2IU 
       28.27        68.94        58.88        43.59       101.52       170.17 
TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AW 
       85.35        54.28        82.88        55.00        38.79        20.45 
TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B5 
       25.55        28.50        46.95        40.83        39.16        48.36 
TCGA-BH-A0B6 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG 
       56.94        51.68        32.02        18.21        25.71        24.85 
TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR 
       44.05        61.68        35.67        48.69        27.19        53.69 
TCGA-BH-A0BS TCGA-BH-A0BW TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE 
       53.95        11.67        41.75        48.13        45.83        31.17 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO 
       23.44        38.01        22.13        13.91        48.23        17.26 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       15.65         3.22         2.56        38.47        45.17        47.41 
TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 
       16.27         4.41        15.68        14.30         9.63        44.81 
TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 
       46.19        32.65        24.43        30.35        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0HB TCGA-BH-A0HI 
       37.78        35.51        24.56        23.08        26.50        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HX 
        5.85         2.50        13.61        36.85        12.89        27.25 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       50.79         5.59        23.93        24.95        42.35        44.81 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M 
        8.81         2.01        20.12        90.84        26.66        72.56 
TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T 
       37.74        30.28        55.63        37.55        66.05         7.36 
TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EV TCGA-BH-A1EW 
       51.39        69.93       113.82        82.85        12.00        55.69 
TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 
       49.58        17.69        25.81        31.53        89.16        97.48 
TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FJ 
      120.62       114.15        33.17        74.73       122.89        63.35 
TCGA-BH-A1FL TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A204 
       55.00       144.59        72.07         6.90        38.60        83.31 
TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
      130.16        10.65         6.44        20.12         0.99       109.28 
TCGA-BH-A42V TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q 
        8.94        11.77        11.77        12.66        11.77         0.07 
TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A131 
       12.66        12.66        12.66        12.66         3.12         1.78 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ 
        0.62         3.85        12.33        10.92        11.34         0.16 
TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 
       10.42         2.30         0.36         8.28         9.67         0.03 
TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 
        0.03         0.03        12.20         0.99         0.03         0.23 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 
       11.90        20.88        13.25        20.58        13.97        14.17 
TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
       13.48        21.14        19.20        17.49        16.50        18.71 
TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ 
       15.78        18.15        12.03        14.01        18.97        20.09 
TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT 
       20.09        19.40        20.38        21.01        12.20        13.32 
TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 
       14.70        18.58        17.79        16.73        25.74        23.90 
TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ 
       27.58         2.66        17.16        15.22        14.73        21.83 
TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS 
       14.50        19.92        17.69         7.96        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 
        6.35        12.99        12.66        16.54        15.32        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27H 
        3.81        14.24        14.14        17.42        13.45        13.05 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R 
        9.44        16.41        13.48         4.80         0.76        10.09 
TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 
       12.53        12.26        14.50        18.51         7.33        43.00 
TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E 
       34.42        27.52        46.59        40.41        37.51        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R 
       28.87        47.15        44.68        40.96        38.24        38.60 
TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y 
       33.17        43.33        34.26        32.02        31.96        28.60 
TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 
       25.41        27.12        23.24        19.43        21.04        23.87 
TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E 
       14.79        25.05        23.34        22.82        17.29        20.71 
TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       18.21        12.92        17.42        19.40         9.04        20.58 
TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 
        7.73        13.02        19.56        14.99        60.53        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD 
       53.03        29.95        32.35        28.50        16.47        17.10 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ 
       38.30        37.41        32.78        33.73        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L8 
       22.65         3.88        20.98        11.08        54.18        39.62 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI 
       19.66        24.59        40.47        28.90       106.75       102.61 
TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 
        8.75        43.04        16.93         5.52        15.72        18.05 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 
       22.26        19.89        19.20        36.82        13.48        12.00 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1QZ 
       13.12        36.56        39.55        35.77        21.57        11.90 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 
       14.30         0.62         6.12         1.38         2.76        21.21 
TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RH TCGA-E9-A1RI 
       32.09        20.81         0.66        34.65        34.59        35.64 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22G TCGA-E9-A22H 
        0.79        12.53        13.32        39.09        23.51        24.10 
TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A24A 
       17.06         0.69         0.85        27.22         0.95        12.56 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA 
        0.72        17.75         0.76        26.07        18.41         0.62 
TCGA-E9-A3X8 TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
       15.72         0.26         0.23        15.39        12.20        39.72 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
        8.48        18.21        18.90        13.25        16.57        15.68 
TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ 
       28.77        25.94        22.82        29.95        29.85        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 
       41.13        39.78        52.96        29.82        18.48        30.08 
TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
       19.99         6.15        13.94        10.52        14.43        34.55 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 
       19.96        55.00        52.73        25.91        22.09        21.27 
TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 
       17.49        10.16        10.59         7.40       109.87        59.57 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH 
      194.27        53.13        53.52        43.04        42.71        42.28 
TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO 
       61.91        62.33        90.84        76.64        77.33        53.36 
TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV 
      110.50        38.20        32.28        53.95        57.63        13.55 
TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 
       18.12        11.84        11.57         8.28         6.67         4.60 
TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM 
        0.66         2.99         3.58         6.90         5.56         4.70 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y 
        3.65         3.19         3.25         2.63         3.88         4.14 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-MS-A51U 
        4.50         4.50         5.59         6.21        15.91         2.79 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.10        12.66        46.55         7.53        44.61        27.65 
TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H 
       24.10        16.87        14.10        10.29         9.80        14.76 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P 
       54.51        33.90        31.07        18.21         7.23         4.44 
TCGA-W8-A86G 
        5.29 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.23               0.03 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            139.17             234.28 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             20.05              21.90 
[1] "0.2 - 139.2 (20.1)" "0.0 - 234.3 (21.9)"
[1] "hr=" "1.7"
D59V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10P LOSS MUTATED         9        6        0        3        54        35
  10P LOSS WILD-TYPE      71       71        9        6       281       189
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10P LOSS MUTATED           1         32          6         11        2
  10P LOSS WILD-TYPE         1        106         21         48       15
                    vv
clus                 STAGE TIS STAGE X
  10P LOSS MUTATED           0       0
  10P LOSS WILD-TYPE         1      16
D59V3, multiclass
            clus
vv           10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                   9                 71
  STAGE IA                  6                 71
  STAGE IB                  0                  9
  STAGE II                  3                  6
  STAGE IIA                54                281
  STAGE IIB                35                189
  STAGE III                 1                  1
  STAGE IIIA               32                106
  STAGE IIIB                6                 21
  STAGE IIIC               11                 48
  STAGE IV                  2                 15
  STAGE TIS                 0                  1
  STAGE X                   0                 16
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  10P LOSS MUTATED    26 107  18   8
  10P LOSS WILD-TYPE 232 474  99  28
D59V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1               26                232
  T2              107                474
  T3               18                 99
  T4                8                 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                  N0  N1  N2  N3
  10P LOSS MUTATED    66  54  26  12
  10P LOSS WILD-TYPE 402 276  85  58
D59V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0               66                402
  N1               54                276
  N2               26                 85
  N3               12                 58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  10P LOSS MUTATED          1 146   2  10
  10P LOSS WILD-TYPE        1 699  15 121
D59V6, multiclass
          clus
vv         10P LOSS MUTATED 10P LOSS WILD-TYPE
  CM0 (I+)                1                  1
  M0                    146                699
  M1                      2                 15
  MX                     10                121
[1] 4 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   159   0
  10P LOSS WILD-TYPE 825  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED    159    0
  10P LOSS WILD-TYPE  825   11
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE              159                825
  MALE                  0                 11
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  10P LOSS MUTATED                            0                           124
  10P LOSS WILD-TYPE                          1                           611
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  10P LOSS MUTATED                               16                   0
  10P LOSS WILD-TYPE                            150                   5
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  10P LOSS MUTATED                                  7                  1
  10P LOSS WILD-TYPE                               22                 13
                    vv
clus                 OTHER  SPECIFY
  10P LOSS MUTATED               10
  10P LOSS WILD-TYPE             34
D59V8, multiclass
                                  clus
vv                                 10P LOSS MUTATED 10P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 124                611
  INFILTRATING LOBULAR CARCINOMA                 16                150
  MEDULLARY CARCINOMA                             0                  5
  MIXED HISTOLOGY (PLEASE SPECIFY)                7                 22
  MUCINOUS CARCINOMA                              1                 13
  OTHER  SPECIFY                                 10                 34
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V9, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    44 115
  10P LOSS WILD-TYPE 238 598
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     44  115
  10P LOSS WILD-TYPE  238  598
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                44                238
  YES              115                598
[1] 2 2
[1] FALSE
D59V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P LOSS MUTATED                                  0    12
  10P LOSS WILD-TYPE                                1    44
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED                          17   112
  10P LOSS WILD-TYPE                       120   596
D59V11, multiclass
                                  clus
vv                                 10P LOSS MUTATED 10P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          12                 44
  BLACK OR AFRICAN AMERICAN                      17                120
  WHITE                                         112                596
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V12, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     3 127
  10P LOSS WILD-TYPE  33 669
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      3  127
  10P LOSS WILD-TYPE   33  669
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 33
  NOT HISPANIC OR LATINO              127                669
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED   183  29
  10Q LOSS WILD-TYPE 677  85
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               212                762 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                29                 85 
$`10Q LOSS MUTATED`
TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A2-A04T TCGA-A2-A0CS 
       13.68        31.79        39.32        19.20        73.84        75.55 
TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D4 TCGA-A2-A0SV 
       75.25         5.19        64.04        21.14        25.22        27.12 
TCGA-A2-A0T0 TCGA-A2-A0T3 TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YJ TCGA-A2-A1FW 
       17.52        18.71        18.21        21.90        18.61        17.36 
TCGA-A2-A1FX TCGA-A2-A1G1 TCGA-A2-A25B TCGA-A2-A3XT TCGA-A2-A4RW TCGA-A2-A4RX 
       36.79        19.20        16.31        83.01         7.30         9.01 
TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13F 
       12.00         3.42        30.61        35.67        31.73        12.72 
TCGA-A7-A26E TCGA-A7-A2KD TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A56D 
       31.36        22.32        13.74        14.50        21.17        14.73 
TCGA-A7-A6VV TCGA-A8-A06R TCGA-A8-A06U TCGA-A8-A076 TCGA-A8-A07I TCGA-A8-A07R 
       10.29        17.98        29.03        53.98        14.01         8.98 
TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08X TCGA-A8-A097 
       15.06        18.05        12.00         9.99        33.99        12.00 
TCGA-A8-A09B TCGA-A8-A09E TCGA-A8-A09R TCGA-A8-A0A6 TCGA-A8-A0AB TCGA-A8-A0AD 
       12.00        31.00         8.98        21.04        17.03        38.04 
TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A62Y 
        0.95         2.66         1.02         0.92         2.27         1.81 
TCGA-AC-A6IW TCGA-AN-A0AK TCGA-AN-A0AT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0XN 
        0.69         7.36         0.33         0.33         0.36         0.33 
TCGA-AN-A0XP TCGA-AN-A0XS TCGA-AN-A0XU TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03N 
        0.30         0.33         0.33         5.59        47.84        66.77 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0JA TCGA-AO-A0JD TCGA-AO-A124 TCGA-AO-A12F 
       59.05        29.13        21.53        72.00       102.58        48.36 
TCGA-AQ-A04J TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TR TCGA-AR-A0TV TCGA-AR-A0TW 
       26.93        21.86         9.99         5.26        29.75        24.30 
TCGA-AR-A0U2 TCGA-AR-A1AY TCGA-AR-A24L TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24W 
       83.87        20.22        73.02        66.05        57.40        50.96 
TCGA-AR-A250 TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LO 
       56.15        39.85        93.83        42.87         7.36        20.81 
TCGA-AR-A2LR TCGA-AR-A5QQ TCGA-B6-A0IK TCGA-B6-A0RE TCGA-B6-A0RL TCGA-B6-A0RS 
       20.38        10.59        18.77       211.56        81.17       100.70 
TCGA-B6-A0RU TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A402 TCGA-B6-A408 TCGA-BH-A0AU 
      131.21        73.51       139.17        54.28        49.94        24.53 
TCGA-BH-A0AV TCGA-BH-A0B3 TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BJ TCGA-BH-A0BT 
       38.79        39.55        56.98        37.22        21.70        45.57 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0EB TCGA-BH-A0EE 
       49.94        11.67        49.05        44.02        24.49        31.00 
TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HW TCGA-BH-A0WA TCGA-BH-A18I 
       23.08        41.00        52.96        51.32        23.05         7.23 
TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1EU TCGA-BH-A1F6 TCGA-BH-A1F8 
        7.36        51.16        91.99        42.28        97.48        24.66 
TCGA-BH-A1FC TCGA-BH-A1FH TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A202 TCGA-BH-A208 
      114.15        36.92        45.63        72.07         0.72        57.83 
TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12U TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A138 
       11.93        11.77        12.66         1.45         0.69         3.75 
TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X 
       11.34        12.03         3.25         0.30         0.23         0.36 
TCGA-C8-A26Y TCGA-C8-A27A TCGA-D8-A13Y TCGA-D8-A142 TCGA-D8-A1J8 TCGA-D8-A1J9 
        0.43        12.20        11.90        13.97        14.17        17.49 
TCGA-D8-A1JG TCGA-D8-A1JK TCGA-D8-A1X5 TCGA-D8-A1XB TCGA-D8-A1XF TCGA-D8-A1XJ 
       12.03        20.12        18.58        18.15        15.22        21.83 
TCGA-D8-A1XQ TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A27F TCGA-D8-A27I TCGA-D8-A27T 
       16.41        12.99        15.16        16.04        14.43        13.08 
TCGA-E2-A10C TCGA-E2-A14N TCGA-E2-A14T TCGA-E2-A14Z TCGA-E2-A159 TCGA-E2-A15F 
       40.11        47.15        33.30        17.03        25.05        21.63 
TCGA-E2-A15P TCGA-E2-A1IE TCGA-E2-A1IN TCGA-E2-A1L7 TCGA-E2-A1LG TCGA-E2-A1LH 
       19.56        38.30        22.19        27.42        18.87       106.75 
TCGA-E2-A1LK TCGA-E2-A56Z TCGA-E2-A574 TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1NI 
        8.75         7.20        19.89        12.59        20.05         9.86 
TCGA-E9-A1R3 TCGA-E9-A1RC TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A226 TCGA-E9-A22B 
        2.10        40.24         6.58        21.27        34.13        22.75 
TCGA-E9-A22E TCGA-E9-A248 TCGA-E9-A2JS TCGA-E9-A54Y TCGA-E9-A5FK TCGA-EW-A1OW 
       12.89         1.94        17.75         0.23         0.39        22.82 
TCGA-EW-A1OZ TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A2FV TCGA-GM-A2DC 
       40.41        23.11         7.86        18.90        25.91        53.52 
TCGA-GM-A3XL TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-OL-A5RW 
       69.30        11.84        11.57         3.22         6.21        26.20 
TCGA-OL-A66I TCGA-S3-A6ZG 
       23.70         6.81 

$`10Q LOSS WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P 
       20.88         7.96        28.01        18.21       104.81        18.02 
TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X 
       41.95        82.16        22.06        63.12        64.04        55.43 
TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
       36.13       125.59        64.57        24.79       112.08        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D2 
       88.60       107.93        63.45        56.81        34.55        33.76 
TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ 
       28.77       101.72        89.36        80.28       107.61        79.76 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW 
       74.40        37.05        35.05        34.29        31.82        29.75 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SX 
       24.72        24.16        99.19        54.64        44.88        50.43 
TCGA-A2-A0SY TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       44.28        17.13         8.38        20.52        17.46        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YH TCGA-A2-A0YI 
       20.75        32.55        25.28        15.42        21.67        14.50 
TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FZ 
       19.33        14.63        31.73        23.77        23.47        22.45 
TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25C 
       20.25        19.56        16.47        52.47       107.70        17.19 
TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS 
       18.15        91.92        10.59        20.88        39.65        33.93 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ 
       29.98        14.07        49.48        38.40        34.98        31.99 
TCGA-A2-A3Y0 TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CE 
       38.37         8.81         8.91         6.74        38.30        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13E TCGA-A7-A13G 
       34.29        35.47        37.45        33.11        10.72        23.61 
TCGA-A7-A13H TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J 
       29.56        24.26        23.74        23.80        21.73        20.61 
TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 
       11.34        10.59        10.29        11.28        13.41        14.70 
TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX 
       11.97        14.93        17.92        12.10        10.72        11.05 
TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q 
        9.37        10.42         8.75        13.02        13.02         1.02 
TCGA-A8-A06T TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A079 
       41.06        31.00        26.01         1.02        17.03         9.01 
TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07J TCGA-A8-A07L 
       33.01        19.99        18.97        18.97        12.00        17.03 
TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z 
        9.99        10.98         7.99         9.96         9.99        28.04 
TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C 
       18.05        36.95        13.02         0.99        23.08        19.99 
TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S 
       19.96        37.05        31.00        31.00         0.99        19.07 
TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 
       93.04        40.01        19.07        16.01        17.95        41.98 
TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09I TCGA-A8-A09K 
        9.99         9.99         1.02        13.02        33.07        29.98 
TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
       15.02         1.02        25.02        19.04        15.02         0.99 
TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A7 TCGA-A8-A0A9 
       14.01        12.00        19.04        13.02         0.99        13.02 
TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB 
        2.37        10.85         1.48        38.53        38.20        40.57 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A3BB 
       55.43        36.99        38.79        26.04        50.70         0.99 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 
        0.69        14.83         9.40         1.12         1.81         1.68 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IV 
        1.55         1.32         1.55         0.07         1.12         1.18 
TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 
        0.43         1.74         0.33         0.33         0.23         0.33 
TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AL 
        0.62         2.96         1.78         1.71         8.02         6.51 
TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ 
        0.16         0.33         0.33         6.44         4.64         7.96 
TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FX 
        7.00         7.59         7.17         6.28         6.02         0.33 
TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XO TCGA-AN-A0XR TCGA-AN-A0XT 
        0.33         0.33         0.33        12.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AO-A03L TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T 
        5.33        80.28        81.63        84.69        68.75        47.87 
TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 
       32.78        21.40        17.65        24.16        37.48        20.32 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF 
       22.36        53.03        50.70        50.86        76.77        21.37 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A125 
       26.24        38.53        62.04        55.33        71.80        99.25 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D 
       93.70        94.59        96.10        90.58        77.56        64.04 
TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ 
       57.30        41.62        28.37        14.73        82.62        61.87 
TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04L TCGA-AQ-A0Y5 
       70.39         0.53        17.79        24.79       130.09         5.65 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS 
       15.62        13.22         2.56        82.88        49.32        37.41 
TCGA-AR-A0TT TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 
       56.88        64.83        55.86        76.14        65.36        70.16 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK 
       76.18        55.36        75.55        61.84        52.77        51.25 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ 
       48.82        62.56        43.73        43.56        39.98        43.07 
TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX 
       17.23        40.83        46.32        42.58        35.24        36.26 
TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
      109.58        50.89        65.46        68.19        65.69         0.85 
TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24X TCGA-AR-A24Z 
       62.07        53.26        53.36        54.18        48.16        51.75 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LM 
       45.17        40.64        34.82       128.65        20.25        40.04 
TCGA-AR-A2LN TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0I1 
       17.10        16.96        54.74        16.04        20.45        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC 
      143.38       149.59        12.13       220.90       129.57        50.70 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IM TCGA-B6-A0IN 
       65.72       146.50       112.37       176.98       126.12        84.59 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
      110.14       110.93       140.88        68.45       189.01       234.28 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT 
       78.02       172.96       162.05       102.77       140.48        89.46 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX 
      157.41        97.48       188.68        79.63        17.98        21.47 
TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
      113.79       129.57       129.70       186.48        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A40B 
       58.88        43.59       101.52       170.17        85.35        82.88 
TCGA-B6-A40C TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 
       55.00        20.45        25.55        28.50        46.95        40.83 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD 
       39.16        48.36        56.94        51.68        32.02        18.21 
TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP 
       25.71        24.85        44.05        61.68        35.67        48.69 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 
       27.19        53.69        53.95        41.75        48.13        42.90 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       45.83        31.17        23.44        38.01        22.13        13.91 
TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT 
       48.23        17.26        15.65         3.22         2.56        38.47 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 
       45.17        47.41        16.27         4.41        15.68        14.30 
TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EI TCGA-BH-A0GY 
        9.63        44.81        46.19        32.65        24.43        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0HB 
       10.78        15.16        37.78        35.51        24.56        26.50 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU 
       20.38         5.85         2.50        13.61        36.85        12.89 
TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 
       27.25        50.79         5.59        23.93        24.95        42.35 
TCGA-BH-A0W7 TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L 
       44.81         8.81         2.01        20.12        90.84        26.66 
TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S 
       72.56        37.74        30.28        55.63        37.55        66.05 
TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EV TCGA-BH-A1EW 
       51.39        69.93       113.82        82.85        12.00        55.69 
TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1FB 
       49.58        17.69        25.81        31.53        89.16       120.62 
TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FR 
       33.17        74.73       122.89        63.35        55.00       144.59 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A28O 
       72.07         6.90        38.60        83.31       130.16        10.65 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12N 
        6.44        20.12         0.99       109.28         8.94        11.77 
TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X 
       12.66        11.77         0.07        12.66        12.66        12.66 
TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF 
        3.12         1.78         0.62         3.85        12.33        10.92 
TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A26Z TCGA-C8-A273 
       11.34         0.16        10.42         2.30         8.28         9.67 
TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 
        0.03         0.03         0.03         0.99         0.03         0.23 
TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 
       20.88        13.25        20.58        14.17        13.48        21.14 
TCGA-D8-A147 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE 
       19.20        16.50        18.71        15.78        18.15        18.90 
TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JL TCGA-D8-A1JM 
       12.03        14.01        18.97        20.09        20.09        19.40 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X6 
       20.38        21.01        12.20        13.32        14.70        17.79 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD 
       16.73        25.74        23.90        27.58         2.66        17.16 
TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR 
       14.73        14.50        19.92        17.69         7.96        15.85 
TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 
       16.31         6.35        12.66        16.54        15.32        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27H 
        3.81        14.24        14.14        17.42        13.45        13.05 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R 
        9.44        16.41        13.48         4.80         0.76        10.09 
TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 
       12.53        12.26        14.50        18.51         7.33        43.00 
TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E 
       34.42        27.52        46.59        40.41        37.51        28.44 
TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S 
       28.87        44.68        40.96        38.24        38.60        33.17 
TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A150 
       43.33        34.26        32.02        31.96        28.60        25.41 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 
       27.12        23.24        19.43        21.04        23.87        14.79 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15H 
       23.34        22.82        17.29        20.71        18.21        12.92 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O 
       17.42        19.40         9.04        20.58         7.73        13.02 
TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 
       17.06        14.07        14.99        60.53        53.62        53.03 
TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IF 
       29.95        32.35        28.50        16.47        17.10        37.41 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       32.78        33.73        33.70        28.44        22.65         3.88 
TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA 
       20.98        11.08        54.18        39.62        19.66        24.59 
TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LI TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 
       40.47        28.90       102.61        43.04        16.93         5.52 
TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 
       15.72        18.05        22.26        19.20        36.82        13.48 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NG 
       12.00        13.12        36.56        39.55        35.77        21.57 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 
       11.90        14.30         0.62         6.12         1.38         2.76 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RH 
       21.21        32.09        20.81         0.66        34.65        34.59 
TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22G 
       35.64         0.79        12.53        13.32        39.09        23.51 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A249 
       24.10        17.06         0.69         0.85        27.22         0.95 
TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA 
       12.56         0.72         0.76        26.07        18.41         0.62 
TCGA-E9-A3X8 TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
       15.72         0.26         0.23        15.39        12.20        39.72 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
        8.48        18.21        18.90        13.25        16.57        15.68 
TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P1 
       28.77        25.94        29.95        29.85        41.13        39.78 
TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PB TCGA-EW-A1PC 
       52.96        29.82        18.48        30.08        19.99         6.15 
TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR 
       13.94        10.52        14.43        34.55        19.96        55.00 
TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 
       52.73        22.09        21.27        17.49        10.16        10.59 
TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DD 
        7.40       109.87        59.57       194.27        53.13        43.04 
TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       42.71        42.28        61.91        62.33        90.84        76.64 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN 
       77.33        53.36       110.50        38.20        32.28        53.95 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 
       57.63        13.55        18.12         8.28         6.67         4.60 
TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM 
        0.66         2.99         3.58         6.90         5.56         4.70 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y 
        3.65         3.19         3.25         2.63         3.88         4.14 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 
        4.50         4.50         5.59        15.91         2.79         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
       12.66        46.55         7.53        44.61        27.65        24.10 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J 
       16.87        14.10        10.29         9.80        14.76        54.51 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-W8-A86G 
       33.90        31.07        18.21         7.23         4.44         5.29 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.23               0.03 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            211.56             234.28 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            20.085             22.310 
[1] "0.2 - 211.6 (20.1)" "0.0 - 234.3 (22.3)"
[1] "hr=" "1.6"
D60V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10Q LOSS MUTATED        15       10        1        4        69        46
  10Q LOSS WILD-TYPE      65       67        8        5       266       178
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10Q LOSS MUTATED           1         38          7         17        3
  10Q LOSS WILD-TYPE         1        100         20         42       14
                    vv
clus                 STAGE TIS STAGE X
  10Q LOSS MUTATED           0       1
  10Q LOSS WILD-TYPE         1      15
D60V3, multiclass
            clus
vv           10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                  15                 65
  STAGE IA                 10                 67
  STAGE IB                  1                  8
  STAGE II                  4                  5
  STAGE IIA                69                266
  STAGE IIB                46                178
  STAGE III                 1                  1
  STAGE IIIA               38                100
  STAGE IIIB                7                 20
  STAGE IIIC               17                 42
  STAGE IV                  3                 14
  STAGE TIS                 0                  1
  STAGE X                   1                 15
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  10Q LOSS MUTATED    39 137  24  12
  10Q LOSS WILD-TYPE 219 444  93  24
D60V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1               39                219
  T2              137                444
  T3               24                 93
  T4               12                 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                  N0  N1  N2  N3
  10Q LOSS MUTATED    93  69  32  18
  10Q LOSS WILD-TYPE 375 261  79  52
D60V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0               93                375
  N1               69                261
  N2               32                 79
  N3               18                 52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  10Q LOSS MUTATED          1 193   3  16
  10Q LOSS WILD-TYPE        1 652  14 115
D60V6, multiclass
          clus
vv         10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CM0 (I+)                1                  1
  M0                    193                652
  M1                      3                 14
  MX                     16                115
[1] 4 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   212   1
  10Q LOSS WILD-TYPE 772  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED    212    1
  10Q LOSS WILD-TYPE  772   10
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE              212                772
  MALE                  1                 10
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  10Q LOSS MUTATED                            0                           170
  10Q LOSS WILD-TYPE                          1                           565
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  10Q LOSS MUTATED                               20                   1
  10Q LOSS WILD-TYPE                            146                   4
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  10Q LOSS MUTATED                                  7                  1
  10Q LOSS WILD-TYPE                               22                 13
                    vv
clus                 OTHER  SPECIFY
  10Q LOSS MUTATED               13
  10Q LOSS WILD-TYPE             31
D60V8, multiclass
                                  clus
vv                                 10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 170                565
  INFILTRATING LOBULAR CARCINOMA                 20                146
  MEDULLARY CARCINOMA                             1                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                7                 22
  MUCINOUS CARCINOMA                              1                 13
  OTHER  SPECIFY                                 13                 31
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V9, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    60 153
  10Q LOSS WILD-TYPE 222 560
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     60  153
  10Q LOSS WILD-TYPE  222  560
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                60                222
  YES              153                560
[1] 2 2
[1] FALSE
D60V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q LOSS MUTATED                                  0    18
  10Q LOSS WILD-TYPE                                1    38
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED                          35   139
  10Q LOSS WILD-TYPE                       102   569
D60V11, multiclass
                                  clus
vv                                 10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          18                 38
  BLACK OR AFRICAN AMERICAN                      35                102
  WHITE                                         139                569
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V12, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     3 175
  10Q LOSS WILD-TYPE  33 621
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      3  175
  10Q LOSS WILD-TYPE   33  621
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 33
  NOT HISPANIC OR LATINO              175                621
[1] 2 2
[1] FALSE

Clustering(61) Variable = 11P LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED   217  31
  11P LOSS WILD-TYPE 643  83
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               248                726 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                31                 83 
$`11P LOSS MUTATED`
TCGA-A1-A0SJ TCGA-A1-A0SN TCGA-A2-A04P TCGA-A2-A04T TCGA-A2-A0CO TCGA-A2-A0CX 
       13.68        39.32        18.02        73.84       112.08        56.81 
TCGA-A2-A0D1 TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ET TCGA-A2-A0SX TCGA-A2-A0T1 
       34.55        79.76        74.40        35.05        50.43        17.13 
TCGA-A2-A0YG TCGA-A2-A0YJ TCGA-A2-A0YT TCGA-A2-A1FX TCGA-A2-A25B TCGA-A2-A25E 
       21.90        18.61        23.77        36.79        16.31        91.92 
TCGA-A2-A3XS TCGA-A2-A3XX TCGA-A2-A3Y0 TCGA-A7-A0CE TCGA-A7-A0DA TCGA-A7-A13D 
       33.93        38.40        38.37        35.31        35.67        31.73 
TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A26E TCGA-A7-A4SA TCGA-A7-A4SE TCGA-A7-A56D 
       10.72        12.72        31.36        14.93        21.17        14.73 
TCGA-A7-A6VV TCGA-A8-A06O TCGA-A8-A06T TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07B 
       10.29        13.02        41.06         1.02         9.01        33.01 
TCGA-A8-A07I TCGA-A8-A07W TCGA-A8-A082 TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08J 
       14.01         9.99        18.05        18.05        19.96        37.05 
TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08X TCGA-A8-A093 
        9.99        31.00         0.99        19.07        33.99        17.95 
TCGA-A8-A097 TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09T 
       12.00        12.00         1.02        31.00        33.07        19.04 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0AB TCGA-AC-A23E TCGA-AC-A2BK TCGA-AC-A2BM 
       12.00        19.04        17.03         2.37        38.53        38.20 
TCGA-AC-A2FG TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A3W5 TCGA-AC-A6IW TCGA-AC-A6IX 
       36.99        26.04         1.02         1.81         0.69         0.43 
TCGA-AN-A041 TCGA-AN-A04A TCGA-AN-A0AL TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FW 
        0.23         2.96         6.51         6.28         6.02         0.36 
TCGA-AN-A0FZ TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AO-A03M TCGA-AO-A03P TCGA-AO-A0J7 
        0.33         0.33         0.33        47.84        84.69        20.32 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JL TCGA-AO-A12E TCGA-AO-A12F 
       53.03        21.53        50.70        55.33        57.30        48.36 
TCGA-AO-A12G TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0TT 
       41.62         0.53        17.79         2.56        21.86        56.88 
TCGA-AR-A0TV TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 
       29.75        76.14        65.36        83.87        76.18        55.36 
TCGA-AR-A1AK TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A24H TCGA-AR-A24R TCGA-AR-A24T 
       51.25        46.32        35.24       109.58        57.40        53.26 
TCGA-AR-A24Z TCGA-AR-A2LL TCGA-AR-A2LO TCGA-B6-A0I9 TCGA-B6-A0IE TCGA-B6-A0IG 
       51.75         7.36        20.81        12.13        65.72       146.50 
TCGA-B6-A0IK TCGA-B6-A0IO TCGA-B6-A0RU TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX 
       18.77       110.14       131.21        79.63        17.98        21.47 
TCGA-B6-A0X1 TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A402 TCGA-B6-A40B TCGA-BH-A0AV 
      186.48       101.52       139.17        54.28        82.88        38.79 
TCGA-BH-A0AY TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0BA TCGA-BH-A0BD TCGA-BH-A0BL 
       25.55        48.36        56.94        37.22        18.21        44.05 
TCGA-BH-A0BP TCGA-BH-A0BV TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 
       48.69        49.94        41.75        44.02        48.13        42.90 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0EE TCGA-BH-A0GZ TCGA-BH-A0H0 
       22.13        13.91        48.23        31.00        10.78        15.16 
TCGA-BH-A0H7 TCGA-BH-A0HA TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A18L TCGA-BH-A18P 
       23.08        52.96        27.25        50.79        26.66        30.28 
TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1F2 TCGA-BH-A1F8 
       55.63         7.36        69.93       113.82        31.53        24.66 
TCGA-BH-A1FC TCGA-BH-A203 TCGA-BH-A28Q TCGA-BH-A42T TCGA-C8-A12L TCGA-C8-A12M 
      114.15        38.60         6.44         0.99        11.93        11.77 
TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12W TCGA-C8-A132 TCGA-C8-A135 
       11.77         0.07        12.66        12.66         1.45         0.62 
TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HN 
        3.75        10.92        11.34        11.34        12.03         3.25 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A278 TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A142 
        0.36         0.43         0.03        11.90        20.88        13.97 
TCGA-D8-A145 TCGA-D8-A1J8 TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JI 
       13.48        14.17        15.78        18.15        18.90        18.97 
TCGA-D8-A1JK TCGA-D8-A1X6 TCGA-D8-A1XJ TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XW 
       20.12        17.79        21.83        16.31        12.99        12.66 
TCGA-D8-A1XZ TCGA-D8-A27G TCGA-D8-A27R TCGA-D8-A27W TCGA-E2-A105 TCGA-E2-A109 
       15.32        13.45        10.09        12.26        43.00        46.59 
TCGA-E2-A10C TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A158 
       40.11        38.60        31.96        17.03        27.12        14.79 
TCGA-E2-A159 TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A1BD TCGA-E2-A1IG TCGA-E2-A1IH 
       25.05        20.71        18.21        17.10        32.78        33.73 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LA TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK 
       27.42        39.62        24.59       106.75       102.61         8.75 
TCGA-E2-A1LL TCGA-E2-A573 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1ND TCGA-E9-A1NF 
       43.04        22.26        13.12        36.56        12.59        20.05 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A228 TCGA-E9-A22B 
        6.58        21.27        34.59        35.64        12.53        22.75 
TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A3HO TCGA-E9-A3QA TCGA-E9-A5UO TCGA-EW-A1OZ 
       12.89        23.51        26.07         0.62         0.23        40.41 
TCGA-EW-A1P4 TCGA-EW-A1PC TCGA-EW-A1PF TCGA-EW-A2FR TCGA-GM-A2DI TCGA-GM-A2DO 
       29.82         6.15        14.43        55.00        61.91        53.36 
TCGA-GM-A3XL TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A7T0 TCGA-LL-A8F5 
       69.30         4.70         3.19         3.25         3.22         6.21 
TCGA-LQ-A4E4 TCGA-OL-A5D6 TCGA-OL-A5RW TCGA-OL-A5RZ TCGA-OL-A66J TCGA-OL-A66K 
       15.91        12.66        26.20        10.29        54.51        33.90 
TCGA-OL-A66O TCGA-S3-A6ZG 
        7.23         6.81 

$`11P LOSS WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ 
       20.88        31.79         7.96        28.01        19.20        18.21 
TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W 
      104.81        41.95        82.16        22.06        63.12        64.04 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CP 
       55.43        36.13       125.59        64.57        24.79        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV 
       88.60       107.93        75.55        75.25         5.19        63.45 
TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM 
       64.04        21.14        33.76        28.77        25.22       101.72 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ES TCGA-A2-A0EU TCGA-A2-A0EV 
       89.36        80.28       107.61        37.05        34.29        31.82 
TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV 
       29.75        24.72        24.16        99.19        54.64        27.12 
TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 
       44.88        44.28        17.52         8.38        18.71        20.52 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE 
       17.46        18.90        20.75        32.55        25.28        18.21 
TCGA-A2-A0YF TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       15.42        21.67        14.50        19.33        14.63        31.73 
TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 
       23.47        17.36        22.45        20.25        19.20        19.56 
TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25F 
       16.47        52.47       107.70        17.19        18.15        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW 
       20.88        39.65        83.01        29.98        14.07        49.48 
TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       34.98        31.99         7.30         9.01         8.81         8.91 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH 
       12.00         6.74         3.42        38.30        34.29        35.47 
TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26F 
       30.61        37.45        33.11        23.61        29.56        24.26 
TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY 
       23.74        23.80        21.73        20.61        22.32        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 
       10.59        10.29        11.28        13.41        14.70        11.97 
TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX 
       13.74        14.50        17.92        12.10        10.72        11.05 
TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R 
        9.37        10.42         8.75        13.02         1.02        17.98 
TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07E 
       29.03        31.00        26.01        17.03        53.98        19.99 
TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P 
       18.97        18.97        12.00        17.03         9.99        10.98 
TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A085 
        8.98         7.99         9.96        28.04        15.06        36.95 
TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08I TCGA-A8-A08O 
       13.02         0.99        23.08        19.99        12.00        31.00 
TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A099 
       93.04        40.01        19.07        16.01        41.98         9.99 
TCGA-A8-A09A TCGA-A8-A09D TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q 
        9.99        13.02        29.98        15.02         1.02        25.02 
TCGA-A8-A09R TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A4 TCGA-A8-A0A6 
        8.98        15.02         0.99        14.01        13.02        21.04 
TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A23H 
        0.99        13.02        38.04         0.95        10.85         2.66 
TCGA-AC-A2B8 TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QI 
        1.48        40.57        55.43        38.79        50.70         0.92 
TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN 
        2.27         0.99         0.69        14.83         9.40         1.12 
TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X 
        1.68         1.55         1.32         1.55         0.07         1.12 
TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A046 
        1.81         1.18         1.74         0.33         0.33         0.33 
TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AM 
        0.62         1.78         1.71         8.02         7.36         0.16 
TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ 
        0.33         0.33         0.33         6.44         4.64         7.96 
TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0FY 
        7.00         7.59         7.17         0.33         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XU 
        0.33         0.33        12.33         0.30         0.33         0.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03R 
        5.33         5.59        80.28        66.77        81.63        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 
       47.87        59.05        29.13        32.78        21.40        17.65 
TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE 
       24.16        37.48        22.36        50.86        72.00        76.77 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A124 
       21.37        26.24        38.53        62.04        71.80       102.58 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B 
       99.25        93.70        94.59        96.10        90.58        77.56 
TCGA-AO-A12D TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR 
       64.04        28.37        14.73        82.62        61.87        70.39 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       24.79        26.93       130.09         5.65        15.62        13.22 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TW 
        9.99        82.88        49.32         5.26        37.41        24.30 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0U1 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ 
       64.83        55.86        70.16        75.55        61.84        52.77 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ 
       48.82        62.56        43.73        43.56        39.98        43.07 
TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K 
       17.23        40.83        42.58        36.26        20.22        50.89 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q 
       73.02        65.46        68.19        65.69         0.85        66.05 
TCGA-AR-A24S TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A250 
       62.07        53.36        54.18        50.96        48.16        56.15 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE 
       45.17        40.64        39.85        34.82        93.83       128.65 
TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ TCGA-AR-A2LR 
       20.25        42.87        40.04        17.10        16.96        20.38 
TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 
       54.74        16.04        20.45        10.59        77.62       143.38 
TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IH TCGA-B6-A0IJ 
      149.59       220.90       129.57        50.70       112.37       176.98 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG 
      126.12        84.59       110.93       140.88       211.56        68.45 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
      189.01       234.28        81.17        78.02       172.96       162.05 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS 
      102.77       140.48       100.70        89.46       157.41        97.48 
TCGA-B6-A0WT TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 
      188.68       113.79       129.57       129.70        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A408 
       58.88        43.59        73.51       170.17        85.35        49.94 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 
       55.00        24.53        20.45        28.50        46.95        40.83 
TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BF 
       39.55        39.16        56.98        51.68        32.02        25.71 
TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR 
       24.85        21.70        61.68        35.67        27.19        53.69 
TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0DD TCGA-BH-A0DE 
       53.95        45.57        11.67        49.05        45.83        31.17 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS 
       23.44        38.01        17.26        15.65         3.22         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 
       38.47        45.17        47.41        16.27         4.41        15.68 
TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB 
       14.30         9.63        44.81        46.19        32.65        24.49 
TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 
       24.43        30.35        37.78        35.51        24.56        41.00 
TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ 
       26.50        20.38         5.85         2.50        13.61        36.85 
TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 
       12.89        51.32         5.59        23.93        24.95        42.35 
TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J 
       44.81        23.05         8.81         2.01         7.23        20.12 
TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U 
       90.84        72.56        37.74        37.55        66.05        51.39 
TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW 
       51.16        91.99        82.85        42.28        12.00        55.69 
TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1FB 
       49.58        17.69        25.81        89.16        97.48       120.62 
TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
       33.17        74.73       122.89        36.92        63.35        55.00 
TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 
       45.63        72.07       144.59        72.07         6.90         0.72 
TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A2L8 TCGA-BH-A42U 
       83.31        57.83       130.16        10.65        20.12       109.28 
TCGA-BH-A42V TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A130 
        8.94        11.77        12.66        12.66        12.66         3.12 
TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HJ TCGA-C8-A1HL 
        1.78         0.69         3.85        12.33         0.16        10.42 
TCGA-C8-A1HM TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 
        2.30         0.30         0.23         8.28         9.67         0.03 
TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A140 
        0.03        12.20         0.99         0.03         0.23        13.25 
TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA 
       20.58        14.17        21.14        19.20        17.49        16.50 
TCGA-D8-A1JB TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JJ TCGA-D8-A1JL 
       18.71        12.03        12.03        14.01        20.09        20.09 
TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU 
       19.40        20.38        21.01        12.20        13.32        14.70 
TCGA-D8-A1X5 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB 
       18.58        16.73        25.74        23.90        27.58        18.15 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XL 
        2.66        17.16        15.22        14.73        14.50        19.92 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XT TCGA-D8-A1XV 
       17.69         7.96        16.41        15.85         6.35        15.16 
TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E 
       16.54        15.52         3.81        14.24        14.14        17.42 
TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M 
       16.04        13.05        14.43         9.44        16.41        13.48 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 
        4.80         0.76        13.08        12.53        14.50        18.51 
TCGA-D8-A4Z1 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E 
        7.33        34.42        27.52        40.41        37.51        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14S 
       28.87        47.15        44.68        40.96        38.24        33.17 
TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A150 
       33.30        43.33        34.26        32.02        28.60        25.41 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15A TCGA-E2-A15C 
       23.24        19.43        21.04        23.87        23.34        22.82 
TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       17.29        21.63        12.92        17.42        19.40         9.04 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
       20.58         7.73        13.02        19.56        17.06        14.07 
TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       14.99        60.53        53.62        53.03        29.95        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1II TCGA-E2-A1IJ 
       28.50        16.47        38.30        37.41        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       22.65         3.88        22.19        20.98        11.08        54.18 
TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-E2-A2P6 
       19.66        40.47        28.90        18.87        16.93         5.52 
TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A574 TCGA-E9-A1N4 TCGA-E9-A1N5 
       15.72         7.20        18.05        19.89        19.20        36.82 
TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NI 
       13.48        12.00        39.55        35.77        21.57         9.86 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 
       11.90        14.30         0.62         2.10         6.12         1.38 
TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD 
        2.76        21.21        32.09        20.81        40.24         0.66 
TCGA-E9-A1RE TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22H 
       34.65        34.13         0.79        13.32        39.09        24.10 
TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 
       17.06         0.69         0.85        27.22         1.94         0.95 
TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3X8 
       12.56         0.72        17.75         0.76        18.41        15.72 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
        0.23         0.39         0.26        15.39        12.20        39.72 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
        8.48        18.21        18.90        13.25        16.57        15.68 
TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1P0 
       28.77        25.94        22.82        29.95        29.85        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 
       39.78        52.96        23.11        18.48        30.08         7.86 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PG TCGA-EW-A1PH 
       18.90        19.99        13.94        10.52        34.55        19.96 
TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 
       52.73        25.91        22.09        21.27        17.49        10.16 
TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       10.59         7.40       109.87        59.57       194.27        53.13 
TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DK TCGA-GM-A2DL 
       53.52        43.04        42.71        42.28        62.33        90.84 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN 
       76.64        77.33       110.50        38.20        32.28        53.95 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U 
       57.63        13.55        18.12        11.84        11.57         8.28 
TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y 
        6.67         4.60         0.66         2.99         3.58         6.90 
TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z 
        5.56         3.65         2.63         3.88         4.14         4.50 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D7 TCGA-OL-A5D8 
        4.50         5.59         2.79         2.10        46.55         7.53 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5S0 
       44.61        27.65        24.10        16.87        14.10         9.80 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66P TCGA-W8-A86G 
       14.76        23.70        31.07        18.21         4.44         5.29 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.03               0.03 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            186.48             234.28 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             21.68              21.32 
[1] "0.0 - 186.5 (21.7)" "0.0 - 234.3 (21.3)"
[1] "hr=" "1.3"
D61V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11P LOSS MUTATED        18       13        2        2        86        51
  11P LOSS WILD-TYPE      62       64        7        7       249       173
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11P LOSS MUTATED           0         46         12         14        4
  11P LOSS WILD-TYPE         2         92         15         45       13
                    vv
clus                 STAGE TIS STAGE X
  11P LOSS MUTATED           1       4
  11P LOSS WILD-TYPE         0      12
D61V3, multiclass
            clus
vv           11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  18                 62
  STAGE IA                 13                 64
  STAGE IB                  2                  7
  STAGE II                  2                  7
  STAGE IIA                86                249
  STAGE IIB                51                173
  STAGE III                 0                  2
  STAGE IIIA               46                 92
  STAGE IIIB               12                 15
  STAGE IIIC               14                 45
  STAGE IV                  4                 13
  STAGE TIS                 1                  0
  STAGE X                   4                 12
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  11P LOSS MUTATED    57 153  27  15
  11P LOSS WILD-TYPE 201 428  90  21
D61V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1               57                201
  T2              153                428
  T3               27                 90
  T4               15                 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                  N0  N1  N2  N3
  11P LOSS MUTATED   112  80  41  16
  11P LOSS WILD-TYPE 356 250  70  54
D61V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0              112                356
  N1               80                250
  N2               41                 70
  N3               16                 54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  11P LOSS MUTATED          0 219   4  30
  11P LOSS WILD-TYPE        2 626  13 101
D61V6, multiclass
          clus
vv         11P LOSS MUTATED 11P LOSS WILD-TYPE
  CM0 (I+)                0                  2
  M0                    219                626
  M1                      4                 13
  MX                     30                101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED   251   2
  11P LOSS WILD-TYPE 733   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED    251    2
  11P LOSS WILD-TYPE  733    9
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE              251                733
  MALE                  2                  9
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  11P LOSS MUTATED                            0                           198
  11P LOSS WILD-TYPE                          1                           537
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  11P LOSS MUTATED                               32                   3
  11P LOSS WILD-TYPE                            134                   2
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  11P LOSS MUTATED                                  9                  2
  11P LOSS WILD-TYPE                               20                 12
                    vv
clus                 OTHER  SPECIFY
  11P LOSS MUTATED                9
  11P LOSS WILD-TYPE             35
D61V8, multiclass
                                  clus
vv                                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 198                537
  INFILTRATING LOBULAR CARCINOMA                 32                134
  MEDULLARY CARCINOMA                             3                  2
  MIXED HISTOLOGY (PLEASE SPECIFY)                9                 20
  MUCINOUS CARCINOMA                              2                 12
  OTHER  SPECIFY                                  9                 35
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V9, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    76 177
  11P LOSS WILD-TYPE 206 536
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     76  177
  11P LOSS WILD-TYPE  206  536
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                76                206
  YES              177                536
[1] 2 2
[1] FALSE
D61V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P LOSS MUTATED                                  1    17
  11P LOSS WILD-TYPE                                0    39
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED                          48   158
  11P LOSS WILD-TYPE                        89   550
D61V11, multiclass
                                  clus
vv                                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                          17                 39
  BLACK OR AFRICAN AMERICAN                      48                 89
  WHITE                                         158                550
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V12, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     4 196
  11P LOSS WILD-TYPE  32 600
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      4  196
  11P LOSS WILD-TYPE   32  600
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 32
  NOT HISPANIC OR LATINO              196                600
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED   299  32
  11Q LOSS WILD-TYPE 561  82
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               331                643 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                32                 82 
$`11Q LOSS MUTATED`
TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SQ 
       14.37        43.43        13.68         7.96        39.32        18.21 
TCGA-A2-A04P TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04V TCGA-A2-A0CK TCGA-A2-A0CM 
       18.02        82.16        73.84        63.12       125.59        24.79 
TCGA-A2-A0CO TCGA-A2-A0CT TCGA-A2-A0CX TCGA-A2-A0D4 TCGA-A2-A0EQ TCGA-A2-A0ER 
      112.08        75.25        56.81        25.22        79.76        74.40 
TCGA-A2-A0ET TCGA-A2-A0EW TCGA-A2-A0SU TCGA-A2-A0SX TCGA-A2-A0T1 TCGA-A2-A0T3 
       35.05        29.75        54.64        50.43        17.13        18.71 
TCGA-A2-A0T4 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YF TCGA-A2-A0YI TCGA-A2-A0YK 
       20.52        20.75        32.55        15.42        14.50        19.33 
TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A25B TCGA-A2-A25E TCGA-A2-A3KC 
       23.77        17.36        36.79        16.31        91.92        20.88 
TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XX TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A7-A0CE 
       39.65        33.93        38.40        38.37         7.30        35.31 
TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13H 
       30.61        35.67        31.73        10.72        12.72        29.56 
TCGA-A7-A26E TCGA-A7-A3J1 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE 
       31.36        11.28        14.93        13.74        14.50        21.17 
TCGA-A7-A56D TCGA-A7-A6VV TCGA-A8-A06O TCGA-A8-A06T TCGA-A8-A06Z TCGA-A8-A079 
       14.73        10.29        13.02        41.06         1.02         9.01 
TCGA-A8-A07B TCGA-A8-A07I TCGA-A8-A07W TCGA-A8-A082 TCGA-A8-A08F TCGA-A8-A08G 
       33.01        14.01         9.99        18.05        18.05        19.96 
TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08X 
       37.05         9.99        31.00        31.00        19.07        33.99 
TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A097 TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D 
       19.07        17.95        12.00        12.00         1.02        13.02 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09R TCGA-A8-A09T 
       31.00        33.07        29.98        15.02         8.98        19.04 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A9 TCGA-A8-A0AB 
       12.00        19.04        13.02        21.04        13.02        17.03 
TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FG TCGA-AC-A2FM 
        0.95         2.37        38.53        38.20        36.99        26.04 
TCGA-AC-A2QH TCGA-AC-A3HN TCGA-AC-A3W5 TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX 
        1.02         0.69         1.81         1.18         0.69         0.43 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A04A TCGA-AN-A0AL TCGA-AN-A0FS TCGA-AN-A0FT 
        0.33         0.23         2.96         6.51         6.28         6.02 
TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XW 
        0.36         0.33         0.33         0.33         0.33         5.59 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03P TCGA-AO-A03T TCGA-AO-A0J3 TCGA-AO-A0J7 
       80.28        47.84        84.69        47.87        21.40        20.32 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JG TCGA-AO-A0JL TCGA-AO-A12E TCGA-AO-A12F 
       53.03        21.53        26.24        55.33        57.30        48.36 
TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A1H2 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0TT 
        0.53        17.79        15.62         2.56        21.86        56.88 
TCGA-AR-A0TV TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 
       29.75        76.14        65.36        70.16        83.87        76.18 
TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AM TCGA-AR-A1AU TCGA-AR-A1AV 
       55.36        61.84        51.25        62.56        46.32        42.58 
TCGA-AR-A1AW TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24R TCGA-AR-A24Z TCGA-AR-A250 
       35.24       109.58        73.02        57.40        51.75        56.15 
TCGA-AR-A255 TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LO TCGA-B6-A0I9 TCGA-B6-A0IB 
       34.82        42.87         7.36        20.81        12.13       129.57 
TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0RG TCGA-B6-A0RL TCGA-B6-A0RU 
      146.50        18.77       126.12        68.45        81.17       131.21 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0X1 TCGA-B6-A0X7 TCGA-B6-A1KF 
       79.63        17.98        21.47       186.48        58.88       101.52 
TCGA-B6-A1KN TCGA-B6-A402 TCGA-B6-A40B TCGA-BH-A0AU TCGA-BH-A0AY TCGA-BH-A0AZ 
      139.17        54.28        82.88        24.53        25.55        28.50 
TCGA-BH-A0B5 TCGA-BH-A0BA TCGA-BH-A0BD TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0BV 
       48.36        37.22        18.21        44.05        48.69        49.94 
TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE 
       41.75        44.02        48.13        42.90        45.83        31.17 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0E2 TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GZ 
       13.91        48.23        14.30        31.00        24.43        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H7 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HP TCGA-BH-A0HU 
       15.16        23.08        52.96        26.50        13.61        12.89 
TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0WA TCGA-BH-A18L TCGA-BH-A18P TCGA-BH-A1EN 
       27.25        50.79        23.05        26.66        30.28        69.93 
TCGA-BH-A1ES TCGA-BH-A1F2 TCGA-BH-A1F8 TCGA-BH-A28Q TCGA-BH-A42T TCGA-C8-A12M 
      113.82        31.53        24.66         6.44         0.99        11.77 
TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12W TCGA-C8-A132 TCGA-C8-A135 
       11.77         0.07        12.66        12.66         1.45         0.62 
TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HN 
        3.75        10.92        11.34        11.34        12.03         3.25 
TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A278 TCGA-C8-A27A 
        0.23         0.36         0.43         8.28         0.03        12.20 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A145 TCGA-D8-A1J8 TCGA-D8-A1JC 
       11.90        20.88        13.97        13.48        14.17        15.78 
TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JI TCGA-D8-A1JK TCGA-D8-A1X6 TCGA-D8-A1X8 
       18.15        18.90        18.97        20.12        17.79        25.74 
TCGA-D8-A1X9 TCGA-D8-A1XF TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XZ TCGA-D8-A1Y0 
       23.90        15.22        16.31        12.99        15.32        15.52 
TCGA-D8-A27G TCGA-D8-A27I TCGA-D8-A27R TCGA-D8-A27V TCGA-D8-A27W TCGA-E2-A105 
       13.45        14.43        10.09        12.53        12.26        43.00 
TCGA-E2-A109 TCGA-E2-A14O TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14V TCGA-E2-A14X 
       46.59        44.68        38.60        33.17        34.26        31.96 
TCGA-E2-A152 TCGA-E2-A155 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15E TCGA-E2-A15G 
       27.12        21.04        14.79        25.05        20.71        18.21 
TCGA-E2-A15K TCGA-E2-A15M TCGA-E2-A1BD TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IU 
        9.04         7.73        17.10        32.78        33.73        11.08 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LA TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A56Z 
       27.42        39.62        24.59         8.75        43.04         7.20 
TCGA-E2-A573 TCGA-E9-A1N5 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1QZ TCGA-E9-A1R2 
       22.26        36.82        13.12        36.56        11.90         0.62 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G 
        6.58        21.27        35.64        22.75        12.89        23.51 
TCGA-E9-A247 TCGA-E9-A295 TCGA-E9-A3HO TCGA-E9-A3QA TCGA-E9-A5UO TCGA-EW-A1IW 
       27.22         0.72        26.07         0.62         0.23        12.20 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OY TCGA-EW-A1OZ 
       18.90        13.25        16.57        15.68        29.85        40.41 
TCGA-EW-A1P4 TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PF TCGA-EW-A2FR TCGA-EW-A2FS 
       29.82         6.15        13.94        14.43        55.00        52.73 
TCGA-EW-A423 TCGA-EW-A424 TCGA-GM-A2D9 TCGA-GM-A2DO TCGA-GM-A3XL TCGA-LD-A7W6 
       10.16        10.59        59.57        53.36        69.30         4.60 
TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A7SZ TCGA-LL-A7T0 
        4.70         3.19         3.25         3.88         5.59         3.22 
TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A5DA TCGA-OL-A5RW TCGA-OL-A5RY 
        6.21        15.91         2.10        44.61        26.20        14.10 
TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66O TCGA-OL-A66P 
       10.29         9.80        54.51        33.90         7.23         4.44 
TCGA-S3-A6ZG 
        6.81 

$`11Q LOSS WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK 
        8.52        48.10        14.27        47.24        20.88        31.79 
TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04U TCGA-A2-A04W 
       28.01        19.20       104.81        41.95        22.06        64.04 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CL TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
       55.43        36.13        64.57        92.48        88.60       107.93 
TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 
       75.55         5.19        63.45        64.04        21.14        34.55 
TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP 
       33.76        28.77       101.72        89.36        80.28       107.61 
TCGA-A2-A0ES TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST 
       37.05        34.29        31.82        24.72        24.16        99.19 
TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0T5 
       27.12        44.88        44.28        17.52         8.38        17.46 
TCGA-A2-A0T6 TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YJ 
       18.90        25.28        18.21        21.90        21.67        18.61 
TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 
       14.63        31.73        23.47        22.45        20.25        19.20 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A25D 
       19.56        16.47        52.47       107.70        17.19        18.15 
TCGA-A2-A25F TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XY 
       10.59        83.01        29.98        14.07        49.48        34.98 
TCGA-A2-A3XZ TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 
       31.99         9.01         8.81         8.91        12.00         6.74 
TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB 
        3.42        38.30        34.29        35.47        37.45        33.11 
TCGA-A7-A13G TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J 
       23.61        24.26        23.74        23.80        21.73        20.61 
TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 
       22.32        11.34        10.59        10.29        13.41        14.70 
TCGA-A7-A426 TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VW 
       11.97        17.92        12.10        10.72        11.05         9.37 
TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06U 
       10.42         8.75        13.02         1.02        17.98        29.03 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07E TCGA-A8-A07F 
       31.00        26.01        17.03        53.98        19.99        18.97 
TCGA-A8-A07G TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R 
       18.97        12.00        17.03         9.99        10.98         8.98 
TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 
        7.99         9.96        28.04        15.06        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08I TCGA-A8-A08R TCGA-A8-A08T 
        0.99        23.08        19.99        12.00         0.99        93.04 
TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09N 
       40.01        16.01        41.98         9.99         9.99         1.02 
TCGA-A8-A09Q TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A7 TCGA-A8-A0AD 
       25.02        15.02         0.99        14.01         0.99        38.04 
TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FK 
       10.85         2.66         1.48        40.57        55.43        38.79 
TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3OD TCGA-AC-A3QP 
       50.70         0.92         2.27         0.99        14.83         9.40 
TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V 
        1.12         1.68         1.55         1.32         1.55         0.07 
TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A046 TCGA-AN-A049 
        1.12         1.81         1.74         0.33         0.33         0.62 
TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0AR 
        1.78         1.71         8.02         7.36         0.16         0.33 
TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK 
        0.33         0.33         6.44         4.64         7.96         7.00 
TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XN 
        7.59         7.17         0.33         0.33         0.33         0.33 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AO-A03N 
       12.33         0.30         0.33         0.33         5.33        66.77 
TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J4 
       81.63        68.75        59.05        29.13        32.78        17.65 
TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD 
       24.16        37.48        22.36        50.70        50.86        72.00 
TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A124 
       76.77        21.37        38.53        62.04        71.80       102.58 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B 
       99.25        93.70        94.59        96.10        90.58        77.56 
TCGA-AO-A12D TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ 
       64.04        41.62        28.37        14.73        82.62        61.87 
TCGA-AO-A1KR TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H3 
       70.39        24.79        26.93       130.09         5.65        13.22 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TW 
        9.99        82.88        49.32         5.26        37.41        24.30 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AL TCGA-AR-A1AN 
       64.83        55.86        75.55        52.77        48.82        43.73 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AX 
       43.56        39.98        43.07        17.23        40.83        36.26 
TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
       20.22        50.89        65.46        68.19        65.69         0.85 
TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W 
       66.05        62.07        53.26        53.36        54.18        50.96 
TCGA-AR-A24X TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LE 
       48.16        45.17        40.64        39.85        93.83       128.65 
TCGA-AR-A2LH TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM 
       20.25        40.04        17.10        16.96        20.38        54.74 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 
       16.04        20.45        10.59        77.62       143.38       149.59 
TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IN 
      220.90        50.70        65.72       112.37       176.98        84.59 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RI 
      110.14       110.93       140.88       211.56       189.01       234.28 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS 
       78.02       172.96       162.05       102.77       140.48       100.70 
TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WY TCGA-B6-A0WZ 
       89.46       157.41        97.48       188.68       113.79       129.57 
TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A2IU 
      129.70        28.27        68.94        43.59        73.51       170.17 
TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0B0 
       85.35        49.94        55.00        38.79        20.45        46.95 
TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 
       40.83        39.55        39.16        56.94        56.98        51.68 
TCGA-BH-A0BC TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO 
       32.02        25.71        24.85        21.70        61.68        35.67 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BW TCGA-BH-A0BZ 
       27.19        53.69        53.95        45.57        11.67        49.05 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ 
       23.44        38.01        22.13        17.26        15.65         3.22 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
        2.56        38.47        45.17        47.41        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB 
       15.68         9.63        44.81        46.19        32.65        24.49 
TCGA-BH-A0GY TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HI 
       30.35        37.78        35.51        24.56        41.00        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HQ TCGA-BH-A0HW TCGA-BH-A0RX TCGA-BH-A0W3 
        5.85         2.50        36.85        51.32         5.59        23.93 
TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I 
       24.95        42.35        44.81         8.81         2.01         7.23 
TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18Q TCGA-BH-A18R 
       20.12        90.84        72.56        37.74        55.63        37.55 
TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ET 
       66.05         7.36        51.39        51.16        91.99        82.85 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 
       42.28        12.00        55.69        49.58        17.69        25.81 
TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE 
       89.16        97.48       120.62       114.15        33.17        74.73 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN 
      122.89        36.92        63.35        55.00        45.63        72.07 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 
      144.59        72.07         6.90         0.72        38.60        83.31 
TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V 
       57.83       130.16        10.65        20.12       109.28         8.94 
TCGA-C8-A12L TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A130 
       11.93        11.77        12.66        12.66        12.66         3.12 
TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HJ TCGA-C8-A1HL 
        1.78         0.69         3.85        12.33         0.16        10.42 
TCGA-C8-A1HM TCGA-C8-A26V TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A27B 
        2.30         0.30         9.67         0.03         0.03         0.99 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A146 
        0.03         0.23        13.25        20.58        14.17        21.14 
TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JF TCGA-D8-A1JG 
       19.20        17.49        16.50        18.71        12.03        12.03 
TCGA-D8-A1JH TCGA-D8-A1JJ TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP 
       14.01        20.09        20.09        19.40        20.38        21.01 
TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X7 TCGA-D8-A1XA 
       12.20        13.32        14.70        18.58        16.73        27.58 
TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK 
       18.15         2.66        17.16        14.73        21.83        14.50 
TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XT 
       19.92        17.69         7.96        16.41        15.85         6.35 
TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 
       15.16        12.66        16.54         3.81        14.24        14.14 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M 
       17.42        16.04        13.05         9.44        16.41        13.48 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 
        4.80         0.76        13.08        14.50        18.51         7.33 
TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E 
       34.42        27.52        40.41        37.51        40.11        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14T TCGA-E2-A14U 
       28.87        47.15        40.96        38.24        33.30        43.33 
TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 
       32.02        28.60        17.03        25.41        23.24        19.43 
TCGA-E2-A156 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15H 
       23.87        23.34        22.82        17.29        21.63        12.92 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R 
       17.42        19.40        20.58        13.02        19.56        17.06 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 
       14.07        14.99        60.53        53.62        53.03        29.95 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1II 
       32.35        28.50        16.47        38.30        37.41        33.70 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1L6 
       28.44        22.65         3.88        22.19        20.98        54.18 
TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI 
       19.66        40.47        28.90        18.87       106.75       102.61 
TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A574 TCGA-E9-A1N4 
       16.93         5.52        15.72        18.05        19.89        19.20 
TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF 
       13.48        12.00        39.55        12.59        35.77        20.05 
TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1R0 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 
       21.57         9.86        14.30         2.10         6.12         1.38 
TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD 
        2.76        21.21        32.09        20.81        40.24         0.66 
TCGA-E9-A1RE TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
       34.65        34.59        34.13         0.79        12.53        13.32 
TCGA-E9-A22A TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A248 
       39.09        24.10        17.06         0.69         0.85         1.94 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3X8 
        0.95        12.56        17.75         0.76        18.41        15.72 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A6HE TCGA-EW-A1IX TCGA-EW-A1IY 
        0.23         0.39         0.26        15.39        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1P0 
       18.21        28.77        25.94        22.82        29.95        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 
       39.78        52.96        23.11        18.48        30.08         7.86 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PE TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FV 
       18.90        19.99        10.52        34.55        19.96        25.91 
TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2DA 
       22.09        21.27        17.49         7.40       109.87       194.27 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI 
       53.13        53.52        43.04        42.71        42.28        61.91 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY 
       62.33        90.84        76.64        77.33       110.50        38.20 
TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW 
       32.28        53.95        57.63        13.55        18.12        11.84 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
       11.57         8.28         6.67         0.66         2.99         3.58 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A73Z 
        6.90         5.56         3.65         2.63         4.14         4.50 
TCGA-LL-A740 TCGA-MS-A51U TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5RU 
        4.50         2.79        12.66        46.55         7.53        27.65 
TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66L TCGA-OL-A66N 
       24.10        16.87        14.76        23.70        31.07        18.21 
TCGA-W8-A86G 
        5.29 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.03               0.03 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            186.48             234.28 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             20.71              22.13 
[1] "0.0 - 186.5 (20.7)" "0.0 - 234.3 (22.1)"
[1] "hr=" "1"  
D62V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11Q LOSS MUTATED        18       22        4        4       113        78
  11Q LOSS WILD-TYPE      62       55        5        5       222       146
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11Q LOSS MUTATED           1         58         12         17        6
  11Q LOSS WILD-TYPE         1         80         15         42       11
                    vv
clus                 STAGE TIS STAGE X
  11Q LOSS MUTATED           0       5
  11Q LOSS WILD-TYPE         1      11
D62V3, multiclass
            clus
vv           11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  18                 62
  STAGE IA                 22                 55
  STAGE IB                  4                  5
  STAGE II                  4                  5
  STAGE IIA               113                222
  STAGE IIB                78                146
  STAGE III                 1                  1
  STAGE IIIA               58                 80
  STAGE IIIB               12                 15
  STAGE IIIC               17                 42
  STAGE IV                  6                 11
  STAGE TIS                 0                  1
  STAGE X                   5                 11
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  11Q LOSS MUTATED    77 209  37  15
  11Q LOSS WILD-TYPE 181 372  80  21
D62V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1               77                181
  T2              209                372
  T3               37                 80
  T4               15                 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                  N0  N1  N2  N3
  11Q LOSS MUTATED   148 112  52  21
  11Q LOSS WILD-TYPE 320 218  59  49
D62V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0              148                320
  N1              112                218
  N2               52                 59
  N3               21                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  11Q LOSS MUTATED          1 280   6  51
  11Q LOSS WILD-TYPE        1 565  11  80
D62V6, multiclass
          clus
vv         11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CM0 (I+)                1                  1
  M0                    280                565
  M1                      6                 11
  MX                     51                 80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED   332   6
  11Q LOSS WILD-TYPE 652   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED    332    6
  11Q LOSS WILD-TYPE  652    5
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE              332                652
  MALE                  6                  5
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  11Q LOSS MUTATED                            0                           250
  11Q LOSS WILD-TYPE                          1                           485
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  11Q LOSS MUTATED                               60                   3
  11Q LOSS WILD-TYPE                            106                   2
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  11Q LOSS MUTATED                                 11                  3
  11Q LOSS WILD-TYPE                               18                 11
                    vv
clus                 OTHER  SPECIFY
  11Q LOSS MUTATED               10
  11Q LOSS WILD-TYPE             34
D62V8, multiclass
                                  clus
vv                                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 250                485
  INFILTRATING LOBULAR CARCINOMA                 60                106
  MEDULLARY CARCINOMA                             3                  2
  MIXED HISTOLOGY (PLEASE SPECIFY)               11                 18
  MUCINOUS CARCINOMA                              3                 11
  OTHER  SPECIFY                                 10                 34
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V9, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED   100 238
  11Q LOSS WILD-TYPE 182 475
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED    100  238
  11Q LOSS WILD-TYPE  182  475
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO               100                182
  YES              238                475
[1] 2 2
[1] FALSE
D62V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q LOSS MUTATED                                  1    21
  11Q LOSS WILD-TYPE                                0    35
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED                          61   216
  11Q LOSS WILD-TYPE                        76   492
D62V11, multiclass
                                  clus
vv                                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                          21                 35
  BLACK OR AFRICAN AMERICAN                      61                 76
  WHITE                                         216                492
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V12, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    12 256
  11Q LOSS WILD-TYPE  24 540
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     12  256
  11Q LOSS WILD-TYPE   24  540
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   12                 24
  NOT HISPANIC OR LATINO              256                540
[1] 2 2
[1] FALSE

Clustering(63) Variable = 12P LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED   117  17
  12P LOSS WILD-TYPE 743  97
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
               134                840 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                17                 97 
$`12P LOSS MUTATED`
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A2-A0D1 TCGA-A2-A0T0 TCGA-A2-A0T7 TCGA-A2-A0YF 
       20.88        13.68        34.55        17.52        20.75        15.42 
TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A3XT TCGA-A2-A3XX TCGA-A2-A3Y0 
       52.47        16.31        17.19        83.01        38.40        38.37 
TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A26I 
        9.01        12.00        30.61        35.67        31.73        21.73 
TCGA-A7-A4SA TCGA-A7-A4SF TCGA-A7-A6VV TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A07G 
       14.93        17.92        10.29        17.98        41.06        18.97 
TCGA-A8-A08F TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A09I TCGA-A8-A09Q 
       18.05         0.99        33.99        40.01        33.07        25.02 
TCGA-AC-A23H TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A6IV TCGA-AN-A0AM TCGA-AN-A0FD 
        2.66         0.92         2.27         1.18         0.16         6.44 
TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FV TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AO-A03O 
        7.00         7.59         0.33         0.33        12.33        81.63 
TCGA-AO-A03T TCGA-AO-A0J4 TCGA-AO-A0JL TCGA-AO-A129 TCGA-AO-A12D TCGA-AR-A0TR 
       47.87        17.65        55.33        96.10        64.04         5.26 
TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AR TCGA-AR-A24K 
       76.14        65.36        61.84        52.77        17.23        50.89 
TCGA-AR-A24M TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LL 
       65.46        45.17        40.64        39.85        93.83         7.36 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0RE TCGA-B6-A0RI 
      146.50       112.37       176.98        18.77       211.56       234.28 
TCGA-B6-A0RP TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A1KF TCGA-B6-A1KN TCGA-BH-A0B2 
      102.77       131.21       157.41       101.52       139.17        40.83 
TCGA-BH-A0B3 TCGA-BH-A0B7 TCGA-BH-A0BP TCGA-BH-A0BW TCGA-BH-A0C0 TCGA-BH-A0C7 
       39.55        56.98        48.69        11.67        41.75        42.90 
TCGA-BH-A0DG TCGA-BH-A0DQ TCGA-BH-A0E6 TCGA-BH-A0EE TCGA-BH-A0H7 TCGA-BH-A1EN 
       23.44         3.22         9.63        31.00        23.08        69.93 
TCGA-BH-A1F6 TCGA-BH-A1FN TCGA-BH-A1FU TCGA-BH-A208 TCGA-C8-A12U TCGA-C8-A131 
       97.48        72.07        72.07        57.83        12.66         1.78 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A26Y TCGA-C8-A27A TCGA-D8-A142 TCGA-D8-A1JE 
        1.45         0.69         0.43        12.20        13.97        18.90 
TCGA-D8-A1JG TCGA-D8-A1X5 TCGA-D8-A1XK TCGA-D8-A1XM TCGA-D8-A1XQ TCGA-D8-A1XT 
       12.03        18.58        14.50        17.69        16.41         6.35 
TCGA-D8-A27F TCGA-E2-A10A TCGA-E2-A14Q TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A155 
       16.04        40.41        38.24        17.03        25.41        21.04 
TCGA-E2-A159 TCGA-E2-A15E TCGA-E2-A1B5 TCGA-E2-A1BD TCGA-E2-A1IO TCGA-E2-A1L7 
       25.05        20.71        32.35        17.10        20.98        27.42 
TCGA-E2-A1LA TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E9-A1R4 TCGA-E9-A22G 
       24.59       106.75       102.61         8.75         6.12        23.51 
TCGA-E9-A3X8 TCGA-E9-A5UO TCGA-EW-A1OY TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A3U0 
       15.72         0.23        29.85         6.15        13.94        17.49 
TCGA-GM-A2DK TCGA-LL-A5YM TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Z TCGA-OL-A5D7 
       62.33         4.70         3.25         3.88         4.50        46.55 
TCGA-OL-A5RW TCGA-OL-A66K 
       26.20        33.90 

$`12P LOSS WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ 
       31.79         7.96        39.32        28.01        19.20        18.21 
TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U 
      104.81        18.02        41.95        82.16        73.84        22.06 
TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL 
       63.12        64.04        55.43        36.13       125.59        64.57 
TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS 
       24.79       112.08        92.48        88.60       107.93        75.55 
TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 
       75.25         5.19        63.45        64.04        56.81        21.14 
TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO 
       33.76        28.77        25.22       101.72        89.36        80.28 
TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU 
      107.61        79.76        74.40        37.05        35.05        34.29 
TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU 
       31.82        29.75        24.72        24.16        99.19        54.64 
TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T1 TCGA-A2-A0T2 
       27.12        44.88        50.43        44.28        17.13         8.38 
TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD 
       18.71        20.52        17.46        18.90        32.55        25.28 
TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK 
       18.21        21.90        21.67        14.50        18.61        19.33 
TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX 
       14.63        31.73        23.77        23.47        17.36        36.79 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A25A 
       22.45        20.25        19.20        19.56        16.47       107.70 
TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS 
       18.15        91.92        10.59        20.88        39.65        33.93 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A4RW 
       29.98        14.07        49.48        34.98        31.99         7.30 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE 
        8.81         8.91         6.74         3.42        38.30        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13E TCGA-A7-A13F 
       34.29        35.47        37.45        33.11        10.72        12.72 
TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H 
       23.61        29.56        31.36        24.26        23.74        23.80 
TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       20.61        22.32        11.34        10.59        10.29        11.28 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE 
       13.41        14.70        11.97        13.74        14.50        21.17 
TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A7-A6VX 
       14.73        12.10        10.72        11.05         9.37        10.42 
TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06U TCGA-A8-A06X 
        8.75        13.02        13.02         1.02        29.03        31.00 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B 
       26.01         1.02        17.03        53.98         9.01        33.01 
TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O 
       19.99        18.97        14.01        12.00        17.03         9.99 
TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z 
       10.98         8.98         7.99         9.96         9.99        28.04 
TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B 
       18.05        15.06        36.95        13.02         0.99        23.08 
TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O 
       19.99        19.96        12.00        37.05         9.99        31.00 
TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 
       31.00        19.07        93.04        19.07        16.01        17.95 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C 
       41.98        12.00         9.99         9.99        12.00         1.02 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R 
       13.02        31.00        29.98        15.02         1.02         8.98 
TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 
       19.04        15.02         0.99        14.01        12.00        19.04 
TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD 
       13.02        21.04         0.99        13.02        17.03        38.04 
TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM 
        0.95         2.37        10.85         1.48        38.53        38.20 
TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO 
       40.57        55.43        36.99        38.79        26.04        50.70 
TCGA-AC-A2QH TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN 
        1.02         0.99         0.69        14.83         9.40         1.12 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V 
        1.81         1.68         1.55         1.32         1.55         0.07 
TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AN-A03X 
        1.12         1.81         0.69         0.43         1.74         0.33 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C 
        0.33         0.23         0.33         0.62         2.96         1.78 
TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AS 
        1.71         8.02         7.36         6.51         0.33         0.33 
TCGA-AN-A0AT TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT 
        0.33         4.64         7.96         7.17         6.28         6.02 
TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XP 
        0.36         0.33         0.33         0.33         0.33         0.30 
TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW 
        0.33         0.33         0.33         0.33         5.33         5.59 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03U 
       80.28        47.84        66.77        84.69        68.75        59.05 
TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 
       29.13        32.78        21.40        24.16        37.48        20.32 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD 
       22.36        53.03        21.53        50.70        50.86        72.00 
TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JM 
       76.77        21.37        26.24        38.53        62.04        71.80 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B 
      102.58        99.25        93.70        94.59        90.58        77.56 
TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       57.30        48.36        41.62        28.37        14.73        82.62 
TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J 
       61.87        70.39         0.53        17.79        24.79        26.93 
TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O 
      130.09         5.65        15.62        13.22         2.56        21.86 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV 
        9.99        82.88        49.32        37.41        56.88        29.75 
TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 
       24.30        64.83        55.86        70.16        83.87        76.18 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
       55.36        75.55        51.25        48.82        62.56        43.73 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
       43.56        39.98        43.07        40.83        46.32        42.58 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24N 
       35.24        36.26        20.22       109.58        73.02        68.19 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T 
       65.69         0.85        66.05        57.40        62.07        53.26 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 
       53.36        54.18        50.96        48.16        51.75        56.15 
TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN 
       34.82       128.65        20.25        42.87        40.04        17.10 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP 
       20.81        16.96        20.38        54.74        16.04        20.45 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA 
       10.59        77.62       143.38       149.59        12.13       220.90 
TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO 
      129.57        50.70        65.72       126.12        84.59       110.14 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RL TCGA-B6-A0RM 
      110.93       140.88        68.45       189.01        81.17        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0WS 
      172.96       162.05       140.48       100.70        89.46        97.48 
TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ 
      188.68        79.63        17.98        21.47       113.79       129.57 
TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC 
      129.70       186.48        28.27        68.94        58.88        43.59 
TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B 
       73.51       170.17        85.35        54.28        49.94        82.88 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ 
       55.00        24.53        38.79        20.45        25.55        28.50 
TCGA-BH-A0B0 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B9 TCGA-BH-A0BA 
       46.95        39.16        48.36        56.94        51.68        37.22 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL 
       32.02        18.21        25.71        24.85        21.70        44.05 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT 
       61.68        35.67        27.19        53.69        53.95        45.57 
TCGA-BH-A0BV TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE 
       49.94        49.05        44.02        48.13        45.83        31.17 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP 
       38.01        22.13        13.91        48.23        17.26        15.65 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
        2.56        38.47        45.17        47.41        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB 
       15.68        14.30        44.81        46.19        32.65        24.49 
TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       24.43        30.35        10.78        15.16        37.78        35.51 
TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK 
       24.56        41.00        52.96        26.50        20.38         5.85 
TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX 
        2.50        13.61        36.85        12.89        51.32        27.25 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       50.79         5.59        23.93        24.95        42.35        44.81 
TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K 
       23.05         8.81         2.01         7.23        20.12        90.84 
TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R 
       26.66        72.56        37.74        30.28        55.63        37.55 
TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ES 
       66.05         7.36        51.39        51.16        91.99       113.82 
TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY 
       82.85        42.28        12.00        55.69        49.58        17.69 
TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC 
       25.81        31.53        89.16        24.66       120.62       114.15 
TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
       33.17        74.73       122.89        36.92        63.35        55.00 
TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 
       45.63       144.59         6.90         0.72        38.60        83.31 
TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
      130.16        10.65         6.44        20.12         0.99       109.28 
TCGA-BH-A42V TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P 
        8.94        11.93        11.77        11.77        12.66        11.77 
TCGA-C8-A12Q TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A135 
        0.07        12.66        12.66        12.66         3.12         0.62 
TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI 
        3.85         3.75        12.33        10.92        11.34        11.34 
TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V 
        0.16        12.03        10.42         2.30         3.25         0.30 
TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
        0.23         0.36         8.28         9.67         0.03         0.03 
TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A13Z 
        0.03         0.99         0.03         0.23        11.90        20.88 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 
       13.25        20.58        14.17        13.48        21.14        19.20 
TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD 
       14.17        17.49        16.50        18.71        15.78        18.15 
TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL 
       12.03        14.01        18.97        20.09        20.12        20.09 
TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU 
       19.40        20.38        21.01        12.20        13.32        14.70 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB 
       17.79        16.73        25.74        23.90        27.58        18.15 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XL 
        2.66        17.16        15.22        14.73        21.83        19.92 
TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW 
        7.96        15.85        16.31        12.99        15.16        12.66 
TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 
       16.54        15.32        15.52         3.81        14.24        14.14 
TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       17.42        13.45        13.05        14.43         9.44        16.41 
TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V 
       13.48         4.80         0.76        10.09        13.08        12.53 
TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A107 
       12.26        14.50        18.51         7.33        43.00        34.42 
TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F 
       27.52        46.59        37.51        40.11        28.44        28.87 
TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T 
       47.15        44.68        40.96        38.60        33.17        33.30 
TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A152 
       43.33        34.26        32.02        31.96        28.60        27.12 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15A TCGA-E2-A15C 
       23.24        19.43        23.87        14.79        23.34        22.82 
TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J 
       17.29        21.63        18.21        12.92        17.42        19.40 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R 
        9.04        20.58         7.73        13.02        19.56        17.06 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 
       14.07        14.99        60.53        53.62        53.03        29.95 
TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       28.50        16.47        38.30        37.41        32.78        33.73 
TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IU 
       33.70        28.44        22.65         3.88        22.19        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG 
       54.18        39.62        19.66        40.47        28.90        18.87 
TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
       43.04        16.93         5.52        15.72         7.20        18.05 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 
       22.26        19.89        19.20        36.82        13.48        12.00 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF 
       13.12        36.56        39.55        12.59        35.77        20.05 
TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 
       21.57         9.86        11.90        14.30         0.62         2.10 
TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC 
        1.38         2.76        21.21        32.09        20.81        40.24 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI 
        0.66        34.65         6.58        21.27        34.59        35.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       34.13         0.79        12.53        13.32        39.09        22.75 
TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A247 
       12.89        24.10        17.06         0.69         0.85        27.22 
TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT 
        1.94         0.95        12.56         0.72        17.75         0.76 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL 
       26.07        18.41         0.62         0.23         0.39         0.26 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 
       15.39        12.20        39.72         8.48        18.21        18.90 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW 
       13.25        16.57        15.68        28.77        25.94        22.82 
TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 
       29.95        40.41        41.13        39.78        52.96        29.82 
TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB 
       23.11        18.48        30.08         7.86        18.90        19.99 
TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS 
       10.52        14.43        34.55        19.96        55.00        52.73 
TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 
       25.91        22.09        21.27        10.16        10.59         7.40 
TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD 
      109.87        59.57       194.27        53.13        53.52        43.04 
TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       42.71        42.28        61.91        90.84        76.64        77.33 
TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN 
       53.36       110.50        38.20        32.28        69.30        53.95 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U 
       57.63        13.55        18.12        11.84        11.57         8.28 
TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y 
        6.67         4.60         0.66         2.99         3.58         6.90 
TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A740 
        5.56         3.65         3.19         2.63         4.14         4.50 
TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 
        5.59         3.22         6.21        15.91         2.79         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX 
       12.66         7.53        44.61        27.65        24.10        16.87 
TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J 
       14.10        10.29         9.80        14.76        23.70        54.51 
TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-S3-A6ZG TCGA-W8-A86G 
       31.07        18.21         7.23         4.44         6.81         5.29 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.16               0.03 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            234.28             220.90 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            22.405             21.385 
[1] "0.2 - 234.3 (22.4)" "0.0 - 220.9 (21.4)"
[1] "hr=" "1.2"
D63V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12P LOSS MUTATED         9        9        0        1        50        36
  12P LOSS WILD-TYPE      71       68        9        8       285       188
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12P LOSS MUTATED           0         17          9          5        1
  12P LOSS WILD-TYPE         2        121         18         54       16
                    vv
clus                 STAGE TIS STAGE X
  12P LOSS MUTATED           0       1
  12P LOSS WILD-TYPE         1      15
D63V3, multiclass
            clus
vv           12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                   9                 71
  STAGE IA                  9                 68
  STAGE IB                  0                  9
  STAGE II                  1                  8
  STAGE IIA                50                285
  STAGE IIB                36                188
  STAGE III                 0                  2
  STAGE IIIA               17                121
  STAGE IIIB                9                 18
  STAGE IIIC                5                 54
  STAGE IV                  1                 16
  STAGE TIS                 0                  1
  STAGE X                   1                 15
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  12P LOSS MUTATED    30  84  13  11
  12P LOSS WILD-TYPE 228 497 104  25
D63V4, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1               30                228
  T2               84                497
  T3               13                104
  T4               11                 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                  N0  N1  N2  N3
  12P LOSS MUTATED    65  50  14   6
  12P LOSS WILD-TYPE 403 280  97  64
D63V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0               65                403
  N1               50                280
  N2               14                 97
  N3                6                 64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  12P LOSS MUTATED          0 127   1  11
  12P LOSS WILD-TYPE        2 718  16 120
D63V6, multiclass
          clus
vv         12P LOSS MUTATED 12P LOSS WILD-TYPE
  CM0 (I+)                0                  2
  M0                    127                718
  M1                      1                 16
  MX                     11                120
[1] 4 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   138   1
  12P LOSS WILD-TYPE 846  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED    138    1
  12P LOSS WILD-TYPE  846   10
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE              138                846
  MALE                  1                 10
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  12P LOSS MUTATED                            0                           121
  12P LOSS WILD-TYPE                          1                           614
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  12P LOSS MUTATED                                8                   1
  12P LOSS WILD-TYPE                            158                   4
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  12P LOSS MUTATED                                  3                  1
  12P LOSS WILD-TYPE                               26                 13
                    vv
clus                 OTHER  SPECIFY
  12P LOSS MUTATED                5
  12P LOSS WILD-TYPE             39
D63V8, multiclass
                                  clus
vv                                 12P LOSS MUTATED 12P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 121                614
  INFILTRATING LOBULAR CARCINOMA                  8                158
  MEDULLARY CARCINOMA                             1                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                3                 26
  MUCINOUS CARCINOMA                              1                 13
  OTHER  SPECIFY                                  5                 39
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V9, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    44  95
  12P LOSS WILD-TYPE 238 618
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     44   95
  12P LOSS WILD-TYPE  238  618
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                44                238
  YES               95                618
[1] 2 2
[1] FALSE
D63V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P LOSS MUTATED                                  0     7
  12P LOSS WILD-TYPE                                1    49
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED                          26    94
  12P LOSS WILD-TYPE                       111   614
D63V11, multiclass
                                  clus
vv                                 12P LOSS MUTATED 12P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           7                 49
  BLACK OR AFRICAN AMERICAN                      26                111
  WHITE                                          94                614
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V12, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     3 116
  12P LOSS WILD-TYPE  33 680
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      3  116
  12P LOSS WILD-TYPE   33  680
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 33
  NOT HISPANIC OR LATINO              116                680
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    96  17
  12Q LOSS WILD-TYPE 764  97
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
               113                861 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                17                 97 
$`12Q LOSS MUTATED`
TCGA-A1-A0SF TCGA-A1-A0SJ TCGA-A2-A0D1 TCGA-A2-A0T0 TCGA-A2-A0YE TCGA-A2-A3XS 
       48.10        13.68        34.55        17.52        18.21        33.93 
TCGA-A2-A3XT TCGA-A2-A3XX TCGA-A2-A3Y0 TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A7-A0CJ 
       83.01        38.40        38.37         9.01        12.00        30.61 
TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A26I TCGA-A7-A4SA TCGA-A7-A4SD 
       35.67        31.73        10.72        21.73        14.93        14.50 
TCGA-A7-A4SF TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A8-A07G TCGA-A8-A08F 
       17.92        10.29         9.37        10.42        18.97        18.05 
TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A09Q TCGA-AC-A2QJ TCGA-AN-A04C TCGA-AN-A0AM 
        0.99        33.99        25.02         2.27         1.78         0.16 
TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0XO TCGA-AO-A0J4 TCGA-AO-A0JL TCGA-AO-A124 
        7.00         7.59        12.33        17.65        55.33       102.58 
TCGA-AO-A129 TCGA-AO-A12F TCGA-AR-A0U0 TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AQ 
       96.10        48.36        65.36        61.84        52.77        43.07 
TCGA-AR-A1AR TCGA-AR-A24K TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A256 TCGA-AR-A2LL 
       17.23        50.89        45.17        40.64        93.83         7.36 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0RE TCGA-B6-A0RI TCGA-B6-A0RP 
      146.50       112.37       176.98       211.56       234.28       102.77 
TCGA-B6-A0RU TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A402 TCGA-BH-A0AV TCGA-BH-A0B2 
      131.21       101.52       139.17        54.28        38.79        40.83 
TCGA-BH-A0B7 TCGA-BH-A0BP TCGA-BH-A0C0 TCGA-BH-A0C7 TCGA-BH-A0DG TCGA-BH-A0E0 
       56.98        48.69        41.75        42.90        23.44         4.41 
TCGA-BH-A0EE TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1F6 TCGA-BH-A1FN 
       31.00        51.16        69.93        91.99        97.48        72.07 
TCGA-BH-A1FU TCGA-BH-A208 TCGA-C8-A12U TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A26Y 
       72.07        57.83        12.66         1.78         1.45         0.43 
TCGA-C8-A27A TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A1JG TCGA-D8-A1XK TCGA-D8-A1XQ 
       12.20        13.97        14.17        12.03        14.50        16.41 
TCGA-D8-A27F TCGA-E2-A10A TCGA-E2-A150 TCGA-E2-A159 TCGA-E2-A15E TCGA-E2-A1AZ 
       16.04        40.41        25.41        25.05        20.71        60.53 
TCGA-E2-A1B5 TCGA-E2-A1BD TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A1LH TCGA-E2-A1LI 
       32.35        17.10        20.98        27.42       106.75       102.61 
TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E9-A1RG TCGA-E9-A22G TCGA-E9-A3X8 TCGA-EW-A1P4 
        8.75        16.93        21.27        23.51        15.72        29.82 
TCGA-EW-A1P8 TCGA-EW-A1PC TCGA-EW-A3U0 TCGA-GI-A2C8 TCGA-GM-A2DK TCGA-LL-A5YP 
        7.86         6.15        17.49         7.40        62.33         3.25 
TCGA-LL-A73Z TCGA-OL-A5D7 TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-OL-A66K 
        4.50        46.55        26.20         9.80        33.90 

$`12Q LOSS WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI 
        8.52        14.37        43.43        14.27        47.24        20.88 
TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ 
       31.79         7.96        39.32        28.01        19.20        18.21 
TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U 
      104.81        18.02        41.95        82.16        73.84        22.06 
TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL 
       63.12        64.04        55.43        36.13       125.59        64.57 
TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS 
       24.79       112.08        92.48        88.60       107.93        75.55 
TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 
       75.25         5.19        63.45        64.04        56.81        21.14 
TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO 
       33.76        28.77        25.22       101.72        89.36        80.28 
TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU 
      107.61        79.76        74.40        37.05        35.05        34.29 
TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU 
       31.82        29.75        24.72        24.16        99.19        54.64 
TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T1 TCGA-A2-A0T2 
       27.12        44.88        50.43        44.28        17.13         8.38 
TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC 
       18.71        20.52        17.46        18.90        20.75        32.55 
TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ 
       25.28        15.42        21.90        21.67        14.50        18.61 
TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW 
       19.33        14.63        31.73        23.77        23.47        17.36 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 
       36.79        22.45        20.25        19.20        19.56        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       52.47       107.70        16.31        17.19        18.15        91.92 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW 
       10.59        20.88        39.65        29.98        14.07        49.48 
TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 
       34.98        31.99         7.30         8.81         8.91         6.74 
TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 
        3.42        38.30        35.31        34.29        35.47        37.45 
TCGA-A7-A0DB TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F 
       33.11        12.72        23.61        29.56        31.36        24.26 
TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ 
       23.74        23.80        20.61        22.32        11.34        10.59 
TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SB 
       10.29        11.28        13.41        14.70        11.97        13.74 
TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VY 
       21.17        14.73        12.10        10.72        11.05         8.75 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U 
       13.02        13.02         1.02        17.98        41.06        29.03 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 
       31.00        26.01         1.02        17.03        53.98         9.01 
TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
       33.01        19.99        18.97        14.01        12.00        17.03 
TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W 
        9.99        10.98         8.98         7.99         9.96         9.99 
TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A 
       28.04        18.05        15.06        36.95        13.02         0.99 
TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L 
       23.08        19.99        19.96        12.00        37.05         9.99 
TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 
       31.00        31.00        19.07        93.04        40.01        19.07 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A 
       16.01        17.95        41.98        12.00         9.99         9.99 
TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K 
       12.00         1.02        13.02        31.00        33.07        29.98 
TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
       15.02         1.02         8.98        19.04        15.02         0.99 
TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 
       14.01        12.00        19.04        13.02        21.04         0.99 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G 
       13.02        17.03        38.04         0.95         2.37        10.85 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF 
        2.66         1.48        38.53        38.20        40.57        55.43 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI 
       36.99        38.79        26.04        50.70         1.02         0.92 
TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 
        0.99         0.69        14.83         9.40         1.12         1.81 
TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X 
        1.68         1.55         1.32         1.55         0.07         1.12 
TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AN-A03X 
        1.81         1.18         0.69         0.43         1.74         0.33 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D 
        0.33         0.23         0.33         0.62         2.96         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT 
        8.02         7.36         6.51         0.33         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT 
        6.44         4.64         7.96         7.17         6.28         6.02 
TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL 
        0.33         0.36         0.33         0.33         0.33         0.33 
TCGA-AN-A0XN TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU 
        0.33         0.30         0.33         0.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O 
        5.33         5.59        80.28        47.84        66.77        81.63 
TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 
       84.69        68.75        47.87        59.05        29.13        32.78 
TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 
       21.40        24.16        37.48        20.32        22.36        53.03 
TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF 
       21.53        50.70        50.86        72.00        76.77        21.37 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 
       26.24        38.53        62.04        71.80        99.25        93.70 
TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G 
       94.59        90.58        77.56        64.04        57.30        41.62 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS 
       28.37        14.73        82.62        61.87        70.39         0.53 
TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 
       17.79        24.79        26.93       130.09         5.65        15.62 
TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ 
       13.22         2.56        21.86         9.99        82.88        49.32 
TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX 
        5.26        37.41        56.88        29.75        24.30        64.83 
TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 
       55.86        76.14        70.16        83.87        76.18        55.36 
TCGA-AR-A1AH TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO 
       75.55        51.25        48.82        62.56        43.73        43.56 
TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX 
       39.98        40.83        46.32        42.58        35.24        36.26 
TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       20.22       109.58        73.02        65.46        68.19        65.69 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U 
        0.85        66.05        57.40        62.07        53.26        53.36 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A254 
       54.18        50.96        48.16        51.75        56.15        39.85 
TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN 
       34.82       128.65        20.25        42.87        40.04        17.10 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP 
       20.81        16.96        20.38        54.74        16.04        20.45 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA 
       10.59        77.62       143.38       149.59        12.13       220.90 
TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
      129.57        50.70        65.72        18.77       126.12        84.59 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RL 
      110.14       110.93       140.88        68.45       189.01        81.17 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT 
       78.02       172.96       162.05       140.48       100.70        89.46 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX 
      157.41        97.48       188.68        79.63        17.98        21.47 
TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
      113.79       129.57       129.70       186.48        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A408 
       58.88        43.59        73.51       170.17        85.35        49.94 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ 
       82.88        55.00        24.53        20.45        25.55        28.50 
TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B9 
       46.95        39.55        39.16        48.36        56.94        51.68 
TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ 
       37.22        32.02        18.21        25.71        24.85        21.70 
TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       44.05        61.68        35.67        27.19        53.69        53.95 
TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C3 
       45.57        49.94        11.67        49.05        44.02        48.13 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL 
       45.83        31.17        38.01        22.13        13.91        48.23 
TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       17.26        15.65         3.22         2.56        38.47        45.17 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 
       47.41        16.27        15.68        14.30         9.63        44.81 
TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ 
       46.19        32.65        24.49        24.43        30.35        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 
       15.16        37.78        35.51        24.56        23.08        41.00 
TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       52.96        26.50        20.38         5.85         2.50        13.61 
TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX 
       36.85        12.89        51.32        27.25        50.79         5.59 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F 
       23.93        24.95        42.35        44.81        23.05         8.81 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M 
        2.01         7.23        20.12        90.84        26.66        72.56 
TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T 
       37.74        30.28        55.63        37.55        66.05         7.36 
TCGA-BH-A18U TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW 
       51.39       113.82        82.85        42.28        12.00        55.69 
TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F8 
       49.58        17.69        25.81        31.53        89.16        24.66 
TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH 
      120.62       114.15        33.17        74.73       122.89        36.92 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A202 
       63.35        55.00        45.63       144.59         6.90         0.72 
TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
       38.60        83.31       130.16        10.65         6.44        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N 
        0.99       109.28         8.94        11.93        11.77        11.77 
TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X 
       12.66        11.77         0.07        12.66        12.66        12.66 
TCGA-C8-A130 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE 
        3.12         0.69         0.62         3.85         3.75        12.33 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL 
       10.92        11.34        11.34         0.16        12.03        10.42 
TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Z 
        2.30         3.25         0.30         0.23         0.36         8.28 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 
        9.67         0.03         0.03         0.03         0.99         0.03 
TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A145 
        0.23        11.90        20.88        13.25        20.58        13.48 
TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
       21.14        19.20        14.17        17.49        16.50        18.71 
TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JI 
       15.78        18.15        18.90        12.03        14.01        18.97 
TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP 
       20.09        20.12        20.09        19.40        20.38        21.01 
TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 
       12.20        13.32        14.70        18.58        17.79        16.73 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD 
       25.74        23.90        27.58        18.15         2.66        17.16 
TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO 
       15.22        14.73        21.83        19.92        17.69         7.96 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW 
       15.85        16.31         6.35        12.99        15.16        12.66 
TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 
       16.54        15.32        15.52         3.81        14.24        14.14 
TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       17.42        13.45        13.05        14.43         9.44        16.41 
TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V 
       13.48         4.80         0.76        10.09        13.08        12.53 
TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A107 
       12.26        14.50        18.51         7.33        43.00        34.42 
TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F 
       27.52        46.59        37.51        40.11        28.44        28.87 
TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S 
       47.15        44.68        40.96        38.24        38.60        33.17 
TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y 
       33.30        43.33        34.26        32.02        31.96        28.60 
TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 
       17.03        27.12        23.24        19.43        21.04        23.87 
TCGA-E2-A158 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15G 
       14.79        23.34        22.82        17.29        21.63        18.21 
TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M 
       12.92        17.42        19.40         9.04        20.58         7.73 
TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 
       13.02        19.56        17.06        14.07        14.99        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF 
       53.03        29.95        28.50        16.47        38.30        37.41 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       32.78        33.73        33.70        28.44        22.65         3.88 
TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA 
       22.19        11.08        54.18        39.62        19.66        24.59 
TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX 
       40.47        28.90        18.87        43.04         5.52        15.72 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N4 TCGA-E9-A1N5 
        7.20        18.05        22.26        19.89        19.20        36.82 
TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND 
       13.48        12.00        13.12        36.56        39.55        12.59 
TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 
       35.77        20.05        21.57         9.86        11.90        14.30 
TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 
        0.62         2.10         6.12         1.38         2.76        21.21 
TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF 
       32.09        20.81        40.24         0.66        34.65         6.58 
TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
       34.59        35.64        34.13         0.79        12.53        13.32 
TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 
       39.09        22.75        12.89        24.10        17.06         0.69 
TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
        0.85        27.22         1.94         0.95        12.56         0.72 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54Y 
       17.75         0.76        26.07        18.41         0.62         0.23 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
        0.39         0.26         0.23        15.39        12.20        39.72 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
        8.48        18.21        18.90        13.25        16.57        15.68 
TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ 
       28.77        25.94        22.82        29.95        29.85        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 
       41.13        39.78        52.96        23.11        18.48        30.08 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
       18.90        19.99        13.94        10.52        14.43        34.55 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 
       19.96        55.00        52.73        25.91        22.09        21.27 
TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       10.16        10.59       109.87        59.57       194.27        53.13 
TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DL 
       53.52        43.04        42.71        42.28        61.91        90.84 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
       76.64        77.33        53.36       110.50        38.20        32.28 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW 
       69.30        53.95        57.63        13.55        18.12        11.84 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 
       11.57         8.28         6.67         4.60         0.66         2.99 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO 
        3.58         6.90         5.56         4.70         3.65         3.19 
TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 
        2.63         3.88         4.14         4.50         5.59         3.22 
TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 
        6.21        15.91         2.79         2.10        12.66         7.53 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       44.61        27.65        24.10        16.87        14.10        10.29 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O 
       14.76        23.70        54.51        31.07        18.21         7.23 
TCGA-OL-A66P TCGA-S3-A6ZG TCGA-W8-A86G 
        4.44         6.81         5.29 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.16               0.03 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            234.28             220.90 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             26.20              21.14 
[1] "0.2 - 234.3 (26.2)" "0.0 - 220.9 (21.1)"
[1] "hr=" "1.1"
D64V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12Q LOSS MUTATED         9        4        0        1        44        32
  12Q LOSS WILD-TYPE      71       73        9        8       291       192
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12Q LOSS MUTATED           0         11          7          6        1
  12Q LOSS WILD-TYPE         2        127         20         53       16
                    vv
clus                 STAGE TIS STAGE X
  12Q LOSS MUTATED           0       1
  12Q LOSS WILD-TYPE         1      15
D64V3, multiclass
            clus
vv           12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                   9                 71
  STAGE IA                  4                 73
  STAGE IB                  0                  9
  STAGE II                  1                  8
  STAGE IIA                44                291
  STAGE IIB                32                192
  STAGE III                 0                  2
  STAGE IIIA               11                127
  STAGE IIIB                7                 20
  STAGE IIIC                6                 53
  STAGE IV                  1                 16
  STAGE TIS                 0                  1
  STAGE X                   1                 15
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  12Q LOSS MUTATED    22  75  10   9
  12Q LOSS WILD-TYPE 236 506 107  27
D64V4, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1               22                236
  T2               75                506
  T3               10                107
  T4                9                 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                  N0  N1  N2  N3
  12Q LOSS MUTATED    61  38  10   6
  12Q LOSS WILD-TYPE 407 292 101  64
D64V5, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0               61                407
  N1               38                292
  N2               10                101
  N3                6                 64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  12Q LOSS MUTATED          0 107   1   9
  12Q LOSS WILD-TYPE        2 738  16 122
D64V6, multiclass
          clus
vv         12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CM0 (I+)                0                  2
  M0                    107                738
  M1                      1                 16
  MX                      9                122
[1] 4 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   117   0
  12Q LOSS WILD-TYPE 867  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED    117    0
  12Q LOSS WILD-TYPE  867   11
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE              117                867
  MALE                  0                 11
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  12Q LOSS MUTATED                            0                           100
  12Q LOSS WILD-TYPE                          1                           635
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  12Q LOSS MUTATED                                7                   2
  12Q LOSS WILD-TYPE                            159                   3
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  12Q LOSS MUTATED                                  1                  0
  12Q LOSS WILD-TYPE                               28                 14
                    vv
clus                 OTHER  SPECIFY
  12Q LOSS MUTATED                7
  12Q LOSS WILD-TYPE             37
D64V8, multiclass
                                  clus
vv                                 12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 100                635
  INFILTRATING LOBULAR CARCINOMA                  7                159
  MEDULLARY CARCINOMA                             2                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)                1                 28
  MUCINOUS CARCINOMA                              0                 14
  OTHER  SPECIFY                                  7                 37
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V9, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    37  80
  12Q LOSS WILD-TYPE 245 633
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     37   80
  12Q LOSS WILD-TYPE  245  633
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                37                245
  YES               80                633
[1] 2 2
[1] FALSE
D64V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q LOSS MUTATED                                  0     6
  12Q LOSS WILD-TYPE                                1    50
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED                          27    78
  12Q LOSS WILD-TYPE                       110   630
D64V11, multiclass
                                  clus
vv                                 12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           6                 50
  BLACK OR AFRICAN AMERICAN                      27                110
  WHITE                                          78                630
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V12, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     3 100
  12Q LOSS WILD-TYPE  33 696
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      3  100
  12Q LOSS WILD-TYPE   33  696
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 33
  NOT HISPANIC OR LATINO              100                696
[1] 2 2
[1] FALSE

Clustering(65) Variable = 13Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED   345  53
  13Q LOSS WILD-TYPE 515  61
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               398                576 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                53                 61 
$`13Q LOSS MUTATED`
TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SN TCGA-A1-A0SO 
       14.37        43.43        20.88        13.68        39.32        28.01 
TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04U TCGA-A2-A04X 
       19.20        18.21        18.02        41.95        22.06        55.43 
TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV 
       24.79       112.08        75.55        75.25         5.19        63.45 
TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D4 TCGA-A2-A0EO 
       64.04        56.81        21.14        34.55        25.22        80.28 
TCGA-A2-A0ER TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0T7 
       74.40        34.29        31.82        27.12        44.88        20.75 
TCGA-A2-A0YE TCGA-A2-A0YI TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV 
       18.21        14.50        14.63        31.73        23.77        23.47 
TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3Y0 TCGA-A2-A4RW 
       83.01        29.98        49.48        38.40        38.37         7.30 
TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A13D 
        9.01        12.00         6.74        38.30        30.61        31.73 
TCGA-A7-A13F TCGA-A7-A26E TCGA-A7-A26G TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3IZ 
       12.72        31.36        23.74        21.73        22.32        10.59 
TCGA-A7-A4SA TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX 
       14.93        14.50        17.92        10.29         9.37        10.42 
TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Y 
        8.75        13.02        17.98        41.06        29.03        26.01 
TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07L 
        1.02        53.98         9.01        33.01        18.97        17.03 
TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07W TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08B 
        9.99        10.98         9.99        36.95        13.02        23.08 
TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08S 
       18.05        12.00         9.99        31.00        31.00        19.07 
TCGA-A8-A08X TCGA-A8-A092 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09I TCGA-A8-A09K 
       33.99        16.01         9.99        12.00        33.07        29.98 
TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09X TCGA-A8-A0A2 TCGA-A8-A0A4 
       15.02         1.02        25.02        14.01        19.04        13.02 
TCGA-A8-A0A9 TCGA-A8-A0AD TCGA-AC-A23E TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2QH 
       13.02        38.04         2.37        38.53        38.20         1.02 
TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A62X TCGA-AC-A62Y 
        2.27         0.99         1.81         1.68         1.12         1.81 
TCGA-AC-A6IW TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A046 TCGA-AN-A04A TCGA-AN-A04C 
        0.69         1.74         0.33         0.33         2.96         1.78 
TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FS TCGA-AN-A0FX 
        1.71         8.02         0.33         0.33         6.28         0.33 
TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW 
        0.33         0.33         0.33         0.33         5.33         5.59 
TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A0J3 TCGA-AO-A0J4 
       80.28        66.77        81.63        68.75        21.40        17.65 
TCGA-AO-A0J6 TCGA-AO-A0JE TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM 
       37.48        76.77        38.53        62.04        55.33        71.80 
TCGA-AO-A124 TCGA-AO-A129 TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A1KQ 
      102.58        96.10        57.30        48.36        41.62        61.87 
TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04L TCGA-AQ-A1H2 
       70.39         0.53        17.79        24.79       130.09        15.62 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TV 
        2.56        21.86         9.99        82.88         5.26        29.75 
TCGA-AR-A0TX TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AH 
       64.83        76.14        65.36        83.87        55.36        75.55 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AR TCGA-AR-A1AW TCGA-AR-A1AY 
       61.84        52.77        51.25        17.23        35.24        20.22 
TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24N TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24T 
       50.89        73.02        68.19        66.05        62.07        53.26 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A255 
       54.18        50.96        51.75        45.17        40.64        34.82 
TCGA-AR-A256 TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A5QM TCGA-AR-A5QQ TCGA-B6-A0I1 
       93.83        42.87         7.36        54.74        10.59        77.62 
TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RL TCGA-B6-A0RP 
      129.57        65.72       140.88        68.45        81.17       102.77 
TCGA-B6-A0RQ TCGA-B6-A0RU TCGA-B6-A0WS TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX 
      140.48       131.21        97.48        79.63        17.98        21.47 
TCGA-B6-A0X5 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU 
       68.94        43.59       101.52        73.51       139.17       170.17 
TCGA-B6-A401 TCGA-B6-A408 TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B3 
       85.35        49.94        38.79        25.55        28.50        39.55 
TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BJ TCGA-BH-A0BP 
       56.94        56.98        37.22        32.02        21.70        48.69 
TCGA-BH-A0BR TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 
       53.69        49.94        11.67        49.05        41.75        44.02 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DH TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP 
       42.90        45.83        38.01        13.91        48.23        15.65 
TCGA-BH-A0E0 TCGA-BH-A0E9 TCGA-BH-A0EE TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H7 
        4.41        46.19        31.00        10.78        15.16        23.08 
TCGA-BH-A0HB TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0WA 
       26.50        12.89        27.25         5.59        23.93        23.05 
TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18Q TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U 
       90.84        26.66        55.63        66.05         7.36        51.39 
TCGA-BH-A1EN TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F6 
       69.93        42.28        12.00        17.69        25.81        97.48 
TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FU 
      114.15        33.17        74.73        36.92        63.35        72.07 
TCGA-BH-A202 TCGA-BH-A209 TCGA-BH-A28Q TCGA-C8-A12M TCGA-C8-A12O TCGA-C8-A12P 
        0.72       130.16         6.44        11.77        12.66        11.77 
TCGA-C8-A12U TCGA-C8-A130 TCGA-C8-A135 TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI 
       12.66         3.12         0.62        10.92        11.34        11.34 
TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26X TCGA-C8-A26Y 
       12.03         2.30         3.25         0.30         0.36         0.43 
TCGA-C8-A274 TCGA-C8-A278 TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 
        0.03         0.03         0.23        11.90        20.88        13.25 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 
       13.97        14.17        13.48        21.14        14.17        17.49 
TCGA-D8-A1JA TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JI 
       16.50        15.78        18.15        18.90        12.03        18.97 
TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JT TCGA-D8-A1X5 TCGA-D8-A1X6 
       20.12        20.09        19.40        13.32        18.58        17.79 
TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XD TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XU 
       23.90        27.58        17.16        14.50        19.92        12.99 
TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27I 
       16.54        15.52         3.81        14.24        14.14        14.43 
TCGA-D8-A27N TCGA-D8-A27T TCGA-E2-A107 TCGA-E2-A10C TCGA-E2-A14N TCGA-E2-A14O 
        4.80        13.08        34.42        40.11        47.15        44.68 
TCGA-E2-A14W TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A155 TCGA-E2-A159 TCGA-E2-A15G 
       32.02        25.41        27.12        21.04        25.05        18.21 
TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A1AZ 
        7.73        13.02        19.56        17.06        14.07        60.53 
TCGA-E2-A1II TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-E2-A1LK 
       33.70        22.19        20.98        39.62        18.87         8.75 
TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A56Z TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA 
       43.04        16.93         7.20        13.48        13.12        36.56 
TCGA-E9-A1NE TCGA-E9-A1NI TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RD 
       35.77         9.86         2.76        32.09        20.81         0.66 
TCGA-E9-A1RG TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A247 TCGA-E9-A249 
       21.27        12.89        23.51        24.10        27.22         0.95 
TCGA-E9-A295 TCGA-E9-A3QA TCGA-E9-A54Y TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW 
        0.72         0.62         0.23         0.23        15.39        12.20 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P3 TCGA-EW-A1P5 
       25.94        22.82        29.85        40.41        52.96        23.11 
TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PC TCGA-EW-A1PF TCGA-EW-A1PH TCGA-EW-A2FS 
        7.86        18.90         6.15        14.43        19.96        52.73 
TCGA-EW-A3U0 TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH 
       17.49        53.13        53.52        43.04        42.71        42.28 
TCGA-GM-A2DL TCGA-GM-A3NW TCGA-GM-A3XL TCGA-LD-A66U TCGA-LD-A74U TCGA-LL-A5YM 
       90.84       110.50        69.30         8.28         6.67         4.70 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-OL-A5D7 
        3.19         3.25         3.88         5.59         3.22        46.55 
TCGA-OL-A5DA TCGA-OL-A5RW TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66I TCGA-OL-A66K 
       44.61        26.20        10.29         9.80        23.70        33.90 
TCGA-OL-A66N TCGA-OL-A66O 
       18.21         7.23 

$`13Q LOSS WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SK TCGA-A1-A0SM 
        8.52        48.10        14.27        47.24        31.79         7.96 
TCGA-A2-A04N TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04Y 
      104.81        82.16        73.84        63.12        64.04        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0D2 
      125.59        64.57        92.48        88.60       107.93        33.76 
TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ES 
       28.77       101.72        89.36       107.61        79.76        37.05 
TCGA-A2-A0ET TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU 
       35.05        29.75        24.72        24.16        99.19        54.64 
TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 
       50.43        44.28        17.52        17.13         8.38        18.71 
TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF 
       20.52        17.46        18.90        32.55        25.28        15.42 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A1FW TCGA-A2-A1FX 
       21.90        21.67        18.61        19.33        17.36        36.79 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       22.45        20.25        19.20        19.56        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
      107.70        16.31        17.19        18.15        91.92        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XV TCGA-A2-A3XY TCGA-A2-A3XZ 
       20.88        39.65        33.93        14.07        34.98        31.99 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH 
        8.81         8.91         3.42        35.31        34.29        35.47 
TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H 
       37.45        35.67        33.11        10.72        23.61        29.56 
TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3J0 TCGA-A7-A3J1 
       24.26        23.80        20.61        11.34        10.29        11.28 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A56D 
       13.41        14.70        11.97        13.74        21.17        14.73 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06X 
       12.10        10.72        11.05        13.02         1.02        31.00 
TCGA-A8-A075 TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07R 
       17.03        19.99        18.97        14.01        12.00         8.98 
TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A08A 
        7.99         9.96        28.04        18.05        15.06         0.99 
TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08Z 
       19.99        19.96        37.05         0.99        93.04        40.01 
TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09C 
       19.07        17.95        41.98        12.00         9.99         1.02 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
       13.02        31.00         8.98        19.04        15.02         0.99 
TCGA-A8-A0A1 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0AB TCGA-AC-A23C TCGA-AC-A23G 
       12.00        21.04         0.99        17.03         0.95        10.85 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
        2.66         1.48        40.57        55.43        36.99        38.79 
TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
       26.04        50.70         0.92         0.69        14.83         9.40 
TCGA-AC-A3TN TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A6IV 
        1.12         1.55         1.32         1.55         0.07         1.18 
TCGA-AC-A6IX TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A0AK TCGA-AN-A0AL 
        0.43         0.33         0.23         0.62         7.36         6.51 
TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK 
        0.16         0.33         6.44         4.64         7.96         7.00 
TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FZ 
        7.59         7.17         6.02         0.33         0.36         0.33 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AO-A03M 
       12.33         0.30         0.33         0.33         0.33        47.84 
TCGA-AO-A03P TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J5 
       84.69        47.87        59.05        29.13        32.78        24.16 
TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC 
       20.32        22.36        53.03        21.53        50.70        50.86 
TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 
       72.00        21.37        26.24        99.25        93.70        94.59 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       90.58        77.56        64.04        28.37        14.73        82.62 
TCGA-AQ-A04J TCGA-AQ-A0Y5 TCGA-AQ-A1H3 TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT 
       26.93         5.65        13.22        49.32        37.41        56.88 
TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A1AL TCGA-AR-A1AM 
       24.30        55.86        70.16        76.18        48.82        62.56 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU 
       43.73        43.56        39.98        43.07        40.83        46.32 
TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A24H TCGA-AR-A24M TCGA-AR-A24O TCGA-AR-A24P 
       42.58        36.26       109.58        65.46        65.69         0.85 
TCGA-AR-A24R TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A254 TCGA-AR-A2LE 
       57.40        53.36        48.16        56.15        39.85       128.65 
TCGA-AR-A2LH TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
       20.25        40.04        17.10        20.81        16.96        20.38 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA 
       16.04        20.45       143.38       149.59        12.13       220.90 
TCGA-B6-A0IC TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM 
       50.70       146.50       112.37       176.98        18.77       126.12 
TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RI 
       84.59       110.14       110.93       211.56       189.01       234.28 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RV 
       78.02       172.96       162.05       100.70        89.46       157.41 
TCGA-B6-A0WT TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
      188.68       113.79       129.57       129.70       186.48        28.27 
TCGA-B6-A0X7 TCGA-B6-A402 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW 
       58.88        54.28        82.88        55.00        24.53        20.45 
TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B9 TCGA-BH-A0BD 
       46.95        40.83        39.16        48.36        51.68        18.21 
TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ 
       25.71        24.85        44.05        61.68        35.67        27.19 
TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0C3 TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DI 
       53.95        45.57        48.13        31.17        23.44        22.13 
TCGA-BH-A0DO TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       17.26         3.22         2.56        38.47        45.17        47.41 
TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0EA 
       16.27        15.68        14.30         9.63        44.81        32.65 
TCGA-BH-A0EB TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       24.49        24.43        30.35        37.78        35.51        24.56 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       41.00        52.96        20.38         5.85         2.50        13.61 
TCGA-BH-A0HQ TCGA-BH-A0HW TCGA-BH-A0HY TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       36.85        51.32        50.79        24.95        42.35        44.81 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18M TCGA-BH-A18N 
        8.81         2.01         7.23        20.12        72.56        37.74 
TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET 
       30.28        37.55        51.16        91.99       113.82        82.85 
TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F8 TCGA-BH-A1FB 
       55.69        49.58        31.53        89.16        24.66       120.62 
TCGA-BH-A1FG TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A201 
      122.89        55.00        45.63        72.07       144.59         6.90 
TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A28O TCGA-BH-A2L8 TCGA-BH-A42T 
       38.60        83.31        57.83        10.65        20.12         0.99 
TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12L TCGA-C8-A12N TCGA-C8-A12Q TCGA-C8-A12V 
      109.28         8.94        11.93        11.77         0.07        12.66 
TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 
       12.66        12.66         1.78         1.45         0.69         3.85 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A26W TCGA-C8-A26Z 
        3.75        12.33         0.16        10.42         0.23         8.28 
TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-D8-A141 
        9.67         0.03        12.20         0.99         0.03        20.58 
TCGA-D8-A147 TCGA-D8-A1JB TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JJ TCGA-D8-A1JN 
       19.20        18.71        12.03        14.01        20.09        20.38 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1XB 
       21.01        12.20        14.70        16.73        25.74        18.15 
TCGA-D8-A1XC TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XM TCGA-D8-A1XO 
        2.66        15.22        14.73        21.83        17.69         7.96 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW 
       16.41        15.85        16.31         6.35        15.16        12.66 
TCGA-D8-A1XZ TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27K 
       15.32        17.42        16.04        13.45        13.05         9.44 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27V TCGA-D8-A27W 
       16.41        13.48         0.76        10.09        12.53        12.26 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A109 
       14.50        18.51         7.33        43.00        27.52        46.59 
TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14P TCGA-E2-A14Q 
       40.41        37.51        28.44        28.87        40.96        38.24 
TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14X 
       38.60        33.17        33.30        43.33        34.26        31.96 
TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A156 TCGA-E2-A158 
       28.60        17.03        23.24        19.43        23.87        14.79 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15H 
       23.34        22.82        17.29        20.71        21.63        12.92 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15T TCGA-E2-A1B0 
       17.42        19.40         9.04        20.58        14.99        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD 
       53.03        29.95        32.35        28.50        16.47        17.10 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK 
       38.30        37.41        32.78        33.73        28.44        22.65 
TCGA-E2-A1IL TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA 
        3.88        11.08        54.18        27.42        19.66        24.59 
TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A2P6 TCGA-E2-A3DX 
       40.47        28.90       106.75       102.61         5.52        15.72 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 
       18.05        22.26        19.89        19.20        36.82        12.00 
TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1QZ TCGA-E9-A1R0 
       39.55        12.59        20.05        21.57        11.90        14.30 
TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RC 
        0.62         2.10         6.12         1.38        21.21        40.24 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
       34.65         6.58        34.59        35.64        34.13         0.79 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A243 TCGA-E9-A244 
       12.53        13.32        39.09        22.75        17.06         0.69 
TCGA-E9-A245 TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO 
        0.85         1.94        12.56        17.75         0.76        26.07 
TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A5FK TCGA-E9-A5FL TCGA-EW-A1IX TCGA-EW-A1IY 
       18.41        15.72         0.39         0.26        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 
       18.21        18.90        13.25        16.57        15.68        28.77 
TCGA-EW-A1OX TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 
       29.95        41.13        39.78        29.82        18.48        30.08 
TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PG TCGA-EW-A2FR TCGA-EW-A2FV 
       19.99        13.94        10.52        34.55        55.00        25.91 
TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 
       22.09        21.27        10.16        10.59         7.40       109.87 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DM TCGA-GM-A2DN 
       59.57       194.27        61.91        62.33        76.64        77.33 
TCGA-GM-A2DO TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV 
       53.36        38.20        32.28        53.95        57.63        13.55 
TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 
       18.12        11.84        11.57         4.60         0.66         2.99 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A6FQ TCGA-LL-A73Y 
        3.58         6.90         5.56         3.65         2.63         4.14 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 
        4.50         4.50         6.21        15.91         2.79         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY 
       12.66         7.53        27.65        24.10        16.87        14.10 
TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66P TCGA-S3-A6ZG TCGA-W8-A86G 
       14.76        54.51        31.07         4.44         6.81         5.29 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.03               0.03 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            170.17             234.28 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            21.795             21.190 
[1] "0.0 - 170.2 (21.8)" "0.0 - 234.3 (21.2)"
[1] "hr=" "1.5"
D65V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  13Q LOSS MUTATED        31       24        3        3       148        95
  13Q LOSS WILD-TYPE      49       53        6        6       187       129
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  13Q LOSS MUTATED           1         58         10         21        7
  13Q LOSS WILD-TYPE         1         80         17         38       10
                    vv
clus                 STAGE TIS STAGE X
  13Q LOSS MUTATED           1       5
  13Q LOSS WILD-TYPE         0      11
D65V3, multiclass
            clus
vv           13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                  31                 49
  STAGE IA                 24                 53
  STAGE IB                  3                  6
  STAGE II                  3                  6
  STAGE IIA               148                187
  STAGE IIB                95                129
  STAGE III                 1                  1
  STAGE IIIA               58                 80
  STAGE IIIB               10                 17
  STAGE IIIC               21                 38
  STAGE IV                  7                 10
  STAGE TIS                 1                  0
  STAGE X                   5                 11
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  13Q LOSS MUTATED    88 253  51  15
  13Q LOSS WILD-TYPE 170 328  66  21
D65V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1               88                170
  T2              253                328
  T3               51                 66
  T4               15                 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                  N0  N1  N2  N3
  13Q LOSS MUTATED   195 133  48  26
  13Q LOSS WILD-TYPE 273 197  63  44
D65V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0              195                273
  N1              133                197
  N2               48                 63
  N3               26                 44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  13Q LOSS MUTATED          1 345   7  55
  13Q LOSS WILD-TYPE        1 500  10  76
D65V6, multiclass
          clus
vv         13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CM0 (I+)                1                  1
  M0                    345                500
  M1                      7                 10
  MX                     55                 76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED   403   5
  13Q LOSS WILD-TYPE 581   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED    403    5
  13Q LOSS WILD-TYPE  581    6
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE              403                581
  MALE                  5                  6
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  13Q LOSS MUTATED                            0                           329
  13Q LOSS WILD-TYPE                          1                           406
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  13Q LOSS MUTATED                               48                   4
  13Q LOSS WILD-TYPE                            118                   1
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  13Q LOSS MUTATED                                 10                  2
  13Q LOSS WILD-TYPE                               19                 12
                    vv
clus                 OTHER  SPECIFY
  13Q LOSS MUTATED               14
  13Q LOSS WILD-TYPE             30
D65V8, multiclass
                                  clus
vv                                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 329                406
  INFILTRATING LOBULAR CARCINOMA                 48                118
  MEDULLARY CARCINOMA                             4                  1
  MIXED HISTOLOGY (PLEASE SPECIFY)               10                 19
  MUCINOUS CARCINOMA                              2                 12
  OTHER  SPECIFY                                 14                 30
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V9, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED   120 288
  13Q LOSS WILD-TYPE 162 425
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED    120  288
  13Q LOSS WILD-TYPE  162  425
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO               120                162
  YES              288                425
[1] 2 2
[1] FALSE
D65V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q LOSS MUTATED                                  0    22
  13Q LOSS WILD-TYPE                                1    34
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED                          71   268
  13Q LOSS WILD-TYPE                        66   440
D65V11, multiclass
                                  clus
vv                                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          22                 34
  BLACK OR AFRICAN AMERICAN                      71                 66
  WHITE                                         268                440
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V12, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    11 316
  13Q LOSS WILD-TYPE  25 480
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     11  316
  13Q LOSS WILD-TYPE   25  480
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   11                 25
  NOT HISPANIC OR LATINO              316                480
[1] 2 2
[1] FALSE

Clustering(66) Variable = 14Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED   201  35
  14Q LOSS WILD-TYPE 659  79
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               236                738 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                35                 79 
$`14Q LOSS MUTATED`
TCGA-A1-A0SK TCGA-A1-A0SP TCGA-A2-A04P TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W 
       31.79        19.20        18.02        73.84        22.06        64.04 
TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0EQ TCGA-A2-A0ET TCGA-A2-A0EU 
        5.19        64.04        21.14        79.76        35.05        34.29 
TCGA-A2-A0SV TCGA-A2-A0SX TCGA-A2-A0YE TCGA-A2-A0YJ TCGA-A2-A0YT TCGA-A2-A1G1 
       27.12        50.43        18.21        18.61        23.77        19.20 
TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XX TCGA-A2-A3Y0 TCGA-A2-A4S1 
       33.93        83.01        29.98        38.40        38.37        12.00 
TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A26G 
        3.42        35.31        31.73        10.72        12.72        23.74 
TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE 
       21.73        22.32        11.28        13.74        14.50        21.17 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06X 
       10.29         9.37        10.42         8.75        13.02        31.00 
TCGA-A8-A06Z TCGA-A8-A07F TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A07W 
        1.02        18.97        17.03         9.99         8.98         9.99 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08L TCGA-A8-A097 TCGA-A8-A09I TCGA-A8-A09K 
       18.05        19.96         9.99        12.00        33.07        29.98 
TCGA-A8-A09N TCGA-A8-A0A6 TCGA-A8-A0AB TCGA-AC-A23C TCGA-AC-A2BK TCGA-AC-A2BM 
        1.02        21.04        17.03         0.95        38.53        38.20 
TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A62X TCGA-AC-A6IW TCGA-AN-A04C TCGA-AN-A0AK 
        1.02         2.27         1.12         0.69         1.78         7.36 
TCGA-AN-A0FJ TCGA-AN-A0FX TCGA-AN-A0XN TCGA-AO-A0J4 TCGA-AO-A0J6 TCGA-AO-A0JL 
        7.96         0.33         0.33        17.65        37.48        55.33 
TCGA-AO-A124 TCGA-AO-A129 TCGA-AO-A12F TCGA-AO-A1KR TCGA-AQ-A04L TCGA-AQ-A0Y5 
      102.58        96.10        48.36        70.39       130.09         5.65 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0U0 
        2.56        21.86         5.26        56.88        29.75        65.36 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AM TCGA-AR-A1AP TCGA-AR-A1AQ 
       75.55        61.84        52.77        62.56        39.98        43.07 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24Q TCGA-AR-A24V TCGA-AR-A251 
       36.26        20.22       109.58        66.05        54.18        45.17 
TCGA-AR-A255 TCGA-AR-A256 TCGA-B6-A0I9 TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IO 
       34.82        93.83        12.13       112.37       176.98       110.14 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RL TCGA-B6-A0WS TCGA-B6-A0WW TCGA-B6-A0WX 
      140.88       211.56        81.17        97.48        17.98        21.47 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW 
       43.59       101.52        73.51        24.53        38.79        20.45 
TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BF TCGA-BH-A0BG 
       39.55        48.36        56.98        51.68        25.71        24.85 
TCGA-BH-A0BJ TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C7 TCGA-BH-A0E0 
       21.70        11.67        49.05        44.02        42.90         4.41 
TCGA-BH-A0E6 TCGA-BH-A0H7 TCGA-BH-A0RX TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18Q 
        9.63        23.08         5.59        23.05         8.81        55.63 
TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EW TCGA-BH-A1EY TCGA-BH-A1F6 TCGA-BH-A1F8 
        7.36        51.39        55.69        17.69        97.48        24.66 
TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A202 TCGA-BH-A42T TCGA-C8-A12L TCGA-C8-A12M 
      114.15        74.73         0.72         0.99        11.93        11.77 
TCGA-C8-A12X TCGA-C8-A134 TCGA-C8-A1HF TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN 
       12.66         0.69        10.92        12.03         2.30         3.25 
TCGA-C8-A26Y TCGA-C8-A27B TCGA-D8-A142 TCGA-D8-A1JC TCGA-D8-A1JG TCGA-D8-A1JJ 
        0.43         0.99        13.97        15.78        12.03        20.09 
TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JP TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XG 
       20.09        19.40        21.01        27.58        18.15        14.73 
TCGA-D8-A1XK TCGA-D8-A1XO TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1Y0 
       14.50         7.96         6.35        12.99        16.54        15.52 
TCGA-D8-A1Y3 TCGA-D8-A27I TCGA-D8-A27M TCGA-D8-A27R TCGA-D8-A27T TCGA-E2-A108 
       14.14        14.43        13.48        10.09        13.08        27.52 
TCGA-E2-A14R TCGA-E2-A14T TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A155 TCGA-E2-A159 
       38.60        33.30        17.03        25.41        21.04        25.05 
TCGA-E2-A15A TCGA-E2-A15F TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A1AZ TCGA-E2-A1IH 
       23.34        21.63         7.73        19.56        60.53        33.73 
TCGA-E2-A1II TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A56Z TCGA-E2-A573 
       33.70        28.90       106.75       102.61         7.20        22.26 
TCGA-E2-A574 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1QZ TCGA-E9-A1R4 
       19.89        13.48        12.00        13.12        11.90         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1RB TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22G 
        1.38         2.76        20.81        39.09        22.75        23.51 
TCGA-E9-A2JS TCGA-E9-A3HO TCGA-E9-A3QA TCGA-EW-A1IZ TCGA-EW-A1J6 TCGA-EW-A1OV 
       17.75        26.07         0.62        18.21        28.77        25.94 
TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P8 TCGA-EW-A1PF TCGA-EW-A1PH TCGA-EW-A2FR 
       22.82        29.82         7.86        14.43        19.96        55.00 
TCGA-EW-A2FV TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C9 TCGA-GM-A2DH 
       25.91        17.49        10.16        10.59       109.87        42.28 
TCGA-GM-A2DK TCGA-GM-A3XL TCGA-GM-A5PX TCGA-JL-A3YX TCGA-LL-A441 TCGA-LL-A5YP 
       62.33        69.30        18.12        11.57         2.99         3.25 
TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-OL-A5D7 TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66I 
        3.22         6.21        46.55        10.29         9.80        23.70 
TCGA-OL-A66K TCGA-OL-A66N 
       33.90        18.21 

$`14Q LOSS WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ 
       20.88        13.68         7.96        39.32        28.01        18.21 
TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04X TCGA-A2-A04Y 
      104.81        41.95        82.16        63.12        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
      125.59        64.57        24.79       112.08        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D1 
      107.93        75.55        75.25        63.45        56.81        34.55 
TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO 
       33.76        28.77        25.22       101.72        89.36        80.28 
TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
      107.61        74.40        37.05        31.82        29.75        24.72 
TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 
       24.16        99.19        54.64        44.88        44.28        17.52 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.13         8.38        18.71        20.52        17.46        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH 
       20.75        32.55        25.28        15.42        21.90        21.67 
TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FW 
       14.50        19.33        14.63        31.73        23.47        17.36 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       36.79        22.45        20.25        19.56        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
      107.70        16.31        17.19        18.15        91.92        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XY TCGA-A2-A3XZ 
       20.88        39.65        14.07        49.48        34.98        31.99 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A7-A0CD 
        7.30         9.01         8.81         8.91         6.74        38.30 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB 
       34.29        35.47        30.61        37.45        35.67        33.11 
TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26J 
       23.61        29.56        31.36        24.26        23.80        20.61 
TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 
       11.34        10.59        10.29        13.41        14.70        11.97 
TCGA-A7-A4SA TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX 
       14.93        17.92        14.73        12.10        10.72        11.05 
TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Y 
       13.02         1.02        17.98        41.06        29.03        26.01 
TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07G 
       17.03        53.98         9.01        33.01        19.99        18.97 
TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07Z 
       14.01        12.00        10.98         7.99         9.96        28.04 
TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B 
       18.05        15.06        36.95        13.02         0.99        23.08 
TCGA-A8-A08C TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R 
       19.99        12.00        37.05        31.00        31.00         0.99 
TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 
       19.07        93.04        33.99        40.01        19.07        16.01 
TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C 
       17.95        41.98         9.99         9.99        12.00         1.02 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T 
       13.02        31.00        15.02        25.02         8.98        19.04 
TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 
       15.02         0.99        14.01        12.00        19.04        13.02 
TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AD TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H 
        0.99        13.02        38.04         2.37        10.85         2.66 
TCGA-AC-A2B8 TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM 
        1.48        40.57        55.43        36.99        38.79        26.04 
TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
       50.70         0.92         0.99         0.69        14.83         9.40 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS 
        1.12         1.81         1.68         1.55         1.32         1.55 
TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AN-A03X 
        0.07         1.81         1.18         0.43         1.74         0.33 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D 
        0.33         0.23         0.33         0.62         2.96         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT 
        8.02         6.51         0.16         0.33         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        6.44         4.64         7.00         7.59         7.17         6.28 
TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL 
        6.02         0.33         0.36         0.33         0.33         0.33 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU 
       12.33         0.30         0.33         0.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O 
        5.33         5.59        80.28        47.84        66.77        81.63 
TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 
       84.69        68.75        47.87        59.05        29.13        32.78 
TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA 
       21.40        24.16        20.32        22.36        53.03        21.53 
TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG 
       50.70        50.86        72.00        76.77        21.37        26.24 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 
       38.53        62.04        71.80        99.25        93.70        94.59 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H 
       90.58        77.56        64.04        57.30        41.62        28.37 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H 
       14.73        82.62        61.87         0.53        17.79        24.79 
TCGA-AQ-A04J TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ 
       26.93        15.62        13.22         9.99        82.88        49.32 
TCGA-AR-A0TS TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 
       37.41        24.30        64.83        55.86        76.14        70.16 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN 
       83.87        76.18        55.36        51.25        48.82        43.73 
TCGA-AR-A1AO TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       43.56        17.23        40.83        46.32        42.58        35.24 
TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
       50.89        73.02        65.46        68.19        65.69         0.85 
TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24W TCGA-AR-A24X 
       57.40        62.07        53.26        53.36        50.96        48.16 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A2LE TCGA-AR-A2LH 
       51.75        56.15        40.64        39.85       128.65        20.25 
TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       42.87         7.36        40.04        17.10        20.81        16.96 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       20.38        54.74        16.04        20.45        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
      143.38       149.59       220.90       129.57        50.70        65.72 
TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0RG 
      146.50        18.77       126.12        84.59       110.93        68.45 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP 
      189.01       234.28        78.02       172.96       162.05       102.77 
TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WT 
      140.48       100.70        89.46       131.21       157.41       188.68 
TCGA-B6-A0WV TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
       79.63       113.79       129.57       129.70       186.48        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 
       68.94        58.88       139.17       170.17        85.35        54.28 
TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 
       49.94        82.88        55.00        25.55        28.50        46.95 
TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
       40.83        39.16        56.94        37.22        32.02        18.21 
TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR 
       44.05        61.68        35.67        48.69        27.19        53.69 
TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0DD 
       53.95        45.57        49.94        41.75        48.13        45.83 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL 
       31.17        23.44        38.01        22.13        13.91        48.23 
TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       17.26        15.65         3.22         2.56        38.47        45.17 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0E9 
       47.41        16.27        15.68        14.30        44.81        46.19 
TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ 
       32.65        24.49        31.00        24.43        30.35        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HA 
       15.16        37.78        35.51        24.56        41.00        52.96 
TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ 
       26.50        20.38         5.85         2.50        13.61        36.85 
TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0W3 TCGA-BH-A0W4 
       12.89        51.32        27.25        50.79        23.93        24.95 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K 
       42.35        44.81         2.01         7.23        20.12        90.84 
TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S 
       26.66        72.56        37.74        30.28        37.55        66.05 
TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU 
       51.16        69.93        91.99       113.82        82.85        42.28 
TCGA-BH-A1EV TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1FB 
       12.00        49.58        25.81        31.53        89.16       120.62 
TCGA-BH-A1FD TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM 
       33.17       122.89        36.92        63.35        55.00        45.63 
TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A204 
       72.07       144.59        72.07         6.90        38.60        83.31 
TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42U 
       57.83       130.16        10.65         6.44        20.12       109.28 
TCGA-BH-A42V TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U 
        8.94        11.77        12.66        11.77         0.07        12.66 
TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A135 
       12.66        12.66         3.12         1.78         1.45         0.62 
TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ 
        3.85         3.75        12.33        11.34        11.34         0.16 
TCGA-C8-A1HL TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 
       10.42         0.30         0.23         0.36         8.28         9.67 
TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A3M7 TCGA-C8-A3M8 
        0.03         0.03         0.03        12.20         0.03         0.23 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A145 
       11.90        20.88        13.25        20.58        14.17        13.48 
TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
       21.14        19.20        14.17        17.49        16.50        18.71 
TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JK 
       18.15        18.90        12.03        14.01        18.97        20.12 
TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 
       20.38        12.20        13.32        14.70        18.58        17.79 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF 
       16.73        25.74        23.90         2.66        17.16        15.22 
TCGA-D8-A1XJ TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS 
       21.83        19.92        17.69        16.41        15.85        16.31 
TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E 
       15.16        12.66        15.32         3.81        14.24        17.42 
TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27N 
       16.04        13.45        13.05         9.44        16.41         4.80 
TCGA-D8-A27P TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 
        0.76        12.53        12.26        14.50        18.51         7.33 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C 
       43.00        34.42        46.59        40.41        37.51        40.11 
TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q 
       28.44        28.87        47.15        44.68        40.96        38.24 
TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y 
       33.17        43.33        34.26        32.02        31.96        28.60 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15C 
       27.12        23.24        19.43        23.87        14.79        22.82 
TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J 
       17.29        20.71        18.21        12.92        17.42        19.40 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
        9.04        20.58        13.02        17.06        14.07        14.99 
TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC 
       53.62        53.03        29.95        32.35        28.50        16.47 
TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IJ TCGA-E2-A1IK 
       17.10        38.30        37.41        32.78        28.44        22.65 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 
        3.88        22.19        20.98        11.08        54.18        27.42 
TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LG TCGA-E2-A1LK 
       39.62        19.66        24.59        40.47        18.87         8.75 
TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E9-A1N4 
       43.04        16.93         5.52        15.72        18.05        19.20 
TCGA-E9-A1N5 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF 
       36.82        36.56        39.55        12.59        35.77        20.05 
TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R7 
       21.57         9.86        14.30         0.62         2.10        21.21 
TCGA-E9-A1RA TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG 
       32.09        40.24         0.66        34.65         6.58        21.27 
TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
       34.59        35.64        34.13         0.79        12.53        13.32 
TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A247 
       12.89        24.10        17.06         0.69         0.85        27.22 
TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JT TCGA-E9-A3Q9 
        1.94         0.95        12.56         0.72         0.76        18.41 
TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE 
       15.72         0.23         0.39         0.26         0.23        15.39 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 
       12.20        39.72         8.48        18.90        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 
       15.68        29.95        29.85        40.41        41.13        39.78 
TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB 
       52.96        23.11        18.48        30.08        18.90        19.99 
TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PG TCGA-EW-A2FS TCGA-EW-A2FW 
        6.15        13.94        10.52        34.55        52.73        22.09 
TCGA-EW-A3E8 TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC 
       21.27         7.40        59.57       194.27        53.13        53.52 
TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       43.04        42.71        61.91        90.84        76.64        77.33 
TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 
       53.36       110.50        38.20        32.28        53.95        57.63 
TCGA-GM-A5PV TCGA-JL-A3YW TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 
       13.55        11.84         8.28         6.67         4.60         0.66 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO 
        3.58         6.90         5.56         4.70         3.65         3.19 
TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ 
        2.63         3.88         4.14         4.50         4.50         5.59 
TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA 
       15.91         2.79         2.10        12.66         7.53        44.61 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A66H 
       27.65        24.10        26.20        16.87        14.10        14.76 
TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P TCGA-S3-A6ZG TCGA-W8-A86G 
       54.51        31.07         7.23         4.44         6.81         5.29 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.33               0.03 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            211.56             234.28 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            21.025             21.865 
[1] "0.3 - 211.6 (21.0)" "0.0 - 234.3 (21.9)"
[1] "hr=" "1.6"
D66V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  14Q LOSS MUTATED        19       19        0        2        90        55
  14Q LOSS WILD-TYPE      61       58        9        7       245       169
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  14Q LOSS MUTATED           0         29          4         14        4
  14Q LOSS WILD-TYPE         2        109         23         45       13
                    vv
clus                 STAGE TIS STAGE X
  14Q LOSS MUTATED           0       3
  14Q LOSS WILD-TYPE         1      13
D66V3, multiclass
            clus
vv           14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                  19                 61
  STAGE IA                 19                 58
  STAGE IB                  0                  9
  STAGE II                  2                  7
  STAGE IIA                90                245
  STAGE IIB                55                169
  STAGE III                 0                  2
  STAGE IIIA               29                109
  STAGE IIIB                4                 23
  STAGE IIIC               14                 45
  STAGE IV                  4                 13
  STAGE TIS                 0                  1
  STAGE X                   3                 13
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  14Q LOSS MUTATED    51 159  24   5
  14Q LOSS WILD-TYPE 207 422  93  31
D66V4, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1               51                207
  T2              159                422
  T3               24                 93
  T4                5                 31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  14Q LOSS MUTATED   131  66  26  14
  14Q LOSS WILD-TYPE 337 264  85  56
D66V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0              131                337
  N1               66                264
  N2               26                 85
  N3               14                 56
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  14Q LOSS MUTATED          0 202   4  34
  14Q LOSS WILD-TYPE        2 643  13  97
D66V6, multiclass
          clus
vv         14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CM0 (I+)                0                  2
  M0                    202                643
  M1                      4                 13
  MX                     34                 97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED   239   1
  14Q LOSS WILD-TYPE 745  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED    239    1
  14Q LOSS WILD-TYPE  745   10
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE              239                745
  MALE                  1                 10
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  14Q LOSS MUTATED                            0                           200
  14Q LOSS WILD-TYPE                          1                           535
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  14Q LOSS MUTATED                               22                   4
  14Q LOSS WILD-TYPE                            144                   1
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  14Q LOSS MUTATED                                  3                  1
  14Q LOSS WILD-TYPE                               26                 13
                    vv
clus                 OTHER  SPECIFY
  14Q LOSS MUTATED                9
  14Q LOSS WILD-TYPE             35
D66V8, multiclass
                                  clus
vv                                 14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 200                535
  INFILTRATING LOBULAR CARCINOMA                 22                144
  MEDULLARY CARCINOMA                             4                  1
  MIXED HISTOLOGY (PLEASE SPECIFY)                3                 26
  MUCINOUS CARCINOMA                              1                 13
  OTHER  SPECIFY                                  9                 35
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V9, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    75 165
  14Q LOSS WILD-TYPE 207 548
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     75  165
  14Q LOSS WILD-TYPE  207  548
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                75                207
  YES              165                548
[1] 2 2
[1] FALSE
D66V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q LOSS MUTATED                                  0    13
  14Q LOSS WILD-TYPE                                1    43
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED                          52   153
  14Q LOSS WILD-TYPE                        85   555
D66V11, multiclass
                                  clus
vv                                 14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          13                 43
  BLACK OR AFRICAN AMERICAN                      52                 85
  WHITE                                         153                555
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V12, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    11 189
  14Q LOSS WILD-TYPE  25 607
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     11  189
  14Q LOSS WILD-TYPE   25  607
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   11                 25
  NOT HISPANIC OR LATINO              189                607
[1] 2 2
[1] FALSE

Clustering(67) Variable = 15Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED   251  40
  15Q LOSS WILD-TYPE 609  74
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               291                683 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                40                 74 
$`15Q LOSS MUTATED`
TCGA-A1-A0SI TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04T 
       20.88        28.01        19.20        18.02        41.95        73.84 
TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CS TCGA-A2-A0CT 
       22.06        64.04        64.57        24.79        75.55        75.25 
TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EQ 
       64.04        56.81        21.14        89.36        80.28        79.76 
TCGA-A2-A0ET TCGA-A2-A0EY TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX 
       35.05        24.16        54.64        27.12        44.88        50.43 
TCGA-A2-A0T0 TCGA-A2-A0T7 TCGA-A2-A0YE TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A1G1 
       17.52        20.75        18.21        18.61        31.73        19.20 
TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XX TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4S1 
       33.93        29.98        38.40        38.37         7.30        12.00 
TCGA-A2-A4S3 TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A26E 
        3.42        30.61        35.67        31.73        10.72        31.36 
TCGA-A7-A26F TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A4SD TCGA-A7-A4SF 
       24.26        21.73        22.32        11.28        14.50        17.92 
TCGA-A7-A56D TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A8-A06R TCGA-A8-A06U 
       14.73        10.29         9.37        10.42        17.98        29.03 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07R 
       26.01         1.02        53.98        33.01        18.97         8.98 
TCGA-A8-A084 TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08X TCGA-A8-A092 
       15.06        12.00         9.99        31.00        33.99        16.01 
TCGA-A8-A093 TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09N TCGA-A8-A09W TCGA-A8-A0AB 
       17.95         9.99         1.02         1.02         0.99        17.03 
TCGA-AC-A23E TCGA-AC-A2BK TCGA-AC-A2FM TCGA-AC-A2QJ TCGA-AC-A3OD TCGA-AC-A62X 
        2.37        38.53        26.04         2.27        14.83         1.12 
TCGA-AC-A6IW TCGA-AC-A8OP TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AR TCGA-AN-A0FD 
        0.69         1.74         8.02         7.36         0.33         6.44 
TCGA-AN-A0FK TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY 
        7.00         6.02         0.33         0.36         0.33         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XS TCGA-AO-A03L TCGA-AO-A03M 
        0.33         0.33        12.33         0.33        80.28        47.84 
TCGA-AO-A03V TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A0JD TCGA-AO-A0JL 
       29.13        37.48        20.32        53.03        72.00        55.33 
TCGA-AO-A129 TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H 
       96.10        48.36        61.87         0.53        17.79        24.79 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TX 
        2.56        21.86         5.26        56.88        29.75        64.83 
TCGA-AR-A0TY TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ 
       55.86        65.36        70.16        75.55        61.84        52.77 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AW TCGA-AR-A1AY TCGA-AR-A24Q TCGA-AR-A24R 
       43.07        17.23        35.24        20.22        66.05        57.40 
TCGA-AR-A24S TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A256 
       62.07        54.18        50.96        51.75        56.15        93.83 
TCGA-AR-A2LK TCGA-AR-A2LR TCGA-B6-A0I1 TCGA-B6-A0IB TCGA-B6-A0IH TCGA-B6-A0IJ 
       42.87        20.38        77.62       129.57       112.37       176.98 
TCGA-B6-A0IO TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RP TCGA-B6-A0RS TCGA-B6-A0RU 
      110.14       211.56        68.45       102.77       100.70       131.21 
TCGA-B6-A0WV TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI 
       79.63        21.47       113.79        43.59       101.52        73.51 
TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0B2 TCGA-BH-A0B5 
       54.28        49.94        55.00        24.53        40.83        48.36 
TCGA-BH-A0B6 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BL TCGA-BH-A0BT TCGA-BH-A0BZ 
       56.94        51.68        37.22        44.05        45.57        49.05 
TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C7 TCGA-BH-A0DP TCGA-BH-A0DX TCGA-BH-A0E0 
       41.75        44.02        42.90        15.65        47.41         4.41 
TCGA-BH-A0E6 TCGA-BH-A0EB TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HP TCGA-BH-A0HU 
        9.63        24.49        23.08        41.00        13.61        12.89 
TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W7 TCGA-BH-A18F TCGA-BH-A18J 
       27.25        50.79         5.59        44.81         8.81        20.12 
TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO 
       90.84        26.66         7.36        51.39        69.93        91.99 
TCGA-BH-A1ES TCGA-BH-A1EV TCGA-BH-A1F6 TCGA-BH-A1FC TCGA-BH-A1FM TCGA-BH-A1FN 
      113.82        12.00        97.48       114.15        45.63        72.07 
TCGA-BH-A208 TCGA-C8-A12P TCGA-C8-A12X TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HF 
       57.83        11.77        12.66         0.62         3.75        10.92 
TCGA-C8-A1HK TCGA-C8-A1HN TCGA-C8-A26Y TCGA-C8-A278 TCGA-C8-A27A TCGA-D8-A13Z 
       12.03         3.25         0.43         0.03        12.20        20.88 
TCGA-D8-A142 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JE TCGA-D8-A1JF 
       13.97        21.14        14.17        17.49        18.90        12.03 
TCGA-D8-A1JG TCGA-D8-A1XB TCGA-D8-A1XF TCGA-D8-A1XJ TCGA-D8-A1XL TCGA-D8-A1XO 
       12.03        18.15        15.22        21.83        19.92         7.96 
TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y1 
       16.41        16.31        12.99        16.54        15.32         3.81 
TCGA-D8-A27M TCGA-E2-A109 TCGA-E2-A10C TCGA-E2-A14O TCGA-E2-A14V TCGA-E2-A150 
       13.48        46.59        40.11        44.68        34.26        25.41 
TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A159 TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A1AZ 
       27.12        19.43        25.05        18.21        12.92        60.53 
TCGA-E2-A1BD TCGA-E2-A1IF TCGA-E2-A1II TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LA 
       17.10        37.41        33.70        27.42        39.62        24.59 
TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N6 TCGA-E9-A1N9 
        8.75        16.93        22.26        19.89        13.48        13.12 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1R4 TCGA-E9-A1RC TCGA-E9-A1RE 
       36.56        39.55        12.59         6.12        40.24        34.65 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A22E TCGA-E9-A22G 
        6.58        21.27        34.59        34.13        12.89        23.51 
TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A295 TCGA-E9-A3HO 
        0.69        27.22         1.94         0.95         0.72        26.07 
TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A5FL TCGA-E9-A5UO TCGA-EW-A1OV TCGA-EW-A1OY 
        0.62        15.72         0.26         0.23        25.94        29.85 
TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P8 TCGA-EW-A1PC TCGA-EW-A1PH TCGA-EW-A2FR 
       40.41        41.13         7.86         6.15        19.96        55.00 
TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A3E8 TCGA-GM-A2DH TCGA-GM-A3XL TCGA-JL-A3YX 
       52.73        25.91        21.27        42.28        69.30        11.57 
TCGA-LL-A441 TCGA-LL-A5YN TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A8F5 TCGA-OL-A5D7 
        2.99         3.65         3.25         3.88         6.21        46.55 
TCGA-OL-A66I TCGA-OL-A66K TCGA-S3-A6ZG 
       23.70        33.90         6.81 

$`15Q LOSS WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SQ TCGA-A2-A04N 
       13.68        31.79         7.96        39.32        18.21       104.81 
TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CO 
       82.16        63.12        55.43        36.13       125.59       112.08 
TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0D1 
       92.48        88.60       107.93         5.19        63.45        34.55 
TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EP TCGA-A2-A0ER 
       33.76        28.77        25.22       101.72       107.61        74.40 
TCGA-A2-A0ES TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST 
       37.05        34.29        31.82        29.75        24.72        99.19 
TCGA-A2-A0SY TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 
       44.28        17.13         8.38        18.71        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH 
       18.90        32.55        25.28        15.42        21.90        21.67 
TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW 
       14.50        19.33        14.63        23.77        23.47        17.36 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       36.79        22.45        20.25        19.56        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
      107.70        16.31        17.19        18.15        91.92        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XY 
       20.88        39.65        83.01        14.07        49.48        34.98 
TCGA-A2-A3XZ TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A7-A0CD 
       31.99         9.01         8.81         8.91         6.74        38.30 
TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13F 
       35.31        34.29        35.47        37.45        33.11        12.72 
TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A3IY 
       23.61        29.56        23.74        23.80        20.61        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA 
       10.59        10.29        13.41        14.70        11.97        14.93 
TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VY 
       13.74        21.17        12.10        10.72        11.05         8.75 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06T TCGA-A8-A06X TCGA-A8-A075 
       13.02        13.02         1.02        41.06        31.00        17.03 
TCGA-A8-A079 TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
        9.01        19.99        18.97        14.01        12.00        17.03 
TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z 
        9.99        10.98         7.99         9.96         9.99        28.04 
TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C 
       18.05        36.95        13.02         0.99        23.08        19.99 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S 
       18.05        19.96        37.05        31.00         0.99        19.07 
TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 
       93.04        40.01        19.07        41.98        12.00         9.99 
TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M 
       12.00        13.02        31.00        33.07        29.98        15.02 
TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09X TCGA-A8-A0A1 
       25.02         8.98        19.04        15.02        14.01        12.00 
TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AD 
       19.04        13.02        21.04         0.99        13.02        38.04 
TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB 
        0.95        10.85         2.66         1.48        38.20        40.57 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI 
       55.43        36.99        38.79        50.70         1.02         0.92 
TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 
        0.99         0.69         9.40         1.12         1.81         1.68 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV 
        1.55         1.32         1.55         0.07         1.81         1.18 
TCGA-AC-A6IX TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 
        0.43         0.33         0.33         0.23         0.33         0.62 
TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AS 
        2.96         1.78         1.71         6.51         0.16         0.33 
TCGA-AN-A0AT TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        0.33         4.64         7.96         7.59         7.17         6.28 
TCGA-AN-A0XL TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV 
        0.33         0.30         0.33         0.33         0.33         5.33 
TCGA-AN-A0XW TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T 
        5.59        66.77        81.63        84.69        68.75        47.87 
TCGA-AO-A03U TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J8 
       59.05        32.78        21.40        17.65        24.16        22.36 
TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG 
       21.53        50.70        50.86        76.77        21.37        26.24 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 
       38.53        62.04        71.80       102.58        99.25        93.70 
TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G 
       94.59        90.58        77.56        64.04        57.30        41.62 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AQ-A04J TCGA-AQ-A04L 
       28.37        14.73        82.62        70.39        26.93       130.09 
TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ 
        5.65        15.62        13.22         9.99        82.88        49.32 
TCGA-AR-A0TS TCGA-AR-A0TW TCGA-AR-A0TZ TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 
       37.41        24.30        76.14        83.87        76.18        55.36 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP 
       51.25        48.82        62.56        43.73        43.56        39.98 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A24H TCGA-AR-A24K 
       40.83        46.32        42.58        36.26       109.58        50.89 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24T 
       73.02        65.46        68.19        65.69         0.85        53.26 
TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 
       53.36        48.16        45.17        40.64        39.85        34.82 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
      128.65        20.25         7.36        40.04        17.10        20.81 
TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I2 
       16.96        54.74        16.04        20.45        10.59       143.38 
TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG 
      149.59        12.13       220.90        50.70        65.72       146.50 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RH 
       18.77       126.12        84.59       110.93       140.88       189.01 
TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ 
      234.28        81.17        78.02       172.96       162.05       140.48 
TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WZ 
       89.46       157.41        97.48       188.68        17.98       129.57 
TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KN 
      129.70       186.48        28.27        68.94        58.88       139.17 
TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A40B TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY 
      170.17        85.35        82.88        38.79        20.45        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B7 TCGA-BH-A0BC 
       28.50        46.95        39.55        39.16        56.98        32.02 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO 
       18.21        25.71        24.85        21.70        61.68        35.67 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW 
       48.69        27.19        53.69        53.95        49.94        11.67 
TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI 
       48.13        45.83        31.17        23.44        38.01        22.13 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT 
       13.91        48.23        17.26         3.22         2.56        38.47 
TCGA-BH-A0DV TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0E9 
       45.17        16.27        15.68        14.30        44.81        46.19 
TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 
       32.65        31.00        24.43        30.35        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI 
       37.78        35.51        24.56        52.96        26.50        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HQ TCGA-BH-A0HW TCGA-BH-A0W3 TCGA-BH-A0W4 
        5.85         2.50        36.85        51.32        23.93        24.95 
TCGA-BH-A0W5 TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18M TCGA-BH-A18N 
       42.35        23.05         2.01         7.23        72.56        37.74 
TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18V TCGA-BH-A1ET 
       30.28        55.63        37.55        66.05        51.16        82.85 
TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 
       42.28        55.69        49.58        17.69        25.81        31.53 
TCGA-BH-A1F5 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG 
       89.16        24.66       120.62        33.17        74.73       122.89 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 
       36.92        63.35        55.00       144.59        72.07         6.90 
TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q 
        0.72        38.60        83.31       130.16        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12L TCGA-C8-A12M 
       20.12         0.99       109.28         8.94        11.93        11.77 
TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W 
       11.77        12.66         0.07        12.66        12.66        12.66 
TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A1HE 
        3.12         1.78         1.45         0.69         3.85        12.33 
TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A26V 
       11.34        11.34         0.16        10.42         2.30         0.30 
TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
        0.23         0.36         8.28         9.67         0.03         0.03 
TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 
        0.99         0.03         0.23        11.90        13.25        20.58 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC 
       14.17        13.48        19.20        16.50        18.71        15.78 
TCGA-D8-A1JD TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL 
       18.15        14.01        18.97        20.09        20.12        20.09 
TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU 
       19.40        20.38        21.01        12.20        13.32        14.70 
TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA 
       18.58        17.79        16.73        25.74        23.90        27.58 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XM TCGA-D8-A1XR 
        2.66        17.16        14.73        14.50        17.69        15.85 
TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A1Y3 
        6.35        15.16        12.66        15.52        14.24        14.14 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K 
       17.42        16.04        13.45        13.05        14.43         9.44 
TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V 
       16.41         4.80         0.76        10.09        13.08        12.53 
TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A107 
       12.26        14.50        18.51         7.33        43.00        34.42 
TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N 
       27.52        40.41        37.51        28.44        28.87        47.15 
TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U 
       40.96        38.24        38.60        33.17        33.30        43.33 
TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A153 TCGA-E2-A155 
       32.02        31.96        28.60        17.03        23.24        21.04 
TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E 
       23.87        14.79        23.34        22.82        17.29        20.71 
TCGA-E2-A15F TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M 
       21.63        17.42        19.40         9.04        20.58         7.73 
TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 
       13.02        19.56        17.06        14.07        14.99        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE 
       53.03        29.95        32.35        28.50        16.47        38.30 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN 
       32.78        33.73        28.44        22.65         3.88        22.19 
TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A1LE 
       20.98        11.08        54.18        19.66        40.47        28.90 
TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX 
       18.87       106.75       102.61        43.04         5.52        15.72 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1NE 
        7.20        18.05        19.20        36.82        12.00        35.77 
TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       20.05        21.57         9.86        11.90        14.30         0.62 
TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB 
        2.10         1.38         2.76        21.21        32.09        20.81 
TCGA-E9-A1RD TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
        0.66        35.64         0.79        12.53        13.32        39.09 
TCGA-E9-A22B TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A245 TCGA-E9-A24A TCGA-E9-A2JS 
       22.75        24.10        17.06         0.85        12.56        17.75 
TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A6HE TCGA-EW-A1IW 
        0.76        18.41         0.23         0.39        15.39        12.20 
TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 
       39.72         8.48        18.21        18.90        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1P1 TCGA-EW-A1P3 
       15.68        28.77        22.82        29.95        39.78        52.96 
TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB 
       29.82        23.11        18.48        30.08        18.90        19.99 
TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FW TCGA-EW-A3U0 
       13.94        10.52        14.43        34.55        22.09        17.49 
TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       10.16        10.59         7.40       109.87        59.57       194.27 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DK 
       53.13        53.52        43.04        42.71        61.91        62.33 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY 
       90.84        76.64        77.33        53.36       110.50        38.20 
TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW 
       32.28        53.95        57.63        13.55        18.12        11.84 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y 
        8.28         6.67         4.60         0.66         3.58         6.90 
TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A73Z 
        5.56         4.70         3.19         2.63         4.14         4.50 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 
        4.50         5.59         3.22        15.91         2.79         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW 
       12.66         7.53        44.61        27.65        24.10        26.20 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J 
       16.87        14.10        10.29         9.80        14.76        54.51 
TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-W8-A86G 
       31.07        18.21         7.23         4.44         5.29 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.03               0.03 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            211.56             234.28 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             24.26              20.71 
[1] "0.0 - 211.6 (24.3)" "0.0 - 234.3 (20.7)"
[1] "hr=" "1.4"
D67V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  15Q LOSS MUTATED        19       19        1        1       111        66
  15Q LOSS WILD-TYPE      61       58        8        8       224       158
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  15Q LOSS MUTATED           1         46          5         16        6
  15Q LOSS WILD-TYPE         1         92         22         43       11
                    vv
clus                 STAGE TIS STAGE X
  15Q LOSS MUTATED           0       4
  15Q LOSS WILD-TYPE         1      12
D67V3, multiclass
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                  19                 61
  STAGE IA                 19                 58
  STAGE IB                  1                  8
  STAGE II                  1                  8
  STAGE IIA               111                224
  STAGE IIB                66                158
  STAGE III                 1                  1
  STAGE IIIA               46                 92
  STAGE IIIB                5                 22
  STAGE IIIC               16                 43
  STAGE IV                  6                 11
  STAGE TIS                 0                  1
  STAGE X                   4                 12
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  15Q LOSS MUTATED    58 195  33   9
  15Q LOSS WILD-TYPE 200 386  84  27
D67V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1               58                200
  T2              195                386
  T3               33                 84
  T4                9                 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                  N0  N1  N2  N3
  15Q LOSS MUTATED   151  82  41  20
  15Q LOSS WILD-TYPE 317 248  70  50
D67V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0              151                317
  N1               82                248
  N2               41                 70
  N3               20                 50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  15Q LOSS MUTATED          0 257   6  33
  15Q LOSS WILD-TYPE        2 588  11  98
D67V6, multiclass
          clus
vv         15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CM0 (I+)                0                  2
  M0                    257                588
  M1                      6                 11
  MX                     33                 98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED   293   3
  15Q LOSS WILD-TYPE 691   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    293    3
  15Q LOSS WILD-TYPE  691    8
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE              293                691
  MALE                  3                  8
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  15Q LOSS MUTATED                            0                           242
  15Q LOSS WILD-TYPE                          1                           493
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  15Q LOSS MUTATED                               26                   3
  15Q LOSS WILD-TYPE                            140                   2
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  15Q LOSS MUTATED                                  9                  2
  15Q LOSS WILD-TYPE                               20                 12
                    vv
clus                 OTHER  SPECIFY
  15Q LOSS MUTATED               14
  15Q LOSS WILD-TYPE             30
D67V8, multiclass
                                  clus
vv                                 15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 242                493
  INFILTRATING LOBULAR CARCINOMA                 26                140
  MEDULLARY CARCINOMA                             3                  2
  MIXED HISTOLOGY (PLEASE SPECIFY)                9                 20
  MUCINOUS CARCINOMA                              2                 12
  OTHER  SPECIFY                                 14                 30
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V9, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    95 201
  15Q LOSS WILD-TYPE 187 512
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     95  201
  15Q LOSS WILD-TYPE  187  512
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                95                187
  YES              201                512
[1] 2 2
[1] FALSE
D67V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q LOSS MUTATED                                  0    13
  15Q LOSS WILD-TYPE                                1    43
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED                          50   206
  15Q LOSS WILD-TYPE                        87   502
D67V11, multiclass
                                  clus
vv                                 15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          13                 43
  BLACK OR AFRICAN AMERICAN                      50                 87
  WHITE                                         206                502
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V12, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     8 240
  15Q LOSS WILD-TYPE  28 556
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      8  240
  15Q LOSS WILD-TYPE   28  556
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    8                 28
  NOT HISPANIC OR LATINO              240                556
[1] 2 2
[1] FALSE

Clustering(68) Variable = 16P LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED   133  19
  16P LOSS WILD-TYPE 727  95
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               152                822 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                19                 95 
$`16P LOSS MUTATED`
TCGA-A1-A0SE TCGA-A1-A0SK TCGA-A1-A0SN TCGA-A2-A04U TCGA-A2-A0CR TCGA-A2-A0CT 
       43.43        31.79        39.32        22.06       107.93        75.25 
TCGA-A2-A0CV TCGA-A2-A0D0 TCGA-A2-A0D4 TCGA-A2-A0EQ TCGA-A2-A0EY TCGA-A2-A0SX 
       63.45        21.14        25.22        79.76        24.16        50.43 
TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A3XT TCGA-A2-A4RY TCGA-A7-A0CG TCGA-A7-A0CH 
       20.75        32.55        83.01         8.81        34.29        35.47 
TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A26J 
       30.61        35.67        31.73        12.72        23.61        20.61 
TCGA-A7-A4SD TCGA-A7-A56D TCGA-A7-A6VW TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A075 
       14.50        14.73         9.37        13.02         1.02        17.03 
TCGA-A8-A07B TCGA-A8-A07L TCGA-A8-A08J TCGA-A8-A08X TCGA-A8-A09M TCGA-A8-A09N 
       33.01        17.03        37.05        33.99        15.02         1.02 
TCGA-A8-A09Q TCGA-A8-A09W TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF 
       25.02         0.99        38.53        38.20        40.57        55.43 
TCGA-AC-A6IW TCGA-AC-A8OP TCGA-AN-A046 TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0FN 
        0.69         1.74         0.33         6.51         0.33         7.17 
TCGA-AN-A0XN TCGA-AN-A0XR TCGA-AO-A0JD TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12G 
        0.33         0.33        72.00        96.10        77.56        41.62 
TCGA-AO-A1KT TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AQ 
       17.79        13.22         2.56        76.18        75.55        43.07 
TCGA-AR-A1AR TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24O TCGA-AR-A24U TCGA-AR-A24V 
       17.23       109.58        50.89        65.69        53.36        54.18 
TCGA-AR-A251 TCGA-AR-A2LR TCGA-B6-A0I5 TCGA-B6-A0IJ TCGA-B6-A0RE TCGA-B6-A0RH 
       45.17        20.38       149.59       176.98       211.56       189.01 
TCGA-B6-A0RL TCGA-B6-A0X0 TCGA-B6-A1KC TCGA-B6-A402 TCGA-BH-A0B4 TCGA-BH-A0B6 
       81.17       129.70        43.59        54.28        39.16        56.94 
TCGA-BH-A0BO TCGA-BH-A0C0 TCGA-BH-A0DE TCGA-BH-A0E0 TCGA-BH-A0E2 TCGA-BH-A0H5 
       35.67        41.75        31.17         4.41        14.30        35.51 
TCGA-BH-A0HP TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A18K TCGA-BH-A18U 
       13.61        51.32        27.25        50.79        90.84        51.39 
TCGA-BH-A1EN TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1FC TCGA-BH-A1FD 
       69.93        82.85        42.28        55.69       114.15        33.17 
TCGA-BH-A1FL TCGA-BH-A203 TCGA-BH-A209 TCGA-BH-A28Q TCGA-C8-A130 TCGA-C8-A26X 
       55.00        38.60       130.16         6.44         3.12         0.36 
TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-D8-A13Z TCGA-D8-A1JC TCGA-D8-A1JE 
        0.03         0.99         0.03        20.88        15.78        18.90 
TCGA-D8-A1JN TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A27V TCGA-D8-A3Z6 TCGA-D8-A4Z1 
       20.38        13.32        14.70        12.53        18.51         7.33 
TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A159 TCGA-E2-A15J TCGA-E2-A15R 
       32.02        28.60        25.41        25.05        19.40        17.06 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1II TCGA-E2-A1IL TCGA-E2-A1L7 
       14.07        14.99        60.53        33.70         3.88        27.42 
TCGA-E2-A1LG TCGA-E2-A1LK TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1ND TCGA-E9-A22G 
       18.87         8.75        22.26        19.89        12.59        23.51 
TCGA-E9-A244 TCGA-E9-A248 TCGA-EW-A1J6 TCGA-EW-A1P8 TCGA-EW-A1PC TCGA-EW-A3U0 
        0.69         1.94        28.77         7.86         6.15        17.49 
TCGA-EW-A423 TCGA-GM-A2D9 TCGA-GM-A2DC TCGA-GM-A2DH TCGA-GM-A2DO TCGA-GM-A3XL 
       10.16        59.57        53.52        42.28        53.36        69.30 
TCGA-GM-A4E0 TCGA-LL-A50Y TCGA-LL-A5YN TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-OL-A5D7 
       57.63         6.90         3.65         3.22         6.21        46.55 
TCGA-OL-A5RW TCGA-OL-A66L 
       26.20        31.07 

$`16P LOSS WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI 
        8.52        14.37        48.10        14.27        47.24        20.88 
TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N 
       13.68         7.96        28.01        19.20        18.21       104.81 
TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04V TCGA-A2-A04W 
       18.02        41.95        82.16        73.84        63.12        64.04 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO 
       55.43        36.13       125.59        64.57        24.79       112.08 
TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0CX 
       92.48        88.60        75.55         5.19        64.04        56.81 
TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO 
       34.55        33.76        28.77       101.72        89.36        80.28 
TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV 
      107.61        74.40        37.05        35.05        34.29        31.82 
TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW 
       29.75        24.72        99.19        54.64        27.12        44.88 
TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 
       44.28        17.52        17.13         8.38        18.71        20.52 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG 
       17.46        18.90        25.28        18.21        15.42        21.90 
TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       21.67        14.50        18.61        19.33        14.63        31.73 
TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 
       23.77        23.47        17.36        36.79        22.45        20.25 
TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B 
       19.20        19.56        16.47        52.47       107.70        16.31 
TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD 
       17.19        18.15        91.92        10.59        20.88        39.65 
TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       33.93        29.98        14.07        49.48        38.40        34.98 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4S0 TCGA-A2-A4S1 
       31.99        38.37         7.30         9.01         8.91        12.00 
TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0D9 TCGA-A7-A0DB 
        6.74         3.42        38.30        35.31        37.45        33.11 
TCGA-A7-A13E TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H 
       10.72        29.56        31.36        24.26        23.74        23.80 
TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       21.73        22.32        11.34        10.59        10.29        11.28 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SE 
       13.41        14.70        11.97        14.93        13.74        21.17 
TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VX 
       17.92        12.10        10.72        11.05        10.29        10.42 
TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X 
        8.75        13.02        17.98        41.06        29.03        31.00 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07E TCGA-A8-A07F 
       26.01         1.02        53.98         9.01        19.99        18.97 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R 
       18.97        14.01        12.00         9.99        10.98         8.98 
TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 
        7.99         9.96         9.99        28.04        18.05        15.06 
TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F 
       36.95        13.02         0.99        23.08        19.99        18.05 
TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R 
       19.96        12.00         9.99        31.00        31.00         0.99 
TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 
       19.07        93.04        40.01        19.07        16.01        17.95 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C 
       41.98        12.00         9.99         9.99        12.00         1.02 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09R TCGA-A8-A09T 
       13.02        31.00        33.07        29.98         8.98        19.04 
TCGA-A8-A09V TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 
       15.02        14.01        12.00        19.04        13.02        21.04 
TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E 
        0.99        13.02        17.03        38.04         0.95         2.37 
TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM 
       10.85         2.66         1.48        36.99        38.79        26.04 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN 
       50.70         1.02         0.92         2.27         0.99         0.69 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI 
       14.83         9.40         1.12         1.81         1.68         1.55 
TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV 
        1.32         1.55         0.07         1.12         1.81         1.18 
TCGA-AC-A6IX TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A04A 
        0.43         0.33         0.33         0.23         0.62         2.96 
TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0AS 
        1.78         1.71         8.02         7.36         0.16         0.33 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL 
        0.33         6.44         4.64         7.96         7.00         7.59 
TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY 
        6.28         6.02         0.33         0.36         0.33         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XS TCGA-AN-A0XT 
        0.33         0.33        12.33         0.30         0.33         0.33 
TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N 
        0.33         5.33         5.59        80.28        47.84        66.77 
TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V 
       81.63        84.69        68.75        47.87        59.05        29.13 
TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 
       32.78        21.40        17.65        24.16        37.48        20.32 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE 
       22.36        53.03        21.53        50.70        50.86        76.77 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM 
       21.37        26.24        38.53        62.04        55.33        71.80 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12D 
      102.58        99.25        93.70        94.59        90.58        64.04 
TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ 
       57.30        48.36        28.37        14.73        82.62        61.87 
TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 
       70.39         0.53        24.79        26.93       130.09         5.65 
TCGA-AQ-A1H2 TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
       15.62        21.86         9.99        82.88        49.32         5.26 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
       37.41        56.88        29.75        24.30        64.83        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AI 
       76.14        65.36        70.16        83.87        55.36        61.84 
TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO 
       52.77        51.25        48.82        62.56        43.73        43.56 
TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX 
       39.98        40.83        46.32        42.58        35.24        36.26 
TCGA-AR-A1AY TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24P TCGA-AR-A24Q 
       20.22        73.02        65.46        68.19         0.85        66.05 
TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
       57.40        62.07        53.26        50.96        48.16        51.75 
TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE 
       56.15        40.64        39.85        34.82        93.83       128.65 
TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       20.25        42.87         7.36        40.04        17.10        20.81 
TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       16.96        54.74        16.04        20.45        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
      143.38        12.13       220.90       129.57        50.70        65.72 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO 
      146.50       112.37        18.77       126.12        84.59       110.14 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN 
      110.93       140.88        68.45       234.28        78.02       172.96 
TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU 
      162.05       102.77       140.48       100.70        89.46       131.21 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX 
      157.41        97.48       188.68        79.63        17.98        21.47 
TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      113.79       129.57       186.48        28.27        68.94        58.88 
TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A408 
      101.52        73.51       139.17       170.17        85.35        49.94 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY 
       82.88        55.00        24.53        38.79        20.45        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0B7 
       28.50        46.95        40.83        39.55        48.36        56.98 
TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG 
       51.68        37.22        32.02        18.21        25.71        24.85 
TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR 
       21.70        44.05        61.68        48.69        27.19        53.69 
TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 
       53.95        45.57        49.94        11.67        49.05        44.02 
TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI 
       48.13        42.90        45.83        23.44        38.01        22.13 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS 
       13.91        48.23        17.26        15.65         3.22         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E6 
       38.47        45.17        47.41        16.27        15.68         9.63 
TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI 
       44.81        46.19        32.65        24.49        31.00        24.43 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H6 TCGA-BH-A0H7 
       30.35        10.78        15.16        37.78        24.56        23.08 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       41.00        52.96        26.50        20.38         5.85         2.50 
TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 
       36.85        12.89         5.59        23.93        24.95        42.35 
TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J 
       44.81        23.05         8.81         2.01         7.23        20.12 
TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R 
       26.66        72.56        37.74        30.28        55.63        37.55 
TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1EV 
       66.05         7.36        51.16        91.99       113.82        12.00 
TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 
       49.58        17.69        25.81        31.53        89.16        97.48 
TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
       24.66       120.62        74.73       122.89        36.92        63.35 
TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 
       45.63        72.07       144.59        72.07         6.90         0.72 
TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A28O TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
       83.31        57.83        10.65        20.12         0.99       109.28 
TCGA-BH-A42V TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P 
        8.94        11.93        11.77        11.77        12.66        11.77 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A131 
        0.07        12.66        12.66        12.66        12.66         1.78 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE 
        1.45         0.69         0.62         3.85         3.75        12.33 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL 
       10.92        11.34        11.34         0.16        12.03        10.42 
TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Y TCGA-C8-A26Z 
        2.30         3.25         0.30         0.23         0.43         8.28 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A3M8 TCGA-D8-A13Y 
        9.67         0.03         0.03        12.20         0.23        11.90 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 
       13.25        20.58        13.97        14.17        13.48        21.14 
TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JD 
       19.20        14.17        17.49        16.50        18.71        18.15 
TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK 
       12.03        12.03        14.01        18.97        20.09        20.12 
TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1X5 TCGA-D8-A1X6 
       20.09        19.40        21.01        12.20        18.58        17.79 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC 
       16.73        25.74        23.90        27.58        18.15         2.66 
TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL 
       17.16        15.22        14.73        21.83        14.50        19.92 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT 
       17.69         7.96        16.41        15.85        16.31         6.35 
TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 
       12.99        15.16        12.66        16.54        15.32        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G 
        3.81        14.24        14.14        17.42        16.04        13.45 
TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N 
       13.05        14.43         9.44        16.41        13.48         4.80 
TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-E2-A105 
        0.76        10.09        13.08        12.26        14.50        43.00 
TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C 
       34.42        27.52        46.59        40.41        37.51        40.11 
TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q 
       28.44        28.87        47.15        44.68        40.96        38.24 
TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14X 
       38.60        33.17        33.30        43.33        34.26        31.96 
TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 
       17.03        27.12        23.24        19.43        21.04        23.87 
TCGA-E2-A158 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F 
       14.79        23.34        22.82        17.29        20.71        21.63 
TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M 
       18.21        12.92        17.42         9.04        20.58         7.73 
TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       13.02        19.56        53.62        53.03        29.95        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       28.50        16.47        17.10        38.30        37.41        32.78 
TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       33.73        28.44        22.65        22.19        20.98        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       54.18        39.62        19.66        24.59        40.47        28.90 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX 
      106.75       102.61        43.04        16.93         5.52        15.72 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 
        7.20        18.05        19.20        36.82        13.48        12.00 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG 
       13.12        36.56        39.55        35.77        20.05        21.57 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 
        9.86        11.90        14.30         0.62         2.10         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC 
        1.38         2.76        21.21        32.09        20.81        40.24 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI 
        0.66        34.65         6.58        21.27        34.59        35.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       34.13         0.79        12.53        13.32        39.09        22.75 
TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A249 
       12.89        24.10        17.06         0.85        27.22         0.95 
TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 
       12.56         0.72        17.75         0.76        26.07        18.41 
TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO 
        0.62        15.72         0.23         0.39         0.26         0.23 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 
       15.39        12.20        39.72         8.48        18.21        18.90 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX 
       13.25        16.57        15.68        25.94        22.82        29.95 
TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 
       29.85        40.41        41.13        39.78        52.96        29.82 
TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PD 
       23.11        18.48        30.08        18.90        19.99        13.94 
TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS 
       10.52        14.43        34.55        19.96        55.00        52.73 
TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 
       25.91        22.09        21.27        10.59         7.40       109.87 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DK 
      194.27        53.13        43.04        42.71        61.91        62.33 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
       90.84        76.64        77.33       110.50        38.20        32.28 
TCGA-GM-A3XN TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U 
       53.95        13.55        18.12        11.84        11.57         8.28 
TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A5YL 
        6.67         4.60         0.66         2.99         3.58         5.56 
TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y 
        4.70         3.19         3.25         2.63         3.88         4.14 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 
        4.50         4.50         5.59        15.91         2.79         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX 
       12.66         7.53        44.61        27.65        24.10        16.87 
TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J 
       14.10        10.29         9.80        14.76        23.70        54.51 
TCGA-OL-A66K TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-S3-A6ZG TCGA-W8-A86G 
       33.90        18.21         7.23         4.44         6.81         5.29 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.03               0.03 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            211.56             234.28 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            27.335             20.930 
[1] "0.0 - 211.6 (27.3)" "0.0 - 234.3 (20.9)"
[1] "hr=" "1.1"
D68V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16P LOSS MUTATED        19        8        1        0        63        26
  16P LOSS WILD-TYPE      61       69        8        9       272       198
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16P LOSS MUTATED           0         19          4         11        1
  16P LOSS WILD-TYPE         2        119         23         48       16
                    vv
clus                 STAGE TIS STAGE X
  16P LOSS MUTATED           0       2
  16P LOSS WILD-TYPE         1      14
D68V3, multiclass
            clus
vv           16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                  19                 61
  STAGE IA                  8                 69
  STAGE IB                  1                  8
  STAGE II                  0                  9
  STAGE IIA                63                272
  STAGE IIB                26                198
  STAGE III                 0                  2
  STAGE IIIA               19                119
  STAGE IIIB                4                 23
  STAGE IIIC               11                 48
  STAGE IV                  1                 16
  STAGE TIS                 0                  1
  STAGE X                   2                 14
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  16P LOSS MUTATED    40  90  17   6
  16P LOSS WILD-TYPE 218 491 100  30
D68V4, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1               40                218
  T2               90                491
  T3               17                100
  T4                6                 30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  16P LOSS MUTATED    84  39  17  13
  16P LOSS WILD-TYPE 384 291  94  57
D68V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0               84                384
  N1               39                291
  N2               17                 94
  N3               13                 57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  16P LOSS MUTATED          0 136   1  17
  16P LOSS WILD-TYPE        2 709  16 114
D68V6, multiclass
          clus
vv         16P LOSS MUTATED 16P LOSS WILD-TYPE
  CM0 (I+)                0                  2
  M0                    136                709
  M1                      1                 16
  MX                     17                114
[1] 4 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   152   2
  16P LOSS WILD-TYPE 832   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED    152    2
  16P LOSS WILD-TYPE  832    9
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE              152                832
  MALE                  2                  9
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  16P LOSS MUTATED                            0                           125
  16P LOSS WILD-TYPE                          1                           610
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  16P LOSS MUTATED                               19                   2
  16P LOSS WILD-TYPE                            147                   3
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  16P LOSS MUTATED                                  3                  0
  16P LOSS WILD-TYPE                               26                 14
                    vv
clus                 OTHER  SPECIFY
  16P LOSS MUTATED                5
  16P LOSS WILD-TYPE             39
D68V8, multiclass
                                  clus
vv                                 16P LOSS MUTATED 16P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 125                610
  INFILTRATING LOBULAR CARCINOMA                 19                147
  MEDULLARY CARCINOMA                             2                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)                3                 26
  MUCINOUS CARCINOMA                              0                 14
  OTHER  SPECIFY                                  5                 39
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V9, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    39 115
  16P LOSS WILD-TYPE 243 598
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     39  115
  16P LOSS WILD-TYPE  243  598
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                39                243
  YES              115                598
[1] 2 2
[1] FALSE
D68V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P LOSS MUTATED                                  0    10
  16P LOSS WILD-TYPE                                1    46
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED                          35    98
  16P LOSS WILD-TYPE                       102   610
D68V11, multiclass
                                  clus
vv                                 16P LOSS MUTATED 16P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          10                 46
  BLACK OR AFRICAN AMERICAN                      35                102
  WHITE                                          98                610
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V12, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     6 126
  16P LOSS WILD-TYPE  30 670
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      6  126
  16P LOSS WILD-TYPE   30  670
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                 30
  NOT HISPANIC OR LATINO              126                670
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16Q LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED   481  53
  16Q LOSS WILD-TYPE 379  61
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               534                440 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                53                 61 
$`16Q LOSS MUTATED`
TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SH TCGA-A1-A0SK TCGA-A1-A0SM 
       14.37        43.43        48.10        47.24        31.79         7.96 
TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A2-A04N TCGA-A2-A04R TCGA-A2-A04U TCGA-A2-A04V 
       39.32        28.01       104.81        82.16        22.06        63.12 
TCGA-A2-A0CK TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS 
      125.59       112.08        92.48        88.60       107.93        75.55 
TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0D4 
       75.25        63.45        21.14        34.55        28.77        25.22 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EQ TCGA-A2-A0EU TCGA-A2-A0EX 
      101.72        89.36        80.28        79.76        34.29        24.72 
TCGA-A2-A0EY TCGA-A2-A0SU TCGA-A2-A0SY TCGA-A2-A0T1 TCGA-A2-A0T4 TCGA-A2-A0T5 
       24.16        54.64        44.28        17.13        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YH 
       18.90        20.75        32.55        25.28        15.42        21.67 
TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1G0 
       19.33        14.63        31.73        23.47        36.79        20.25 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A4RY 
       52.47       107.70        20.88        39.65        83.01         8.81 
TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0DB 
        3.42        38.30        34.29        35.47        30.61        33.11 
TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26I 
       31.73        12.72        23.61        29.56        31.36        21.73 
TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IZ TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A4SA 
       20.61        22.32        10.59        11.28        11.97        14.93 
TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZW TCGA-A7-A5ZX 
       13.74        14.50        21.17        14.73        10.72        11.05 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06U 
       10.29         9.37        13.02        13.02         1.02        29.03 
TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F 
       31.00        17.03         9.01        33.01        19.99        18.97 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A084 
       12.00        17.03        10.98         8.98         7.99        15.06 
TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08J 
       13.02         0.99        23.08        19.99        19.96        37.05 
TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z 
       31.00        31.00        19.07        93.04        33.99        40.01 
TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09B 
       19.07        16.01        17.95        41.98         9.99        12.00 
TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T 
       29.98        15.02         1.02        25.02         8.98        19.04 
TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 
       15.02         0.99        14.01        12.00        19.04        13.02 
TCGA-A8-A0A6 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23E TCGA-AC-A23G 
       21.04        13.02        17.03        38.04         2.37        10.85 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG 
        1.48        38.53        38.20        40.57        55.43        36.99 
TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
       26.04        50.70         0.92         0.69        14.83         9.40 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5XS TCGA-AC-A62X TCGA-AC-A6IW 
        1.12         1.81         1.68         1.55         1.12         0.69 
TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A046 TCGA-AN-A0AJ 
        0.43         1.74         0.33         0.33         0.33         8.02 
TCGA-AN-A0AK TCGA-AN-A0AR TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0XL 
        7.36         0.33         7.00         7.17         6.28         0.33 
TCGA-AN-A0XN TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU 
        0.33         0.30         0.33         0.33         0.33         0.33 
TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A0J3 
       80.28        66.77        81.63        84.69        68.75        21.40 
TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JD TCGA-AO-A0JF 
       20.32        22.36        53.03        21.53        72.00        21.37 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12A 
       38.53        62.04        99.25        93.70        96.10        90.58 
TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A1KP TCGA-AO-A1KS TCGA-AO-A1KT 
       77.56        57.30        41.62        82.62         0.53        17.79 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AR-A0TZ TCGA-AR-A0U2 TCGA-AR-A0U3 
       15.62        13.22         2.56        76.14        83.87        76.18 
TCGA-AR-A1AH TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AP 
       75.55        51.25        48.82        62.56        43.73        39.98 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AX TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24N 
       43.07        17.23        36.26       109.58        50.89        68.19 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V 
       65.69         0.85        62.07        53.26        53.36        54.18 
TCGA-AR-A24X TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A2LE TCGA-AR-A2LK TCGA-AR-A2LL 
       48.16        45.17        39.85       128.65        42.87         7.36 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A5QN TCGA-B6-A0I5 TCGA-B6-A0IA 
       40.04        17.10        20.81        16.04       149.59       220.90 
TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IH TCGA-B6-A0IM TCGA-B6-A0IP TCGA-B6-A0IQ 
      129.57        50.70       112.37       126.12       110.93       140.88 
TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RN 
      211.56        68.45       189.01       234.28        81.17       172.96 
TCGA-B6-A0RP TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WW TCGA-B6-A0WZ TCGA-B6-A0X0 
      102.77       157.41        97.48        17.98       129.57       129.70 
TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A2IU TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B 
       58.88        43.59       170.17        54.28        49.94        82.88 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0B2 
       55.00        24.53        38.79        25.55        46.95        40.83 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BF 
       39.16        48.36        56.94        56.98        37.22        25.71 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0C0 
       61.68        35.67        48.69        27.19        53.95        41.75 
TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DH TCGA-BH-A0DK 
       44.02        48.13        42.90        31.17        38.01        13.91 
TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DZ 
       17.26        15.65         2.56        38.47        45.17        16.27 
TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 
        4.41        15.68        14.30         9.63        44.81        46.19 
TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0GY TCGA-BH-A0H0 TCGA-BH-A0H3 
       32.65        24.49        31.00        30.35        15.16        37.78 
TCGA-BH-A0H5 TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ 
       35.51        20.38         5.85         2.50        13.61        36.85 
TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0W3 TCGA-BH-A0W4 
       12.89        51.32        27.25        50.79        23.93        24.95 
TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18N 
       44.81        23.05         8.81        20.12        90.84        37.74 
TCGA-BH-A18P TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ET 
       30.28         7.36        51.39        69.93        91.99        82.85 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EY TCGA-BH-A1F2 TCGA-BH-A1F5 
       42.28        12.00        55.69        17.69        31.53        89.16 
TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FL 
      120.62       114.15        33.17        74.73       122.89        55.00 
TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A209 TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T 
        0.72        38.60       130.16         6.44        20.12         0.99 
TCGA-BH-A42V TCGA-C8-A12N TCGA-C8-A130 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE 
        8.94        11.77         3.12         3.85         3.75        12.33 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26W 
       10.92        11.34        11.34         2.30         3.25         0.23 
TCGA-C8-A26X TCGA-C8-A274 TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-D8-A13Y 
        0.36         0.03         0.03         0.99         0.03        11.90 
TCGA-D8-A13Z TCGA-D8-A141 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 
       20.88        20.58        13.48        21.14        14.17        17.49 
TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JI TCGA-D8-A1JJ 
       15.78        18.15        18.90        12.03        18.97        20.09 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 
       20.38        21.01        12.20        13.32        14.70        18.58 
TCGA-D8-A1X6 TCGA-D8-A1X8 TCGA-D8-A1XK TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR 
       17.79        25.74        14.50         7.96        16.41        15.85 
TCGA-D8-A1XS TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27G 
       16.31        16.54        15.52         3.81        14.14        13.45 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 
        9.44        16.41         0.76        13.08        12.53        14.50 
TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A107 TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A10E 
       18.51         7.33        34.42        40.41        40.11        28.44 
TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14Y 
       44.68        38.24        33.17        43.33        32.02        28.60 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A159 
       17.03        25.41        23.24        21.04        23.87        25.05 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I 
       22.82        17.29        20.71        18.21        12.92        17.42 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15R TCGA-E2-A15S 
       19.40         9.04        20.58        13.02        17.06        14.07 
TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B4 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE 
       14.99        60.53        29.95        16.47        17.10        38.30 
TCGA-E2-A1IF TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IL TCGA-E2-A1IU TCGA-E2-A1L6 
       37.41        33.73        33.70         3.88        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LA TCGA-E2-A1LG TCGA-E2-A1LK TCGA-E2-A2P5 
       27.42        39.62        24.59        18.87         8.75        16.93 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N4 
        5.52        15.72        18.05        22.26        19.89        19.20 
TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI 
       36.82        12.00        12.59        20.05        21.57         9.86 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 
       11.90        14.30         2.10         6.12         1.38         2.76 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RG 
       21.21        32.09        20.81         0.66        34.65        21.27 
TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H 
       35.64        34.13         0.79        12.89        23.51        24.10 
TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A3HO 
        0.69         1.94         0.95        12.56         0.72        26.07 
TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IY TCGA-EW-A1IZ 
       15.72         0.23        15.39        12.20         8.48        18.21 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OZ 
       13.25        16.57        15.68        28.77        25.94        40.41 
TCGA-EW-A1P6 TCGA-EW-A1P8 TCGA-EW-A1PC TCGA-EW-A1PE TCGA-EW-A1PG TCGA-EW-A2FS 
       18.48         7.86         6.15        10.52        34.55        52.73 
TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GM-A2D9 
       21.27        17.49        10.16        10.59         7.40        59.57 
TCGA-GM-A2DC TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
       53.52        42.28        61.91        77.33        53.36       110.50 
TCGA-GM-A3NY TCGA-GM-A3XL TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YX 
       38.20        69.30        57.63        13.55        18.12        11.57 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN 
        8.28         6.67         4.60         6.90         5.56         3.65 
TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OL-A5D6 TCGA-OL-A5D7 
        3.22         6.21        15.91         2.79        12.66        46.55 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5S0 
        7.53        44.61        24.10        26.20        16.87         9.80 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-S3-A6ZG TCGA-W8-A86G 
       54.51        33.90        31.07        18.21         6.81         5.29 

$`16Q LOSS WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SG TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SP TCGA-A1-A0SQ 
        8.52        14.27        20.88        13.68        19.20        18.21 
TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04T TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
       18.02        41.95        73.84        64.04        55.43        36.13 
TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D2 
       64.57        24.79         5.19        64.04        56.81        33.76 
TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EV TCGA-A2-A0EW 
      107.61        74.40        37.05        35.05        31.82        29.75 
TCGA-A2-A0ST TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0T0 TCGA-A2-A0T2 
       99.19        27.12        44.88        50.43        17.52         8.38 
TCGA-A2-A0T3 TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YT 
       18.71        18.21        21.90        14.50        18.61        23.77 
TCGA-A2-A1FW TCGA-A2-A1FZ TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A25B 
       17.36        22.45        19.20        19.56        16.47        16.31 
TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3XS TCGA-A2-A3XU 
       17.19        18.15        91.92        10.59        33.93        29.98 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 
       14.07        49.48        38.40        34.98        31.99        38.37 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CE 
        7.30         9.01         8.91        12.00         6.74        35.31 
TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A13E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H 
       37.45        35.67        10.72        24.26        23.74        23.80 
TCGA-A7-A3IY TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SF TCGA-A7-A5ZV 
       11.34        10.29        13.41        14.70        17.92        12.10 
TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06Y TCGA-A8-A06Z 
       10.42         8.75        17.98        41.06        26.01         1.02 
TCGA-A8-A076 TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07O TCGA-A8-A07U TCGA-A8-A07W 
       53.98        18.97        14.01         9.99         9.96         9.99 
TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08L 
       28.04        18.05        36.95        18.05        12.00         9.99 
TCGA-A8-A08R TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E 
        0.99        12.00         9.99         1.02        13.02        31.00 
TCGA-A8-A09I TCGA-A8-A0A7 TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A2FK TCGA-AC-A2QH 
       33.07         0.99         0.95         2.66        38.79         1.02 
TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A62V TCGA-AC-A62Y 
        2.27         0.99         1.55         1.32         0.07         1.81 
TCGA-AC-A6IV TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D 
        1.18         0.23         0.62         2.96         1.78         1.71 
TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF 
        6.51         0.16         0.33         0.33         6.44         4.64 
TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX 
        7.96         7.59         6.02         0.33         0.36         0.33 
TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XO TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03M 
        0.33         0.33        12.33         5.33         5.59        47.84 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J5 
       47.87        59.05        29.13        32.78        17.65        24.16 
TCGA-AO-A0J6 TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JG TCGA-AO-A0JL 
       37.48        50.70        50.86        76.77        26.24        55.33 
TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A128 TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A12H 
       71.80       102.58        94.59        64.04        48.36        28.37 
TCGA-AO-A1KO TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       14.73        61.87        70.39        24.79        26.93       130.09 
TCGA-AQ-A0Y5 TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
        5.65        21.86         9.99        82.88        49.32         5.26 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
       37.41        56.88        29.75        24.30        64.83        55.86 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AO 
       65.36        70.16        55.36        61.84        52.77        43.56 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AY TCGA-AR-A24L 
       40.83        46.32        42.58        35.24        20.22        73.02 
TCGA-AR-A24M TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24W TCGA-AR-A24Z TCGA-AR-A250 
       65.46        66.05        57.40        50.96        51.75        56.15 
TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LH TCGA-AR-A2LQ TCGA-AR-A2LR 
       40.64        34.82        93.83        20.25        16.96        20.38 
TCGA-AR-A5QM TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I9 
       54.74        20.45        10.59        77.62       143.38        12.13 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IN TCGA-B6-A0IO 
       65.72       146.50       176.98        18.77        84.59       110.14 
TCGA-B6-A0RM TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU 
       78.02       162.05       140.48       100.70        89.46       131.21 
TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0X1 TCGA-B6-A0X4 
      188.68        79.63        21.47       113.79       186.48        28.27 
TCGA-B6-A0X5 TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A401 TCGA-BH-A0AW 
       68.94       101.52        73.51       139.17        85.35        20.45 
TCGA-BH-A0AZ TCGA-BH-A0B3 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BG 
       28.50        39.55        51.68        32.02        18.21        24.85 
TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BR TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW 
       21.70        44.05        53.69        45.57        49.94        11.67 
TCGA-BH-A0BZ TCGA-BH-A0DD TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DL TCGA-BH-A0DQ 
       49.05        45.83        23.44        22.13        48.23         3.22 
TCGA-BH-A0DX TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 
       47.41        24.43        10.78        24.56        23.08        41.00 
TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0RX TCGA-BH-A0W5 TCGA-BH-A18G TCGA-BH-A18I 
       52.96        26.50         5.59        42.35         2.01         7.23 
TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18V 
       26.66        72.56        55.63        37.55        66.05        51.16 
TCGA-BH-A1ES TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FH 
      113.82        49.58        25.81        97.48        24.66        36.92 
TCGA-BH-A1FJ TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 
       63.35        45.63        72.07       144.59        72.07         6.90 
TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A28O TCGA-BH-A42U TCGA-C8-A12L TCGA-C8-A12M 
       83.31        57.83        10.65       109.28        11.93        11.77 
TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W 
       12.66        11.77         0.07        12.66        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A1HJ 
       12.66         1.78         1.45         0.69         0.62         0.16 
TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A26V TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 
       12.03        10.42         0.30         0.43         8.28         9.67 
TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A3M8 TCGA-D8-A140 TCGA-D8-A142 TCGA-D8-A143 
        0.03        12.20         0.23        13.25        13.97        14.17 
TCGA-D8-A147 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JK 
       19.20        16.50        18.71        12.03        14.01        20.12 
TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1X7 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB 
       20.09        19.40        16.73        23.90        27.58        18.15 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XL 
        2.66        17.16        15.22        14.73        21.83        19.92 
TCGA-D8-A1XM TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XZ 
       17.69         6.35        12.99        15.16        12.66        15.32 
TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27M 
       14.24        17.42        16.04        13.05        14.43        13.48 
TCGA-D8-A27N TCGA-D8-A27R TCGA-D8-A27W TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A109 
        4.80        10.09        12.26        43.00        27.52        46.59 
TCGA-E2-A10B TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14R TCGA-E2-A14T 
       37.51        28.87        47.15        40.96        38.60        33.30 
TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A158 TCGA-E2-A15A 
       34.26        31.96        27.12        19.43        14.79        23.34 
TCGA-E2-A15F TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B5 
       21.63         7.73        19.56        53.62        53.03        32.35 
TCGA-E2-A1B6 TCGA-E2-A1IG TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IN TCGA-E2-A1IO 
       28.50        32.78        28.44        22.65        22.19        20.98 
TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LL 
       19.66        40.47        28.90       106.75       102.61        43.04 
TCGA-E2-A56Z TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1NE 
        7.20        13.48        13.12        36.56        39.55        35.77 
TCGA-E9-A1R2 TCGA-E9-A1RC TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A228 TCGA-E9-A229 
        0.62        40.24         6.58        34.59        12.53        13.32 
TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A243 TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A2JS 
       39.09        22.75        17.06         0.85        27.22        17.75 
TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO 
        0.76        18.41         0.62         0.39         0.26         0.23 
TCGA-EW-A1IX TCGA-EW-A1J1 TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1P0 
       39.72        18.90        22.82        29.95        29.85        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P7 TCGA-EW-A1PA 
       39.78        52.96        29.82        23.11        30.08        18.90 
TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PF TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FV 
       19.99        13.94        14.43        19.96        55.00        25.91 
TCGA-EW-A2FW TCGA-GI-A2C9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DF 
       22.09       109.87       194.27        53.13        43.04        42.71 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A3XG TCGA-GM-A3XN TCGA-JL-A3YW 
       62.33        90.84        76.64        32.28        53.95        11.84 
TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A5YP 
        0.66         2.99         3.58         4.70         3.19         3.25 
TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ 
        2.63         3.88         4.14         4.50         4.50         5.59 
TCGA-OK-A5Q2 TCGA-OL-A5RU TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I 
        2.10        27.65        14.10        10.29        14.76        23.70 
TCGA-OL-A66O TCGA-OL-A66P 
        7.23         4.44 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.03               0.03 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            234.28             194.27 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             21.09              22.16 
[1] "0.0 - 234.3 (21.1)" "0.0 - 194.3 (22.2)"
[1] "hr=" "1.4"
D69V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16Q LOSS MUTATED        52       39        4        6       192       117
  16Q LOSS WILD-TYPE      28       38        5        3       143       107
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16Q LOSS MUTATED           1         71         12         36        6
  16Q LOSS WILD-TYPE         1         67         15         23       11
                    vv
clus                 STAGE TIS STAGE X
  16Q LOSS MUTATED           0      10
  16Q LOSS WILD-TYPE         1       6
D69V3, multiclass
            clus
vv           16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                  52                 28
  STAGE IA                 39                 38
  STAGE IB                  4                  5
  STAGE II                  6                  3
  STAGE IIA               192                143
  STAGE IIB               117                107
  STAGE III                 1                  1
  STAGE IIIA               71                 67
  STAGE IIIB               12                 15
  STAGE IIIC               36                 23
  STAGE IV                  6                 11
  STAGE TIS                 0                  1
  STAGE X                  10                  6
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  16Q LOSS MUTATED   146 312  70  17
  16Q LOSS WILD-TYPE 112 269  47  19
D69V4, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1              146                112
  T2              312                269
  T3               70                 47
  T4               17                 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                  N0  N1  N2  N3
  16Q LOSS MUTATED   271 167  57  45
  16Q LOSS WILD-TYPE 197 163  54  25
D69V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0              271                197
  N1              167                163
  N2               57                 54
  N3               45                 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                 CM0 (I+)  M0  M1  MX
  16Q LOSS MUTATED          0 463   6  77
  16Q LOSS WILD-TYPE        2 382  11  54
D69V6, multiclass
          clus
vv         16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CM0 (I+)                0                  2
  M0                    463                382
  M1                      6                 11
  MX                     77                 54
[1] 4 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   542   4
  16Q LOSS WILD-TYPE 442   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED    542    4
  16Q LOSS WILD-TYPE  442    7
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE              542                442
  MALE                  4                  7
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  16Q LOSS MUTATED                            0                           379
  16Q LOSS WILD-TYPE                          1                           356
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  16Q LOSS MUTATED                              130                   2
  16Q LOSS WILD-TYPE                             36                   3
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  16Q LOSS MUTATED                                 19                  1
  16Q LOSS WILD-TYPE                               10                 13
                    vv
clus                 OTHER  SPECIFY
  16Q LOSS MUTATED               14
  16Q LOSS WILD-TYPE             30
D69V8, multiclass
                                  clus
vv                                 16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 379                356
  INFILTRATING LOBULAR CARCINOMA                130                 36
  MEDULLARY CARCINOMA                             2                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)               19                 10
  MUCINOUS CARCINOMA                              1                 13
  OTHER  SPECIFY                                 14                 30
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V9, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED   141 405
  16Q LOSS WILD-TYPE 141 308
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED    141  405
  16Q LOSS WILD-TYPE  141  308
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO               141                141
  YES              405                308
[1] 2 2
[1] FALSE
D69V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q LOSS MUTATED                                  1    27
  16Q LOSS WILD-TYPE                                0    29
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED                          73   386
  16Q LOSS WILD-TYPE                        64   322
D69V11, multiclass
                                  clus
vv                                 16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                          27                 29
  BLACK OR AFRICAN AMERICAN                      73                 64
  WHITE                                         386                322
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V12, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    18 426
  16Q LOSS WILD-TYPE  18 370
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     18  426
  16Q LOSS WILD-TYPE   18  370
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   18                 18
  NOT HISPANIC OR LATINO              426                370
[1] 2 2
[1] FALSE

Clustering(70) Variable = 17P LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED   453  66
  17P LOSS WILD-TYPE 407  48
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               519                455 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                66                 48 
$`17P LOSS MUTATED`
TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK 
       14.37        43.43        48.10        47.24        20.88        31.79 
TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04P TCGA-A2-A04R 
       39.32        28.01        19.20        18.21        18.02        82.16 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04Y TCGA-A2-A0CK 
       73.84        22.06        63.12        64.04        36.13       125.59 
TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CR TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV 
       24.79       112.08       107.93        75.25         5.19        63.45 
TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D4 TCGA-A2-A0EN TCGA-A2-A0EO 
       64.04        21.14        34.55        25.22        89.36        80.28 
TCGA-A2-A0EQ TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX 
       79.76        24.72        24.16        27.12        44.88        50.43 
TCGA-A2-A0SY TCGA-A2-A0T1 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T7 TCGA-A2-A0YC 
       44.28        17.13        18.71        20.52        20.75        32.55 
TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A1FV 
       18.21        21.90        21.67        19.33        14.63        23.47 
TCGA-A2-A1FW TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A2-A25B 
       17.36        20.25        19.20        19.56       107.70        16.31 
TCGA-A2-A25D TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XY 
       18.15        39.65        83.01        14.07        49.48        34.98 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CG 
       38.37         7.30         9.01        12.00         3.42        34.29 
TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A13H 
       30.61        37.45        35.67        31.73        12.72        29.56 
TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A2KD 
       31.36        24.26        23.74        23.80        21.73        22.32 
TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D 
       14.93        13.74        14.50        21.17        17.92        14.73 
TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06Q 
       11.05         9.37        10.42         8.75        13.02         1.02 
TCGA-A8-A06R TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 
       17.98        29.03        31.00         1.02        17.03        53.98 
TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07L 
        9.01        33.01        19.99        18.97        14.01        17.03 
TCGA-A8-A07R TCGA-A8-A07W TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08B 
        8.98         9.99        15.06        36.95        13.02        23.08 
TCGA-A8-A08F TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A092 
       18.05         9.99        31.00         0.99        33.99        16.01 
TCGA-A8-A093 TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M 
       17.95         9.99         1.02        33.07        29.98        15.02 
TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09X TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A7 
        1.02         8.98        14.01        19.04        13.02         0.99 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A2BK TCGA-AC-A2BM 
       17.03        38.04         0.95         2.37        38.53        38.20 
TCGA-AC-A2FB TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3OD TCGA-AC-A3TN 
       40.57         0.92         2.27         0.99        14.83         1.12 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A62X TCGA-AC-A62Y TCGA-AN-A041 TCGA-AN-A046 
        1.81         1.68         1.12         1.81         0.23         0.33 
TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AS 
        1.78         1.71         8.02         6.51         0.16         0.33 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FT TCGA-AN-A0FV 
        0.33         6.44         7.96         7.59         6.02         0.33 
TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO 
        0.36         0.33         0.33         0.33         0.33        12.33 
TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XW TCGA-AO-A03M 
        0.30         0.33         0.33         0.33         5.59        47.84 
TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03V 
       66.77        81.63        84.69        68.75        47.87        29.13 
TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JD 
       32.78        21.40        17.65        21.53        50.70        72.00 
TCGA-AO-A0JE TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12D 
       76.77        62.04        71.80        93.70        96.10        64.04 
TCGA-AO-A12G TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       41.62        70.39         0.53        24.79        26.93       130.09 
TCGA-AQ-A0Y5 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0TP TCGA-AR-A0TR 
        5.65        13.22         2.56        21.86        82.88         5.26 
TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 
       56.88        24.30        55.86        76.14        70.16        83.87 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AM 
       76.18        55.36        75.55        61.84        52.77        62.56 
TCGA-AR-A1AN TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AX 
       43.73        43.07        17.23        40.83        46.32        36.26 
TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24S 
       20.22       109.58        73.02        65.69         0.85        62.07 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A254 
       53.26        53.36        54.18        51.75        56.15        39.85 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LM TCGA-AR-A5QM TCGA-B6-A0I9 
       34.82        93.83       128.65        40.04        54.74        12.13 
TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK 
      129.57        65.72       146.50       112.37       176.98        18.77 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG 
      126.12        84.59       110.14       140.88       211.56        68.45 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS 
      189.01       234.28       100.70       131.21       157.41        97.48 
TCGA-B6-A0WV TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X7 TCGA-B6-A1KN TCGA-B6-A402 
       79.63       113.79       129.57        58.88       139.17        54.28 
TCGA-B6-A408 TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B5 
       49.94        38.79        25.55        46.95        40.83        48.36 
TCGA-BH-A0B6 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BF TCGA-BH-A0BM 
       56.94        51.68        37.22        32.02        25.71        61.68 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 
       48.69        27.19        53.69        11.67        49.05        44.02 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP 
       45.83        31.17        22.13        13.91        48.23        15.65 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E9 
       47.41        16.27         4.41        14.30         9.63        46.19 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0H0 TCGA-BH-A0H7 TCGA-BH-A0HA TCGA-BH-A0HB 
       31.00        24.43        15.16        23.08        52.96        26.50 
TCGA-BH-A0HK TCGA-BH-A0HP TCGA-BH-A0HU TCGA-BH-A0W4 TCGA-BH-A0WA TCGA-BH-A18F 
        5.85        13.61        12.89        24.95        23.05         8.81 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18L TCGA-BH-A18P TCGA-BH-A18Q 
        2.01         7.23        20.12        26.66        30.28        55.63 
TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO 
       66.05         7.36        51.39        51.16        69.93        91.99 
TCGA-BH-A1ES TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EY TCGA-BH-A1F6 TCGA-BH-A1F8 
      113.82        42.28        12.00        17.69        97.48        24.66 
TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FM 
       33.17        74.73       122.89        36.92        63.35        45.63 
TCGA-BH-A1FN TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A209 
       72.07         6.90         0.72        38.60        57.83       130.16 
TCGA-BH-A42T TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q 
        0.99        11.93        11.77        12.66        11.77         0.07 
TCGA-C8-A12U TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 
       12.66         1.78         0.69         0.62         3.85         3.75 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM 
       10.92        11.34         0.16        12.03        10.42         2.30 
TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A278 
        0.30         0.23         0.36         0.43         8.28         0.03 
TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A145 
       12.20         0.99         0.03        11.90        20.88        13.48 
TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JC 
       21.14        19.20        14.17        17.49        16.50        15.78 
TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JK TCGA-D8-A1JM TCGA-D8-A1JN 
       18.15        18.90        12.03        20.12        19.40        20.38 
TCGA-D8-A1JP TCGA-D8-A1JT TCGA-D8-A1X5 TCGA-D8-A1X7 TCGA-D8-A1X9 TCGA-D8-A1XA 
       21.01        13.32        18.58        16.73        23.90        27.58 
TCGA-D8-A1XF TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XQ 
       15.22        21.83        14.50        19.92        17.69        16.41 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 
        6.35        12.99        16.54        15.32        15.52         3.81 
TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27M TCGA-D8-A27N 
       14.24        14.14        13.45        13.05        13.48         4.80 
TCGA-D8-A27R TCGA-D8-A27T TCGA-E2-A105 TCGA-E2-A10C TCGA-E2-A10F TCGA-E2-A14Q 
       10.09        13.08        43.00        40.11        28.87        38.24 
TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z 
       38.60        33.17        34.26        31.96        28.60        17.03 
TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A158 TCGA-E2-A159 
       25.41        27.12        23.24        21.04        14.79        25.05 
TCGA-E2-A15A TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15M 
       23.34        20.71        18.21        12.92        17.42         7.73 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1IE TCGA-E2-A1IG TCGA-E2-A1IH 
       14.07        14.99        60.53        38.30        32.78        33.73 
TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LA 
       33.70        28.44        20.98        27.42        39.62        24.59 
TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A56Z 
       28.90        18.87        43.04        16.93         5.52         7.20 
TCGA-E2-A573 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA 
       22.26        36.82        13.48        12.00        13.12        36.56 
TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1R4 TCGA-E9-A1R7 TCGA-E9-A1RA 
       39.55        12.59        20.05         6.12        21.21        32.09 
TCGA-E9-A1RB TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A226 
       20.81        34.65         6.58        21.27        35.64        34.13 
TCGA-E9-A228 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A247 
       12.53        39.09        22.75        23.51         0.69        27.22 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A3HO TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A5FL 
        0.72        17.75        26.07         0.62        15.72         0.26 
TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 
        0.23        15.39        12.20        18.90        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OZ TCGA-EW-A1P3 TCGA-EW-A1P4 
       15.68        28.77        25.94        40.41        52.96        29.82 
TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
       23.11         7.86        18.90        13.94        10.52        14.43 
TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A3E8 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2DA 
       55.00        25.91        21.27         7.40       109.87       194.27 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI 
       53.13        53.52        43.04        42.71        42.28        61.91 
TCGA-GM-A2DL TCGA-GM-A3XL TCGA-JL-A3YW TCGA-LD-A74U TCGA-LL-A5YM TCGA-LL-A5YN 
       90.84        69.30        11.84         6.67         4.70         3.65 
TCGA-LL-A5YO TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LQ-A4E4 
        3.19         4.50         4.50         3.22         6.21        15.91 
TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RW TCGA-OL-A5RZ 
       12.66        46.55         7.53        44.61        26.20        10.29 
TCGA-OL-A5S0 TCGA-OL-A66I TCGA-W8-A86G 
        9.80        23.70         5.29 

$`17P LOSS WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SG TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A2-A04N TCGA-A2-A04Q 
        8.52        14.27        13.68         7.96       104.81        41.95 
TCGA-A2-A04X TCGA-A2-A0CL TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CS TCGA-A2-A0CX 
       55.43        64.57        92.48        88.60        75.55        56.81 
TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES 
       33.76        28.77       101.72       107.61        74.40        37.05 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0ST TCGA-A2-A0SU 
       35.05        34.29        31.82        29.75        99.19        54.64 
TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YD TCGA-A2-A0YF 
       17.52         8.38        17.46        18.90        25.28        15.42 
TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FX TCGA-A2-A1FZ 
       14.50        18.61        31.73        23.77        36.79        22.45 
TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25C TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
       16.47        52.47        17.19        91.92        10.59        20.88 
TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XX TCGA-A2-A3XZ TCGA-A2-A4RY TCGA-A2-A4S0 
       33.93        29.98        38.40        31.99         8.81         8.91 
TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CH TCGA-A7-A0DB TCGA-A7-A13E 
        6.74        38.30        35.31        35.47        33.11        10.72 
TCGA-A7-A13G TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       23.61        20.61        11.34        10.59        10.29        11.28 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VV 
       13.41        14.70        11.97        12.10        10.72        10.29 
TCGA-A8-A06P TCGA-A8-A06T TCGA-A8-A06Y TCGA-A8-A07F TCGA-A8-A07J TCGA-A8-A07O 
       13.02        41.06        26.01        18.97        12.00         9.99 
TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A08A 
       10.98         7.99         9.96        28.04        18.05         0.99 
TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08S 
       19.99        19.96        12.00        37.05        31.00        19.07 
TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 
       93.04        40.01        19.07        41.98        12.00         9.99 
TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A09V 
       12.00        13.02        31.00        25.02        19.04        15.02 
TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A6 TCGA-A8-A0A9 TCGA-AC-A23G TCGA-AC-A23H 
        0.99        12.00        21.04        13.02        10.85         2.66 
TCGA-AC-A2B8 TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO 
        1.48        55.43        36.99        38.79        26.04        50.70 
TCGA-AC-A2QH TCGA-AC-A3HN TCGA-AC-A3QP TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS 
        1.02         0.69         9.40         1.55         1.32         1.55 
TCGA-AC-A62V TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AN-A03X 
        0.07         1.18         0.69         0.43         1.74         0.33 
TCGA-AN-A03Y TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A0AK TCGA-AN-A0AR TCGA-AN-A0FF 
        0.33         0.62         2.96         7.36         0.33         4.64 
TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FX TCGA-AN-A0XS TCGA-AN-A0XV 
        7.00         7.17         6.28         0.33         0.33         5.33 
TCGA-AO-A03L TCGA-AO-A03U TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 
       80.28        59.05        24.16        37.48        20.32        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JC TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JL 
       53.03        50.86        21.37        26.24        38.53        55.33 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E 
      102.58        99.25        94.59        90.58        77.56        57.30 
TCGA-AO-A12F TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KT 
       48.36        28.37        14.73        82.62        61.87        17.79 
TCGA-AQ-A1H2 TCGA-AQ-A7U7 TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TV TCGA-AR-A0TX 
       15.62         9.99        49.32        37.41        29.75        64.83 
TCGA-AR-A0U0 TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AV 
       65.36        51.25        48.82        43.56        39.98        42.58 
TCGA-AR-A1AW TCGA-AR-A24K TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24Q TCGA-AR-A24R 
       35.24        50.89        65.46        68.19        66.05        57.40 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A2LH TCGA-AR-A2LK 
       50.96        48.16        45.17        40.64        20.25        42.87 
TCGA-AR-A2LL TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QN 
        7.36        17.10        20.81        16.96        20.38        16.04 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IA 
       20.45        10.59        77.62       143.38       149.59       220.90 
TCGA-B6-A0IC TCGA-B6-A0IP TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
       50.70       110.93        81.17        78.02       172.96       162.05 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX 
      102.77       140.48        89.46       188.68        17.98        21.47 
TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A1KC TCGA-B6-A1KF 
      129.70       186.48        28.27        68.94        43.59       101.52 
TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
       73.51       170.17        85.35        82.88        55.00        24.53 
TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B7 TCGA-BH-A0BD 
       20.45        28.50        39.55        39.16        56.98        18.21 
TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BO TCGA-BH-A0BS TCGA-BH-A0BT 
       24.85        21.70        44.05        35.67        53.95        45.57 
TCGA-BH-A0BV TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DG TCGA-BH-A0DH 
       49.94        41.75        48.13        42.90        23.44        38.01 
TCGA-BH-A0DO TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0E1 
       17.26         3.22         2.56        38.47        45.17        15.68 
TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H3 
       44.81        32.65        24.49        30.35        10.78        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HI TCGA-BH-A0HO TCGA-BH-A0HQ 
       35.51        24.56        41.00        20.38         2.50        36.85 
TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W5 
       51.32        27.25        50.79         5.59        23.93        42.35 
TCGA-BH-A0W7 TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18R TCGA-BH-A1ET 
       44.81        90.84        72.56        37.74        37.55        82.85 
TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1FB 
       55.69        49.58        25.81        31.53        89.16       120.62 
TCGA-BH-A1FC TCGA-BH-A1FL TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A204 TCGA-BH-A28O 
      114.15        55.00       144.59        72.07        83.31        10.65 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12N TCGA-C8-A12V 
        6.44        20.12       109.28         8.94        11.77        12.66 
TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A132 TCGA-C8-A1HE TCGA-C8-A1HI 
       12.66        12.66         3.12         1.45        12.33        11.34 
TCGA-C8-A1HN TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A3M8 TCGA-D8-A140 
        3.25         9.67         0.03         0.03         0.23        13.25 
TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A1JB TCGA-D8-A1JF TCGA-D8-A1JH 
       20.58        13.97        14.17        18.71        12.03        14.01 
TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JL TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X6 
       18.97        20.09        20.09        12.20        14.70        17.79 
TCGA-D8-A1X8 TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XO 
       25.74        18.15         2.66        17.16        14.73         7.96 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A27E TCGA-D8-A27F 
       15.85        16.31        15.16        12.66        17.42        16.04 
TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27P TCGA-D8-A27V TCGA-D8-A27W 
       14.43         9.44        16.41         0.76        12.53        12.26 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 
       14.50        18.51         7.33        34.42        27.52        46.59 
TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P 
       40.41        37.51        28.44        47.15        44.68        40.96 
TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A154 TCGA-E2-A156 TCGA-E2-A15C 
       33.30        43.33        32.02        19.43        23.87        22.82 
TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15O 
       17.29        21.63        19.40         9.04        20.58        13.02 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       19.56        17.06        53.62        53.03        29.95        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IF TCGA-E2-A1IK TCGA-E2-A1IL 
       28.50        16.47        17.10        37.41        22.65         3.88 
TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A1LH 
       22.19        11.08        54.18        19.66        40.47       106.75 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A574 TCGA-E9-A1N4 
      102.61         8.75        15.72        18.05        19.89        19.20 
TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       35.77        21.57         9.86        11.90        14.30         0.62 
TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RH 
        2.10         1.38         2.76        40.24         0.66        34.59 
TCGA-E9-A227 TCGA-E9-A229 TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A245 
        0.79        13.32        12.89        24.10        17.06         0.85 
TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A54Y 
        1.94         0.95        12.56         0.76        18.41         0.23 
TCGA-E9-A5FK TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1OW TCGA-EW-A1OX 
        0.39        39.72         8.48        18.21        22.82        29.95 
TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PB 
       29.85        41.13        39.78        18.48        30.08        19.99 
TCGA-EW-A1PC TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A3U0 
        6.15        34.55        19.96        52.73        22.09        17.49 
TCGA-EW-A423 TCGA-EW-A424 TCGA-GM-A2D9 TCGA-GM-A2DK TCGA-GM-A2DM TCGA-GM-A2DN 
       10.16        10.59        59.57        62.33        76.64        77.33 
TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 
       53.36       110.50        38.20        32.28        53.95        57.63 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A7W6 TCGA-LL-A440 
       13.55        18.12        11.57         8.28         4.60         0.66 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YP TCGA-LL-A6FQ 
        2.99         3.58         6.90         5.56         3.25         2.63 
TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A7SZ TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5RU 
        3.88         4.14         5.59         2.79         2.10        27.65 
TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K 
       24.10        16.87        14.10        14.76        54.51        33.90 
TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-S3-A6ZG 
       31.07        18.21         7.23         4.44         6.81 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.03               0.03 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            234.28             220.90 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             21.53              21.37 
[1] "0.0 - 234.3 (21.5)" "0.0 - 220.9 (21.4)"
[1] "hr=" "1.2"
D70V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17P LOSS MUTATED        41       34        2        3       176       132
  17P LOSS WILD-TYPE      39       43        7        6       159        92
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17P LOSS MUTATED           0         79         10         33       10
  17P LOSS WILD-TYPE         2         59         17         26        7
                    vv
clus                 STAGE TIS STAGE X
  17P LOSS MUTATED           1      10
  17P LOSS WILD-TYPE         0       6
D70V3, multiclass
            clus
vv           17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                  41                 39
  STAGE IA                 34                 43
  STAGE IB                  2                  7
  STAGE II                  3                  6
  STAGE IIA               176                159
  STAGE IIB               132                 92
  STAGE III                 0                  2
  STAGE IIIA               79                 59
  STAGE IIIB               10                 17
  STAGE IIIC               33                 26
  STAGE IV                 10                  7
  STAGE TIS                 1                  0
  STAGE X                  10                  6
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  17P LOSS MUTATED   117 332  66  15
  17P LOSS WILD-TYPE 141 249  51  21
D70V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1              117                141
  T2              332                249
  T3               66                 51
  T4               15                 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                  N0  N1  N2  N3
  17P LOSS MUTATED   250 171  63  37
  17P LOSS WILD-TYPE 218 159  48  33
D70V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0              250                218
  N1              171                159
  N2               63                 48
  N3               37                 33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  17P LOSS MUTATED          1 456  10  65
  17P LOSS WILD-TYPE        1 389   7  66
D70V6, multiclass
          clus
vv         17P LOSS MUTATED 17P LOSS WILD-TYPE
  CM0 (I+)                1                  1
  M0                    456                389
  M1                     10                  7
  MX                     65                 66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   528   4
  17P LOSS WILD-TYPE 456   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    528    4
  17P LOSS WILD-TYPE  456    7
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE              528                456
  MALE                  4                  7
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  17P LOSS MUTATED                            0                           412
  17P LOSS WILD-TYPE                          1                           323
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  17P LOSS MUTATED                               72                   4
  17P LOSS WILD-TYPE                             94                   1
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  17P LOSS MUTATED                                 18                  4
  17P LOSS WILD-TYPE                               11                 10
                    vv
clus                 OTHER  SPECIFY
  17P LOSS MUTATED               21
  17P LOSS WILD-TYPE             23
D70V8, multiclass
                                  clus
vv                                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 412                323
  INFILTRATING LOBULAR CARCINOMA                 72                 94
  MEDULLARY CARCINOMA                             4                  1
  MIXED HISTOLOGY (PLEASE SPECIFY)               18                 11
  MUCINOUS CARCINOMA                              4                 10
  OTHER  SPECIFY                                 21                 23
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V9, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   152 380
  17P LOSS WILD-TYPE 130 333
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    152  380
  17P LOSS WILD-TYPE  130  333
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO               152                130
  YES              380                333
[1] 2 2
[1] FALSE
D70V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P LOSS MUTATED                                  1    36
  17P LOSS WILD-TYPE                                0    20
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED                          79   367
  17P LOSS WILD-TYPE                        58   341
D70V11, multiclass
                                  clus
vv                                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                          36                 20
  BLACK OR AFRICAN AMERICAN                      79                 58
  WHITE                                         367                341
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V12, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    19 432
  17P LOSS WILD-TYPE  17 364
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     19  432
  17P LOSS WILD-TYPE   17  364
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                   19                 17
  NOT HISPANIC OR LATINO              432                364
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17Q LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED   214  30
  17Q LOSS WILD-TYPE 646  84
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
               244                730 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                30                 84 
$`17Q LOSS MUTATED`
TCGA-A1-A0SK TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A04P TCGA-A2-A04T 
       31.79        39.32        28.01        19.20        18.02        73.84 
TCGA-A2-A04U TCGA-A2-A0CK TCGA-A2-A0CM TCGA-A2-A0CR TCGA-A2-A0CT TCGA-A2-A0CV 
       22.06       125.59        24.79       107.93        75.25        63.45 
TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0EN TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0T1 
       21.14        34.55        89.36        44.88        50.43        17.13 
TCGA-A2-A0YC TCGA-A2-A0YE TCGA-A2-A0YK TCGA-A2-A1FW TCGA-A2-A1G1 TCGA-A2-A25A 
       32.55        18.21        19.33        17.36        19.20       107.70 
TCGA-A2-A25B TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RX 
       16.31        83.01        14.07        34.98        38.37         9.01 
TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CG TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A13D 
       12.00         3.42        34.29        30.61        37.45        31.73 
TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26I TCGA-A7-A4SB TCGA-A7-A4SD 
       31.36        24.26        23.74        21.73        13.74        14.50 
TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY 
       21.17        14.73        10.29         9.37        10.42         8.75 
TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B 
        1.02        17.98        31.00        53.98         9.01        33.01 
TCGA-A8-A07E TCGA-A8-A07I TCGA-A8-A07L TCGA-A8-A07R TCGA-A8-A084 TCGA-A8-A086 
       19.99        14.01        17.03         8.98        15.06        13.02 
TCGA-A8-A08B TCGA-A8-A08I TCGA-A8-A08X TCGA-A8-A093 TCGA-A8-A09K TCGA-A8-A09N 
       23.08        12.00        33.99        17.95        29.98         1.02 
TCGA-A8-A0A7 TCGA-A8-A0AB TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2QJ TCGA-AC-A3BB 
        0.99        17.03        38.53        38.20         2.27         0.99 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A62Y TCGA-AN-A046 TCGA-AN-A04C TCGA-AN-A0AL 
        1.81         1.68         1.81         0.33         1.78         6.51 
TCGA-AN-A0AS TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW 
        0.33         7.96         7.59         6.02         0.33         0.36 
TCGA-AN-A0FY TCGA-AN-A0XR TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AO-A03N TCGA-AO-A03V 
        0.33         0.33         0.33         0.33        66.77        29.13 
TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0JD TCGA-AO-A0JL TCGA-AO-A129 TCGA-AO-A12D 
       32.78        21.40        72.00        55.33        96.10        64.04 
TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AR-A0TP TCGA-AR-A0TY 
       70.39         0.53         5.65         2.56        82.88        55.86 
TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AN 
       70.16        76.18        75.55        61.84        52.77        43.73 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AY TCGA-AR-A24S TCGA-AR-A24U TCGA-AR-A250 
       43.07        17.23        20.22        62.07        53.36        56.15 
TCGA-B6-A0IB TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IO TCGA-B6-A0IQ TCGA-B6-A0RE 
      129.57       112.37       176.98       110.14       140.88       211.56 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WY TCGA-B6-A1KN 
       68.45       189.01       100.70       131.21       113.79       139.17 
TCGA-B6-A402 TCGA-B6-A408 TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0B5 
       54.28        49.94        38.79        25.55        46.95        48.36 
TCGA-BH-A0B6 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BP TCGA-BH-A0BR 
       56.94        51.68        37.22        32.02        48.69        53.69 
TCGA-BH-A0BW TCGA-BH-A0C1 TCGA-BH-A0E0 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E9 
       11.67        44.02         4.41        14.30         9.63        46.19 
TCGA-BH-A0EE TCGA-BH-A0H7 TCGA-BH-A0HB TCGA-BH-A0HP TCGA-BH-A18F TCGA-BH-A18G 
       31.00        23.08        26.50        13.61         8.81         2.01 
TCGA-BH-A18I TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1ES 
        7.23        30.28        55.63        51.16        69.93       113.82 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EY TCGA-BH-A1F6 TCGA-BH-A1FD TCGA-BH-A1FH 
       42.28        12.00        17.69        97.48        33.17        36.92 
TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A208 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12P 
       45.63        72.07        57.83        11.93        11.77        11.77 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A131 TCGA-C8-A137 TCGA-C8-A1HK TCGA-C8-A26W 
        0.07        12.66         1.78         3.85        12.03         0.23 
TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-D8-A13Y 
        0.36         8.28         0.03         0.99         0.03        11.90 
TCGA-D8-A13Z TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA 
       20.88        13.48        19.20        14.17        17.49        16.50 
TCGA-D8-A1JC TCGA-D8-A1JK TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1XJ TCGA-D8-A1XK 
       15.78        20.12        19.40        20.38        21.83        14.50 
TCGA-D8-A1XQ TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XZ TCGA-D8-A27M TCGA-E2-A14V 
       16.41         6.35        12.99        15.32        13.48        34.26 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 
       31.96        28.60        17.03        25.41        27.12        23.24 
TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15G TCGA-E2-A15M TCGA-E2-A1AZ TCGA-E2-A1II 
       14.79        25.05        18.21         7.73        60.53        33.70 
TCGA-E2-A1L7 TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A573 TCGA-E9-A1N6 TCGA-E9-A1RA 
       27.42        43.04        16.93        22.26        13.48        32.09 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A244 TCGA-E9-A295 TCGA-E9-A3QA TCGA-E9-A3X8 
        6.58        21.27         0.69         0.72         0.62        15.72 
TCGA-E9-A5FL TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OZ TCGA-EW-A1P4 TCGA-EW-A1P8 
        0.26        28.77        25.94        40.41        29.82         7.86 
TCGA-EW-A2FV TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DD 
       25.91         7.40       109.87       194.27        53.13        43.04 
TCGA-GM-A2DI TCGA-JL-A3YW TCGA-LD-A74U TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A73Z 
       61.91        11.84         6.67         3.65         3.19         4.50 
TCGA-OL-A5D7 TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-OL-A66I 
       46.55        26.20         9.80        23.70 

$`17Q LOSS WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04Q 
       20.88        13.68         7.96        18.21       104.81        41.95 
TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CL 
       82.16        63.12        64.04        55.43        36.13        64.57 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CW 
      112.08        92.48        88.60        75.55         5.19        64.04 
TCGA-A2-A0CX TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EO 
       56.81        33.76        28.77        25.22       101.72        80.28 
TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU 
      107.61        79.76        74.40        37.05        35.05        34.29 
TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU 
       31.82        29.75        24.72        24.16        99.19        54.64 
TCGA-A2-A0SV TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 
       27.12        44.28        17.52         8.38        18.71        20.52 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG 
       17.46        18.90        20.75        25.28        15.42        21.90 
TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT 
       21.67        14.50        18.61        14.63        31.73        23.77 
TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 
       23.47        36.79        22.45        20.25        19.56        16.47 
TCGA-A2-A259 TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
       52.47        17.19        18.15        91.92        10.59        20.88 
TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XZ 
       39.65        33.93        29.98        49.48        38.40        31.99 
TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CE 
        7.30         8.81         8.91         6.74        38.30        35.31 
TCGA-A7-A0CH TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G 
       35.47        35.67        33.11        10.72        12.72        23.61 
TCGA-A7-A13H TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ 
       29.56        23.80        20.61        22.32        11.34        10.59 
TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA 
       10.29        11.28        13.41        14.70        11.97        14.93 
TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A8-A06O TCGA-A8-A06P 
       17.92        12.10        10.72        11.05        13.02        13.02 
TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A07F 
       41.06        29.03        26.01         1.02        17.03        18.97 
TCGA-A8-A07G TCGA-A8-A07J TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U 
       18.97        12.00         9.99        10.98         7.99         9.96 
TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A08A TCGA-A8-A08C 
        9.99        28.04        18.05        36.95         0.99        19.99 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P 
       18.05        19.96        37.05         9.99        31.00        31.00 
TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 
        0.99        19.07        93.04        40.01        19.07        16.01 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C 
       41.98        12.00         9.99         9.99        12.00         1.02 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R 
       13.02        31.00        33.07        15.02        25.02         8.98 
TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 
       19.04        15.02         0.99        14.01        12.00        19.04 
TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A9 TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E 
       13.02        21.04        13.02        38.04         0.95         2.37 
TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG 
       10.85         2.66         1.48        40.57        55.43        36.99 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3HN 
       38.79        26.04        50.70         1.02         0.92         0.69 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS 
       14.83         9.40         1.12         1.55         1.32         1.55 
TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A8OP 
        0.07         1.12         1.18         0.69         0.43         1.74 
TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D 
        0.33         0.33         0.23         0.62         2.96         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD 
        8.02         7.36         0.16         0.33         0.33         6.44 
TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FX TCGA-AN-A0FZ 
        4.64         7.00         7.17         6.28         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XS TCGA-AN-A0XV 
        0.33         0.33        12.33         0.30         0.33         5.33 
TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R 
        5.59        80.28        47.84        81.63        84.69        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 
       47.87        59.05        17.65        24.16        37.48        20.32 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE 
       22.36        53.03        21.53        50.70        50.86        76.77 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A124 
       21.37        26.24        38.53        62.04        71.80       102.58 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E 
       99.25        93.70        94.59        90.58        77.56        57.30 
TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ 
       48.36        41.62        28.37        14.73        82.62        61.87 
TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       17.79        24.79        26.93       130.09        15.62        13.22 
TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT 
       21.86         9.99        49.32         5.26        37.41        56.88 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U2 
       29.75        24.30        64.83        76.14        65.36        83.87 
TCGA-AR-A0U4 TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AO TCGA-AR-A1AP 
       55.36        51.25        48.82        62.56        43.56        39.98 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24H 
       40.83        46.32        42.58        35.24        36.26       109.58 
TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
       50.89        73.02        65.46        68.19        65.69         0.85 
TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X 
       66.05        57.40        53.26        54.18        50.96        48.16 
TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
       51.75        45.17        40.64        39.85        34.82        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN 
      128.65        20.25        42.87         7.36        40.04        17.10 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP 
       20.81        16.96        20.38        54.74        16.04        20.45 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA 
       10.59        77.62       143.38       149.59        12.13       220.90 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
       50.70        65.72       146.50        18.77       126.12        84.59 
TCGA-B6-A0IP TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
      110.93       234.28        81.17        78.02       172.96       162.05 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT 
      102.77       140.48        89.46       157.41        97.48       188.68 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 
       79.63        17.98        21.47       129.57       129.70       186.48 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI 
       28.27        68.94        58.88        43.59       101.52        73.51 
TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW 
      170.17        85.35        82.88        55.00        24.53        20.45 
TCGA-BH-A0AZ TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B7 TCGA-BH-A0BD 
       28.50        40.83        39.55        39.16        56.98        18.21 
TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO 
       25.71        24.85        21.70        44.05        61.68        35.67 
TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BZ TCGA-BH-A0C0 
       27.19        53.95        45.57        49.94        49.05        41.75 
TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH 
       48.13        42.90        45.83        31.17        23.44        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ 
       22.13        13.91        48.23        17.26        15.65         3.22 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 
        2.56        38.47        45.17        47.41        16.27        15.68 
TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ 
       44.81        32.65        24.49        24.43        30.35        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HA 
       15.16        37.78        35.51        24.56        41.00        52.96 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW 
       20.38         5.85         2.50        36.85        12.89        51.32 
TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 
       27.25        50.79         5.59        23.93        24.95        42.35 
TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M 
       44.81        23.05        20.12        90.84        26.66        72.56 
TCGA-BH-A18N TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EO 
       37.74        37.55        66.05         7.36        51.39        91.99 
TCGA-BH-A1ET TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 
       82.85        55.69        49.58        25.81        31.53        89.16 
TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FJ 
       24.66       120.62       114.15        74.73       122.89        63.35 
TCGA-BH-A1FL TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 
       55.00       144.59        72.07         6.90         0.72        38.60 
TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T 
       83.31       130.16        10.65         6.44        20.12         0.99 
TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12V TCGA-C8-A12W 
      109.28         8.94        11.77        12.66        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A138 
       12.66         3.12         1.45         0.69         0.62         3.75 
TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HL 
       12.33        10.92        11.34        11.34         0.16        10.42 
TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A274 
        2.30         3.25         0.30         0.43         9.67         0.03 
TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A3M8 TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 
        0.03        12.20         0.23        13.25        20.58        13.97 
TCGA-D8-A143 TCGA-D8-A146 TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF 
       14.17        21.14        18.71        18.15        18.90        12.03 
TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JL TCGA-D8-A1JP 
       12.03        14.01        18.97        20.09        20.09        21.01 
TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 
       12.20        13.32        14.70        18.58        17.79        16.73 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD 
       25.74        23.90        27.58        18.15         2.66        17.16 
TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR 
       15.22        14.73        19.92        17.69         7.96        15.85 
TCGA-D8-A1XS TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       16.31        15.16        12.66        16.54        15.52         3.81 
TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H 
       14.24        14.14        17.42        16.04        13.45        13.05 
TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R 
       14.43         9.44        16.41         4.80         0.76        10.09 
TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 
       13.08        12.53        12.26        14.50        18.51         7.33 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B 
       43.00        34.42        27.52        46.59        40.41        37.51 
TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P 
       40.11        28.44        28.87        47.15        44.68        40.96 
TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14W 
       38.24        38.60        33.17        33.30        43.33        32.02 
TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D 
       19.43        21.04        23.87        23.34        22.82        17.29 
TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       20.71        21.63        12.92        17.42        19.40         9.04 
TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
       20.58        13.02        19.56        17.06        14.07        14.99 
TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC 
       53.62        53.03        29.95        32.35        28.50        16.47 
TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ 
       17.10        38.30        37.41        32.78        33.73        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       22.65         3.88        22.19        20.98        11.08        54.18 
TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG 
       39.62        19.66        24.59        40.47        28.90        18.87 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z 
      106.75       102.61         8.75         5.52        15.72         7.20 
TCGA-E2-A570 TCGA-E2-A574 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 
       18.05        19.89        19.20        36.82        12.00        13.12 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG 
       36.56        39.55        12.59        35.77        20.05        21.57 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 
        9.86        11.90        14.30         0.62         2.10         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD 
        1.38         2.76        21.21        20.81        40.24         0.66 
TCGA-E9-A1RE TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 
       34.65        34.59        35.64        34.13         0.79        12.53 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H 
       13.32        39.09        22.75        12.89        23.51        24.10 
TCGA-E9-A243 TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A 
       17.06         0.85        27.22         1.94         0.95        12.56 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A54Y TCGA-E9-A5FK 
       17.75         0.76        26.07        18.41         0.23         0.39 
TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
        0.23        15.39        12.20        39.72         8.48        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OW TCGA-EW-A1OX 
       18.90        13.25        16.57        15.68        22.82        29.95 
TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 
       29.85        41.13        39.78        52.96        23.11        18.48 
TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE 
       30.08        18.90        19.99         6.15        13.94        10.52 
TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FW 
       14.43        34.55        19.96        55.00        52.73        22.09 
TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-GM-A2D9 TCGA-GM-A2DC 
       21.27        17.49        10.16        10.59        59.57        53.52 
TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       42.71        42.28        62.33        90.84        76.64        77.33 
TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN 
       53.36       110.50        38.20        32.28        69.30        53.95 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A7W6 
       57.63        13.55        18.12        11.57         8.28         4.60 
TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM 
        0.66         2.99         3.58         6.90         5.56         4.70 
TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A740 TCGA-LL-A7SZ 
        3.25         2.63         3.88         4.14         4.50         5.59 
TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
        3.22         6.21        15.91         2.79         2.10        12.66 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY 
        7.53        44.61        27.65        24.10        16.87        14.10 
TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       10.29        14.76        54.51        33.90        31.07        18.21 
TCGA-OL-A66O TCGA-OL-A66P TCGA-S3-A6ZG TCGA-W8-A86G 
        7.23         4.44         6.81         5.29 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.03               0.03 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            211.56             234.28 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             21.78              21.32 
[1] "0.0 - 211.6 (21.8)" "0.0 - 234.3 (21.3)"
[1] "hr=" "1"  
D71V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17Q LOSS MUTATED        20       16        1        0        86        56
  17Q LOSS WILD-TYPE      60       61        8        9       249       168
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17Q LOSS MUTATED           0         39          6         15        5
  17Q LOSS WILD-TYPE         2         99         21         44       12
                    vv
clus                 STAGE TIS STAGE X
  17Q LOSS MUTATED           0       5
  17Q LOSS WILD-TYPE         1      11
D71V3, multiclass
            clus
vv           17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                  20                 60
  STAGE IA                 16                 61
  STAGE IB                  1                  8
  STAGE II                  0                  9
  STAGE IIA                86                249
  STAGE IIB                56                168
  STAGE III                 0                  2
  STAGE IIIA               39                 99
  STAGE IIIB                6                 21
  STAGE IIIC               15                 44
  STAGE IV                  5                 12
  STAGE TIS                 0                  1
  STAGE X                   5                 11
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  17Q LOSS MUTATED    56 150  33  10
  17Q LOSS WILD-TYPE 202 431  84  26
D71V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1               56                202
  T2              150                431
  T3               33                 84
  T4               10                 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                  N0  N1  N2  N3
  17Q LOSS MUTATED   124  72  33  18
  17Q LOSS WILD-TYPE 344 258  78  52
D71V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0              124                344
  N1               72                258
  N2               33                 78
  N3               18                 52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  17Q LOSS MUTATED          1 219   5  25
  17Q LOSS WILD-TYPE        1 626  12 106
D71V6, multiclass
          clus
vv         17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CM0 (I+)                1                  1
  M0                    219                626
  M1                      5                 12
  MX                     25                106
[1] 4 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   250   0
  17Q LOSS WILD-TYPE 734  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED    250    0
  17Q LOSS WILD-TYPE  734   11
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE              250                734
  MALE                  0                 11
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  17Q LOSS MUTATED                            0                           205
  17Q LOSS WILD-TYPE                          1                           530
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  17Q LOSS MUTATED                               27                   3
  17Q LOSS WILD-TYPE                            139                   2
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  17Q LOSS MUTATED                                  4                  0
  17Q LOSS WILD-TYPE                               25                 14
                    vv
clus                 OTHER  SPECIFY
  17Q LOSS MUTATED               11
  17Q LOSS WILD-TYPE             33
D71V8, multiclass
                                  clus
vv                                 17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 205                530
  INFILTRATING LOBULAR CARCINOMA                 27                139
  MEDULLARY CARCINOMA                             3                  2
  MIXED HISTOLOGY (PLEASE SPECIFY)                4                 25
  MUCINOUS CARCINOMA                              0                 14
  OTHER  SPECIFY                                 11                 33
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V9, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    71 179
  17Q LOSS WILD-TYPE 211 534
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     71  179
  17Q LOSS WILD-TYPE  211  534
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                71                211
  YES              179                534
[1] 2 2
[1] FALSE
D71V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q LOSS MUTATED                                  1    19
  17Q LOSS WILD-TYPE                                0    37
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED                          46   160
  17Q LOSS WILD-TYPE                        91   548
D71V11, multiclass
                                  clus
vv                                 17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                          19                 37
  BLACK OR AFRICAN AMERICAN                      46                 91
  WHITE                                         160                548
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V12, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     9 198
  17Q LOSS WILD-TYPE  27 598
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      9  198
  17Q LOSS WILD-TYPE   27  598
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    9                 27
  NOT HISPANIC OR LATINO              198                598
[1] 2 2
[1] FALSE

Clustering(72) Variable = 18P LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED   234  51
  18P LOSS WILD-TYPE 626  63
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               285                689 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                51                 63 
$`18P LOSS MUTATED`
TCGA-A1-A0SD TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A04W 
       14.37        20.88        13.68        28.01        18.02        64.04 
TCGA-A2-A04X TCGA-A2-A0CU TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D4 TCGA-A2-A0EN 
       55.43         5.19        21.14        34.55        25.22        89.36 
TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EY TCGA-A2-A0SX TCGA-A2-A0T4 TCGA-A2-A0T7 
       34.29        31.82        24.16        50.43        20.52        20.75 
TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT 
       18.21        21.90        14.50        19.33        14.63        23.77 
TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1G1 TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A3XT 
       17.36        36.79        19.20        17.19        18.15        83.01 
TCGA-A2-A3XU TCGA-A2-A4S1 TCGA-A7-A0CG TCGA-A7-A13F TCGA-A7-A26F TCGA-A7-A2KD 
       29.98        12.00        34.29        12.72        24.26        22.32 
TCGA-A7-A3J1 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A6VX 
       11.28        14.93        13.74        17.92        14.73        10.42 
TCGA-A8-A06R TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A076 TCGA-A8-A07G TCGA-A8-A07P 
       17.98        29.03        26.01        53.98        18.97        10.98 
TCGA-A8-A07W TCGA-A8-A084 TCGA-A8-A08B TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A092 
        9.99        15.06        23.08        37.05         9.99        16.01 
TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q 
       12.00        13.02        31.00        15.02         1.02        25.02 
TCGA-A8-A09X TCGA-A8-A0A2 TCGA-AC-A23H TCGA-AC-A2FF TCGA-AC-A2FM TCGA-AC-A2FO 
       14.01        19.04         2.66        55.43        26.04        50.70 
TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A62V TCGA-AC-A8OP 
        2.27         0.99         1.81         1.68         0.07         1.74 
TCGA-AN-A03X TCGA-AN-A04A TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM 
        0.33         2.96         8.02         7.36         6.51         0.16 
TCGA-AN-A0AR TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XP TCGA-AN-A0XU 
        0.33         0.33         0.36         0.33         0.30         0.33 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A0J4 TCGA-AO-A0J5 
       80.28        47.84        66.77        81.63        17.65        24.16 
TCGA-AO-A0J7 TCGA-AO-A0JA TCGA-AO-A0JG TCGA-AO-A129 TCGA-AO-A12E TCGA-AQ-A04H 
       20.32        21.53        26.24        96.10        57.30        24.79 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A54O TCGA-AR-A0TT 
       26.93       130.09         5.65        15.62        21.86        56.88 
TCGA-AR-A0TX TCGA-AR-A0U2 TCGA-AR-A1AI TCGA-AR-A1AP TCGA-AR-A1AV TCGA-AR-A1AW 
       64.83        83.87        61.84        39.98        42.58        35.24 
TCGA-AR-A24H TCGA-AR-A24R TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A252 TCGA-AR-A255 
      109.58        57.40        54.18        50.96        40.64        34.82 
TCGA-AR-A256 TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QQ TCGA-B6-A0IJ TCGA-B6-A0IK 
       93.83        54.74        16.04        10.59       176.98        18.77 
TCGA-B6-A0IO TCGA-B6-A0RH TCGA-B6-A0RL TCGA-B6-A0RP TCGA-B6-A0RS TCGA-B6-A0WV 
      110.14       189.01        81.17       102.77       100.70        79.63 
TCGA-B6-A0WW TCGA-B6-A0WY TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A402 
       17.98       113.79       101.52        73.51       139.17        54.28 
TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0B3 TCGA-BH-A0B6 TCGA-BH-A0BA TCGA-BH-A0BD 
       38.79        25.55        39.55        56.94        37.22        18.21 
TCGA-BH-A0BP TCGA-BH-A0BT TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C7 TCGA-BH-A0DH 
       48.69        45.57        49.05        41.75        42.90        38.01 
TCGA-BH-A0DX TCGA-BH-A0E6 TCGA-BH-A0GY TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0HA 
       47.41         9.63        30.35        24.56        23.08        52.96 
TCGA-BH-A0HI TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0W3 TCGA-BH-A18F TCGA-BH-A18K 
       20.38        27.25        50.79        23.93         8.81        90.84 
TCGA-BH-A18L TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1EU 
       26.66        51.39        51.16        69.93        91.99        42.28 
TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F6 
       12.00        55.69        17.69        25.81        31.53        97.48 
TCGA-BH-A1F8 TCGA-BH-A1FD TCGA-BH-A1FM TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A204 
       24.66        33.17        45.63         6.90        38.60        83.31 
TCGA-BH-A209 TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12W TCGA-C8-A132 
      130.16        12.66        11.77         0.07        12.66         1.45 
TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HI 
        0.69         0.62         3.75        12.33        10.92        11.34 
TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26X TCGA-C8-A26Y 
        0.16        12.03         2.30         3.25         0.36         0.43 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A278 TCGA-C8-A3M7 TCGA-D8-A13Y 
        8.28         9.67         0.03         0.03         0.03        11.90 
TCGA-D8-A142 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JD 
       13.97        21.14        14.17        17.49        16.50        18.15 
TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JM 
       18.90        12.03        14.01        18.97        20.09        19.40 
TCGA-D8-A1JN TCGA-D8-A1X5 TCGA-D8-A1XA TCGA-D8-A1XJ TCGA-D8-A1XL TCGA-D8-A1XR 
       20.38        18.58        27.58        21.83        19.92        15.85 
TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1Y3 TCGA-D8-A27M TCGA-D8-A27R TCGA-D8-A3Z6 
       12.99        16.54        14.14        13.48        10.09        18.51 
TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A14O TCGA-E2-A14Q 
       34.42        46.59        40.11        28.44        44.68        38.24 
TCGA-E2-A14R TCGA-E2-A14V TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A158 
       38.60        34.26        17.03        27.12        19.43        14.79 
TCGA-E2-A159 TCGA-E2-A15E TCGA-E2-A15M TCGA-E2-A1AZ TCGA-E2-A1BD TCGA-E2-A1IH 
       25.05        20.71         7.73        60.53        17.10        33.73 
TCGA-E2-A1IO TCGA-E2-A1LE TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A573 
       20.98        28.90         8.75        43.04         5.52        22.26 
TCGA-E2-A574 TCGA-E9-A1N4 TCGA-E9-A1NA TCGA-E9-A1ND TCGA-E9-A1NG TCGA-E9-A1R6 
       19.89        19.20        36.56        12.59        21.57         2.76 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A22E TCGA-E9-A248 TCGA-E9-A295 
        6.58        21.27        35.64        12.89         1.94         0.72 
TCGA-E9-A2JS TCGA-E9-A54Y TCGA-E9-A5FL TCGA-EW-A1IW TCGA-EW-A1J1 TCGA-EW-A1J6 
       17.75         0.23         0.26        12.20        18.90        28.77 
TCGA-EW-A1OV TCGA-EW-A1OY TCGA-EW-A1P3 TCGA-EW-A1P8 TCGA-EW-A1PC TCGA-EW-A1PF 
       25.94        29.85        52.96         7.86         6.15        14.43 
TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A423 TCGA-GI-A2C8 TCGA-GM-A2DH TCGA-GM-A2DL 
       55.00        25.91        10.16         7.40        42.28        90.84 
TCGA-JL-A3YW TCGA-LD-A74U TCGA-LL-A441 TCGA-LL-A5YM TCGA-LL-A7T0 TCGA-LQ-A4E4 
       11.84         6.67         2.99         4.70         3.22        15.91 
TCGA-OL-A5D6 TCGA-OL-A5S0 TCGA-OL-A66N 
       12.66         9.80        18.21 

$`18P LOSS WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SK 
        8.52        43.43        48.10        14.27        47.24        31.79 
TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04Q 
        7.96        39.32        19.20        18.21       104.81        41.95 
TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CK 
       82.16        73.84        22.06        63.12        36.13       125.59 
TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
       64.57        24.79       112.08        92.48        88.60       107.93 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D2 
       75.55        75.25        63.45        64.04        56.81        33.76 
TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER 
       28.77       101.72        80.28       107.61        79.76        74.40 
TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU 
       37.05        35.05        29.75        24.72        99.19        54.64 
TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 
       27.12        44.88        44.28        17.52        17.13         8.38 
TCGA-A2-A0T3 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF 
       18.71        17.46        18.90        32.55        25.28        15.42 
TCGA-A2-A0YH TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FZ TCGA-A2-A1G0 
       21.67        18.61        31.73        23.47        22.45        20.25 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25E 
       19.56        16.47        52.47       107.70        16.31        91.92 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XV TCGA-A2-A3XW 
       10.59        20.88        39.65        33.93        14.07        49.48 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX 
       38.40        34.98        31.99        38.37         7.30         9.01 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE 
        8.81         8.91         6.74         3.42        38.30        35.31 
TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D 
       35.47        30.61        37.45        35.67        33.11        31.73 
TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26G TCGA-A7-A26H 
       10.72        23.61        29.56        31.36        23.74        23.80 
TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF 
       21.73        20.61        11.34        10.59        10.29        13.41 
TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A5ZV TCGA-A7-A5ZW 
       14.70        11.97        14.50        21.17        12.10        10.72 
TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P 
       11.05        10.29         9.37         8.75        13.02        13.02 
TCGA-A8-A06Q TCGA-A8-A06T TCGA-A8-A06X TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A079 
        1.02        41.06        31.00         1.02        17.03         9.01 
TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
       33.01        19.99        18.97        14.01        12.00        17.03 
TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07Z TCGA-A8-A082 
        9.99         8.98         7.99         9.96        28.04        18.05 
TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G 
       36.95        13.02         0.99        19.99        18.05        19.96 
TCGA-A8-A08I TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T 
       12.00        31.00        31.00         0.99        19.07        93.04 
TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 
       33.99        40.01        19.07        17.95        41.98        12.00 
TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09R 
        9.99         9.99         1.02        33.07        29.98         8.98 
TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A4 TCGA-A8-A0A6 
       19.04        15.02         0.99        12.00        13.02        21.04 
TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E 
        0.99        13.02        17.03        38.04         0.95         2.37 
TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FG 
       10.85         1.48        38.53        38.20        40.57        36.99 
TCGA-AC-A2FK TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
       38.79         1.02         0.92         0.69        14.83         9.40 
TCGA-AC-A3TN TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62X TCGA-AC-A62Y 
        1.12         1.55         1.32         1.55         1.12         1.81 
TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 
        1.18         0.69         0.43         0.33         0.23         0.33 
TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD 
        0.62         1.78         1.71         0.33         0.33         6.44 
TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        4.64         7.96         7.00         7.59         7.17         6.28 
TCGA-AN-A0FT TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO 
        6.02         0.33         0.33         0.33         0.33        12.33 
TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03P 
        0.33         0.33         0.33         5.33         5.59        84.69 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 
       68.75        47.87        59.05        29.13        32.78        21.40 
TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD 
       37.48        22.36        53.03        50.70        50.86        72.00 
TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM 
       76.77        21.37        38.53        62.04        55.33        71.80 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B 
      102.58        99.25        93.70        94.59        90.58        77.56 
TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       64.04        48.36        41.62        28.37        14.73        82.62 
TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A1H3 TCGA-AQ-A54N 
       61.87        70.39         0.53        17.79        13.22         2.56 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TV 
        9.99        82.88        49.32         5.26        37.41        29.75 
TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 
       24.30        55.86        76.14        65.36        70.16        76.18 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM 
       55.36        75.55        52.77        51.25        48.82        62.56 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU 
       43.73        43.56        43.07        17.23        40.83        46.32 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       36.26        20.22        50.89        73.02        65.46        68.19 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U 
       65.69         0.85        66.05        62.07        53.26        53.36 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A2LE 
       48.16        51.75        56.15        45.17        39.85       128.65 
TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       20.25        42.87         7.36        40.04        17.10        20.81 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QP TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 
       16.96        20.38        20.45        77.62       143.38       149.59 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG 
       12.13       220.90       129.57        50.70        65.72       146.50 
TCGA-B6-A0IH TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE 
      112.37       126.12        84.59       110.93       140.88       211.56 
TCGA-B6-A0RG TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ 
       68.45       234.28        78.02       172.96       162.05       140.48 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WX 
       89.46       131.21       157.41        97.48       188.68        21.47 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      129.57       129.70       186.48        28.27        68.94        58.88 
TCGA-B6-A1KC TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C 
       43.59       170.17        85.35        49.94        82.88        55.00 
TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 
       24.53        20.45        28.50        46.95        40.83        39.16 
TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BF TCGA-BH-A0BG 
       48.36        56.98        51.68        32.02        25.71        24.85 
TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR 
       21.70        44.05        61.68        35.67        27.19        53.69 
TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0DD 
       53.95        49.94        11.67        44.02        48.13        45.83 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO 
       31.17        23.44        22.13        13.91        48.23        17.26 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DZ 
       15.65         3.22         2.56        38.47        45.17        16.27 
TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA 
        4.41        15.68        14.30        44.81        46.19        32.65 
TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       24.49        31.00        24.43        10.78        15.16        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H9 TCGA-BH-A0HB TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       35.51        41.00        26.50         5.85         2.50        13.61 
TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A0W5 
       36.85        12.89        51.32         5.59        24.95        42.35 
TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18M 
       44.81        23.05         2.01         7.23        20.12        72.56 
TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T 
       37.74        30.28        55.63        37.55        66.05         7.36 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EX TCGA-BH-A1F5 TCGA-BH-A1FB TCGA-BH-A1FC 
      113.82        82.85        49.58        89.16       120.62       114.15 
TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN 
       74.73       122.89        36.92        63.35        55.00        72.07 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A202 TCGA-BH-A208 TCGA-BH-A28O TCGA-BH-A28Q 
      144.59        72.07         0.72        57.83        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12L TCGA-C8-A12M 
       20.12         0.99       109.28         8.94        11.93        11.77 
TCGA-C8-A12N TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A131 
       11.77        12.66        12.66        12.66         3.12         1.78 
TCGA-C8-A137 TCGA-C8-A1HG TCGA-C8-A1HL TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A275 
        3.85        11.34        10.42         0.30         0.23         0.03 
TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M8 TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 
       12.20         0.99         0.23        20.88        13.25        20.58 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JF 
       14.17        13.48        19.20        18.71        15.78        12.03 
TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU 
       20.12        20.09        21.01        12.20        13.32        14.70 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XB TCGA-D8-A1XC 
       17.79        16.73        25.74        23.90        18.15         2.66 
TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XM TCGA-D8-A1XO 
       17.16        15.22        14.73        14.50        17.69         7.96 
TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XZ 
       16.41        16.31         6.35        15.16        12.66        15.32 
TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G 
       15.52         3.81        14.24        17.42        16.04        13.45 
TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P 
       13.05        14.43         9.44        16.41         4.80         0.76 
TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A4Z1 TCGA-E2-A105 
       13.08        12.53        12.26        14.50         7.33        43.00 
TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P 
       27.52        40.41        37.51        28.87        47.15        40.96 
TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y 
       33.17        33.30        43.33        32.02        31.96        28.60 
TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15A TCGA-E2-A15C 
       25.41        23.24        21.04        23.87        23.34        22.82 
TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J 
       17.29        21.63        18.21        12.92        17.42        19.40 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
        9.04        20.58        13.02        19.56        17.06        14.07 
TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       14.99        53.62        53.03        29.95        32.35        28.50 
TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1II TCGA-E2-A1IJ 
       16.47        38.30        37.41        32.78        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 
       22.65         3.88        22.19        11.08        54.18        27.42 
TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LG TCGA-E2-A1LH 
       39.62        19.66        24.59        40.47        18.87       106.75 
TCGA-E2-A1LI TCGA-E2-A2P5 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E9-A1N5 
      102.61        16.93        15.72         7.20        18.05        36.82 
TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NF 
       13.48        12.00        13.12        39.55        35.77        20.05 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 
        9.86        11.90        14.30         0.62         2.10         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD 
        1.38        21.21        32.09        20.81        40.24         0.66 
TCGA-E9-A1RE TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
       34.65        34.59        34.13         0.79        12.53        13.32 
TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 
       39.09        22.75        23.51        24.10        17.06         0.69 
TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3HO 
        0.85        27.22         0.95        12.56         0.76        26.07 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A6HE 
       18.41         0.62        15.72         0.39         0.23        15.39 
TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
       39.72         8.48        18.21        13.25        16.57        15.68 
TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 
       22.82        29.95        40.41        41.13        39.78        29.82 
TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PD 
       23.11        18.48        30.08        18.90        19.99        13.94 
TCGA-EW-A1PE TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A3E8 
       10.52        34.55        19.96        52.73        22.09        21.27 
TCGA-EW-A3U0 TCGA-EW-A424 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       17.49        10.59       109.87        59.57       194.27        53.13 
TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DM 
       53.52        43.04        42.71        61.91        62.33        76.64 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL 
       77.33        53.36       110.50        38.20        32.28        69.30 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YX TCGA-LD-A66U 
       53.95        57.63        13.55        18.12        11.57         8.28 
TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN 
        4.60         0.66         3.58         6.90         5.56         3.65 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z 
        3.19         3.25         2.63         3.88         4.14         4.50 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D7 
        4.50         5.59         6.21         2.79         2.10        46.55 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX 
        7.53        44.61        27.65        24.10        26.20        16.87 
TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K 
       14.10        10.29        14.76        23.70        54.51        33.90 
TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P TCGA-S3-A6ZG TCGA-W8-A86G 
       31.07         7.23         4.44         6.81         5.29 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.03               0.03 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            189.01             234.28 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             20.32              22.45 
[1] "0.0 - 189.0 (20.3)" "0.0 - 234.3 (22.4)"
[1] "hr=" "2.5"
D72V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18P LOSS MUTATED        24       22        0        1        92        64
  18P LOSS WILD-TYPE      56       55        9        8       243       160
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18P LOSS MUTATED           0         47         15         21        4
  18P LOSS WILD-TYPE         2         91         12         38       13
                    vv
clus                 STAGE TIS STAGE X
  18P LOSS MUTATED           0       2
  18P LOSS WILD-TYPE         1      14
D72V3, multiclass
            clus
vv           18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                  24                 56
  STAGE IA                 22                 55
  STAGE IB                  0                  9
  STAGE II                  1                  8
  STAGE IIA                92                243
  STAGE IIB                64                160
  STAGE III                 0                  2
  STAGE IIIA               47                 91
  STAGE IIIB               15                 12
  STAGE IIIC               21                 38
  STAGE IV                  4                 13
  STAGE TIS                 0                  1
  STAGE X                   2                 14
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  18P LOSS MUTATED    66 174  34  19
  18P LOSS WILD-TYPE 192 407  83  17
D72V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1               66                192
  T2              174                407
  T3               34                 83
  T4               19                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  18P LOSS MUTATED   129  97  39  22
  18P LOSS WILD-TYPE 339 233  72  48
D72V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0              129                339
  N1               97                233
  N2               39                 72
  N3               22                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  18P LOSS MUTATED          0 252   4  37
  18P LOSS WILD-TYPE        2 593  13  94
D72V6, multiclass
          clus
vv         18P LOSS MUTATED 18P LOSS WILD-TYPE
  CM0 (I+)                0                  2
  M0                    252                593
  M1                      4                 13
  MX                     37                 94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED   290   3
  18P LOSS WILD-TYPE 694   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    290    3
  18P LOSS WILD-TYPE  694    8
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE              290                694
  MALE                  3                  8
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  18P LOSS MUTATED                            0                           236
  18P LOSS WILD-TYPE                          1                           499
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  18P LOSS MUTATED                               37                   2
  18P LOSS WILD-TYPE                            129                   3
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  18P LOSS MUTATED                                  6                  0
  18P LOSS WILD-TYPE                               23                 14
                    vv
clus                 OTHER  SPECIFY
  18P LOSS MUTATED               12
  18P LOSS WILD-TYPE             32
D72V8, multiclass
                                  clus
vv                                 18P LOSS MUTATED 18P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 236                499
  INFILTRATING LOBULAR CARCINOMA                 37                129
  MEDULLARY CARCINOMA                             2                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)                6                 23
  MUCINOUS CARCINOMA                              0                 14
  OTHER  SPECIFY                                 12                 32
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V9, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    84 209
  18P LOSS WILD-TYPE 198 504
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     84  209
  18P LOSS WILD-TYPE  198  504
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                84                198
  YES              209                504
[1] 2 2
[1] FALSE
D72V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P LOSS MUTATED                                  0    26
  18P LOSS WILD-TYPE                                1    30
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED                          37   202
  18P LOSS WILD-TYPE                       100   506
D72V11, multiclass
                                  clus
vv                                 18P LOSS MUTATED 18P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          26                 30
  BLACK OR AFRICAN AMERICAN                      37                100
  WHITE                                         202                506
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V12, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    12 236
  18P LOSS WILD-TYPE  24 560
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     12  236
  18P LOSS WILD-TYPE   24  560
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                   12                 24
  NOT HISPANIC OR LATINO              236                560
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18Q LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED   243  43
  18Q LOSS WILD-TYPE 617  71
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               286                688 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                43                 71 
$`18Q LOSS MUTATED`
TCGA-A1-A0SD TCGA-A1-A0SI TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A04W TCGA-A2-A04X 
       14.37        20.88        28.01        18.02        64.04        55.43 
TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0EN TCGA-A2-A0EU TCGA-A2-A0EV 
        5.19        64.04        21.14        89.36        34.29        31.82 
TCGA-A2-A0SV TCGA-A2-A0SX TCGA-A2-A0T4 TCGA-A2-A0T7 TCGA-A2-A0YE TCGA-A2-A0YG 
       27.12        50.43        20.52        20.75        18.21        21.90 
TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX 
       14.50        19.33        14.63        23.77        17.36        36.79 
TCGA-A2-A1G1 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A3XT TCGA-A2-A3XU 
       19.20        16.31        17.19        18.15        83.01        29.98 
TCGA-A2-A4S1 TCGA-A7-A0CG TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A26F 
       12.00        34.29        35.67        31.73        12.72        24.26 
TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A4SF 
       22.32        11.28        14.93        13.74        21.17        17.92 
TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A6VV TCGA-A7-A6VX TCGA-A8-A06R TCGA-A8-A06U 
       14.73        12.10        10.29        10.42        17.98        29.03 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07G TCGA-A8-A07W 
       26.01         1.02        17.03        53.98        18.97         9.99 
TCGA-A8-A084 TCGA-A8-A08B TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A092 
       15.06        23.08        37.05        31.00         0.99        16.01 
TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09M TCGA-A8-A09N 
        9.99        12.00        13.02        31.00        15.02         1.02 
TCGA-A8-A09Q TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A2 TCGA-AC-A23H TCGA-AC-A2FF 
       25.02         0.99        14.01        19.04         2.66        55.43 
TCGA-AC-A2FM TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A62V 
       26.04         2.27         0.99         1.81         1.68         0.07 
TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A04A TCGA-AN-A0AK TCGA-AN-A0AL 
        0.43         1.74         0.33         2.96         7.36         6.51 
TCGA-AN-A0AM TCGA-AN-A0FL TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XP 
        0.16         7.59         0.33         0.36         0.33         0.30 
TCGA-AN-A0XU TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J7 
        0.33        80.28        66.77        32.78        17.65        20.32 
TCGA-AO-A0JA TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A1KT TCGA-AQ-A04H 
       21.53        96.10        64.04        57.30        17.79        24.79 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A54O TCGA-AR-A0TS 
       26.93       130.09         5.65        15.62        21.86        37.41 
TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A1AP TCGA-AR-A1AV 
       56.88        24.30        70.16        83.87        39.98        42.58 
TCGA-AR-A1AW TCGA-AR-A24H TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24V TCGA-AR-A24W 
       35.24       109.58        57.40        62.07        54.18        50.96 
TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A2LR TCGA-AR-A5QM 
       56.15        45.17        40.64        34.82        20.38        54.74 
TCGA-AR-A5QQ TCGA-B6-A0IK TCGA-B6-A0IO TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RL 
       10.59        18.77       110.14       211.56       189.01        81.17 
TCGA-B6-A0RP TCGA-B6-A0RS TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WY TCGA-B6-A1KF 
      102.77       100.70        79.63        17.98       113.79       101.52 
TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A402 TCGA-BH-A0AZ TCGA-BH-A0B6 TCGA-BH-A0BA 
       73.51       170.17        54.28        28.50        56.94        37.22 
TCGA-BH-A0BD TCGA-BH-A0BG TCGA-BH-A0BP TCGA-BH-A0BT TCGA-BH-A0BW TCGA-BH-A0BZ 
       18.21        24.85        48.69        45.57        11.67        49.05 
TCGA-BH-A0C7 TCGA-BH-A0DH TCGA-BH-A0DQ TCGA-BH-A0GY TCGA-BH-A0H7 TCGA-BH-A0H9 
       42.90        38.01         3.22        30.35        23.08        41.00 
TCGA-BH-A0HA TCGA-BH-A0HI TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0W3 TCGA-BH-A0WA 
       52.96        20.38        12.89        27.25        23.93        23.05 
TCGA-BH-A18F TCGA-BH-A18K TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO 
        8.81        90.84        51.39        51.16        69.93        91.99 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F6 
       42.28        12.00        17.69        25.81        31.53        97.48 
TCGA-BH-A1F8 TCGA-BH-A1FM TCGA-BH-A201 TCGA-BH-A204 TCGA-BH-A209 TCGA-C8-A12P 
       24.66        45.63         6.90        83.31       130.16        11.77 
TCGA-C8-A12Q TCGA-C8-A12W TCGA-C8-A132 TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HE 
        0.07        12.66         1.45         0.62         3.75        12.33 
TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A26X TCGA-C8-A26Y 
       11.34         0.16        12.03         2.30         0.36         0.43 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A3M7 
        8.28         9.67         0.03         0.03         0.03         0.03 
TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA 
       20.88        13.97        21.14        14.17        17.49        16.50 
TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ 
       15.78        18.90        12.03        14.01        18.97        20.09 
TCGA-D8-A1JN TCGA-D8-A1X5 TCGA-D8-A1XA TCGA-D8-A1XJ TCGA-D8-A1XL TCGA-D8-A1XR 
       20.38        18.58        27.58        21.83        19.92        15.85 
TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1Y3 TCGA-D8-A27M TCGA-D8-A27R TCGA-D8-A3Z6 
       12.99        16.54        14.14        13.48        10.09        18.51 
TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A14O TCGA-E2-A14Z 
       34.42        46.59        40.11        28.44        44.68        17.03 
TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15E 
       25.41        27.12        19.43        25.05        23.34        20.71 
TCGA-E2-A15M TCGA-E2-A1AZ TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1IO TCGA-E2-A1LE 
        7.73        60.53        17.10        33.73        20.98        28.90 
TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N4 
        8.75        43.04         5.52        22.26        19.89        19.20 
TCGA-E9-A1NA TCGA-E9-A1ND TCGA-E9-A1R6 TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI 
       36.56        12.59         2.76         6.58        21.27        35.64 
TCGA-E9-A22E TCGA-E9-A248 TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A54Y TCGA-E9-A5FL 
       12.89         1.94         0.72        17.75         0.23         0.26 
TCGA-EW-A1IW TCGA-EW-A1J1 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OY TCGA-EW-A1OZ 
       12.20        18.90        28.77        25.94        29.85        40.41 
TCGA-EW-A1P3 TCGA-EW-A1P8 TCGA-EW-A1PC TCGA-EW-A1PF TCGA-EW-A2FR TCGA-EW-A2FV 
       52.96         7.86         6.15        14.43        55.00        25.91 
TCGA-EW-A423 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2DH TCGA-GM-A2DL TCGA-JL-A3YW 
       10.16         7.40       109.87        42.28        90.84        11.84 
TCGA-LD-A74U TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A6FR 
        6.67         2.99         5.56         4.70         3.19         3.88 
TCGA-LQ-A4E4 TCGA-OL-A5D6 TCGA-OL-A5S0 TCGA-OL-A66N 
       15.91        12.66         9.80        18.21 

$`18Q LOSS WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SJ 
        8.52        43.43        48.10        14.27        47.24        13.68 
TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N 
       31.79         7.96        39.32        19.20        18.21       104.81 
TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04Y 
       41.95        82.16        73.84        22.06        63.12        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
      125.59        64.57        24.79       112.08        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D1 
      107.93        75.55        75.25        63.45        56.81        34.55 
TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EO TCGA-A2-A0EP 
       33.76        28.77        25.22       101.72        80.28       107.61 
TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EW TCGA-A2-A0EX 
       79.76        74.40        37.05        35.05        29.75        24.72 
TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 
       24.16        99.19        54.64        44.88        44.28        17.52 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC 
       17.13         8.38        18.71        17.46        18.90        32.55 
TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YH TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A1FV 
       25.28        15.42        21.67        18.61        31.73        23.47 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A 
       22.45        20.25        19.56        16.47        52.47       107.70 
TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XV 
       91.92        10.59        20.88        39.65        33.93        14.07 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW 
       49.48        38.40        34.98        31.99        38.37         7.30 
TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD 
        9.01         8.81         8.91         6.74         3.42        38.30 
TCGA-A7-A0CE TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13E 
       35.31        35.47        30.61        37.45        33.11        10.72 
TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I 
       23.61        29.56        31.36        23.74        23.80        21.73 
TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 
       20.61        11.34        10.59        10.29        13.41        14.70 
TCGA-A7-A426 TCGA-A7-A4SD TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A7-A6VY 
       11.97        14.50        10.72        11.05         9.37         8.75 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06T TCGA-A8-A06X TCGA-A8-A079 
       13.02        13.02         1.02        41.06        31.00         9.01 
TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
       33.01        19.99        18.97        14.01        12.00        17.03 
TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07Z 
        9.99        10.98         8.98         7.99         9.96        28.04 
TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08F 
       18.05        36.95        13.02         0.99        19.99        18.05 
TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08S TCGA-A8-A08T 
       19.96        12.00         9.99        31.00        19.07        93.04 
TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 
       33.99        40.01        19.07        17.95        41.98        12.00 
TCGA-A8-A099 TCGA-A8-A09C TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09R TCGA-A8-A09T 
        9.99         1.02        33.07        29.98         8.98        19.04 
TCGA-A8-A09V TCGA-A8-A0A1 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 
       15.02        12.00        13.02        21.04         0.99        13.02 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2B8 
       17.03        38.04         0.95         2.37        10.85         1.48 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO 
       38.53        38.20        40.57        36.99        38.79        50.70 
TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN 
        1.02         0.92         0.69        14.83         9.40         1.12 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV 
        1.55         1.32         1.55         1.12         1.81         1.18 
TCGA-AC-A6IW TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04C 
        0.69         0.33         0.23         0.33         0.62         1.78 
TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD 
        1.71         8.02         0.33         0.33         0.33         6.44 
TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT 
        4.64         7.96         7.00         7.17         6.28         6.02 
TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XR 
        0.33         0.33         0.33         0.33        12.33         0.33 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03O 
        0.33         0.33         5.33         5.59        47.84        81.63 
TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J3 
       84.69        68.75        47.87        59.05        29.13        21.40 
TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JB TCGA-AO-A0JC 
       24.16        37.48        22.36        53.03        50.70        50.86 
TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ 
       72.00        76.77        21.37        26.24        38.53        62.04 
TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 
       55.33        71.80       102.58        99.25        93.70        94.59 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
       90.58        77.56        48.36        41.62        28.37        14.73 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A1H3 TCGA-AQ-A54N 
       82.62        61.87        70.39         0.53        13.22         2.56 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TV TCGA-AR-A0TX 
        9.99        82.88        49.32         5.26        29.75        64.83 
TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH 
       55.86        76.14        65.36        76.18        55.36        75.55 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
       61.84        52.77        51.25        48.82        62.56        43.73 
TCGA-AR-A1AO TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AX 
       43.56        43.07        17.23        40.83        46.32        36.26 
TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       20.22        50.89        73.02        65.46        68.19        65.69 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A24Z 
        0.85        66.05        53.26        53.36        48.16        51.75 
TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LL 
       39.85        93.83       128.65        20.25        42.87         7.36 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP 
       40.04        17.10        20.81        16.96        16.04        20.45 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB 
       77.62       143.38       149.59        12.13       220.90       129.57 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IM 
       50.70        65.72       146.50       112.37       176.98       126.12 
TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RI TCGA-B6-A0RM 
       84.59       110.93       140.88        68.45       234.28        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV 
      172.96       162.05       140.48        89.46       131.21       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 
       97.48       188.68        21.47       129.57       129.70       186.48 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KN TCGA-B6-A401 
       28.27        68.94        58.88        43.59       139.17        85.35 
TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW 
       49.94        82.88        55.00        24.53        38.79        20.45 
TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 
       25.55        46.95        40.83        39.55        39.16        48.36 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BL 
       56.98        51.68        32.02        25.71        21.70        44.05 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV 
       61.68        35.67        27.19        53.69        53.95        49.94 
TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG 
       41.75        44.02        48.13        45.83        31.17        23.44 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DS 
       22.13        13.91        48.23        17.26        15.65         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 
       38.47        45.17        47.41        16.27         4.41        15.68 
TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB 
       14.30         9.63        44.81        46.19        32.65        24.49 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       31.00        24.43        10.78        15.16        37.78        35.51 
TCGA-BH-A0H6 TCGA-BH-A0HB TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ 
       24.56        26.50         5.85         2.50        13.61        36.85 
TCGA-BH-A0HW TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       51.32        50.79         5.59        24.95        42.35        44.81 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N 
        2.01         7.23        20.12        26.66        72.56        37.74 
TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A1ES 
       30.28        55.63        37.55        66.05         7.36       113.82 
TCGA-BH-A1ET TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F5 TCGA-BH-A1FB TCGA-BH-A1FC 
       82.85        55.69        49.58        89.16       120.62       114.15 
TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
       33.17        74.73       122.89        36.92        63.35        55.00 
TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 
       72.07       144.59        72.07         0.72        38.60        57.83 
TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V 
       10.65         6.44        20.12         0.99       109.28         8.94 
TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12U TCGA-C8-A12V 
       11.93        11.77        11.77        12.66        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A1HF 
       12.66         3.12         1.78         0.69         3.85        10.92 
TCGA-C8-A1HG TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A27A 
       11.34        10.42         3.25         0.30         0.23        12.20 
TCGA-C8-A27B TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 
        0.99         0.23        11.90        13.25        20.58        14.17 
TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JF TCGA-D8-A1JK 
       13.48        19.20        18.71        18.15        12.03        20.12 
TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU 
       20.09        19.40        21.01        12.20        13.32        14.70 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XB TCGA-D8-A1XC 
       17.79        16.73        25.74        23.90        18.15         2.66 
TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XM TCGA-D8-A1XO 
       17.16        15.22        14.73        14.50        17.69         7.96 
TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XZ 
       16.41        16.31         6.35        15.16        12.66        15.32 
TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G 
       15.52         3.81        14.24        17.42        16.04        13.45 
TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P 
       13.05        14.43         9.44        16.41         4.80         0.76 
TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A4Z1 TCGA-E2-A105 
       13.08        12.53        12.26        14.50         7.33        43.00 
TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P 
       27.52        40.41        37.51        28.87        47.15        40.96 
TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V 
       38.24        38.60        33.17        33.30        43.33        34.26 
TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 
       32.02        31.96        28.60        23.24        21.04        23.87 
TCGA-E2-A158 TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H 
       14.79        22.82        17.29        21.63        18.21        12.92 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15P 
       17.42        19.40         9.04        20.58        13.02        19.56 
TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 
       17.06        14.07        14.99        53.62        53.03        29.95 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       32.35        28.50        16.47        38.30        37.41        32.78 
TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IU 
       33.70        28.44        22.65         3.88        22.19        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB 
       54.18        27.42        39.62        19.66        24.59        40.47 
TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A2P5 TCGA-E2-A3DX TCGA-E2-A56Z 
       18.87       106.75       102.61        16.93        15.72         7.20 
TCGA-E2-A570 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NC 
       18.05        36.82        13.48        12.00        13.12        39.55 
TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 
       35.77        20.05        21.57         9.86        11.90        14.30 
TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RA 
        0.62         2.10         6.12         1.38        21.21        32.09 
TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RH TCGA-E9-A226 
       20.81        40.24         0.66        34.65        34.59        34.13 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22G 
        0.79        12.53        13.32        39.09        22.75        23.51 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A249 
       24.10        17.06         0.69         0.85        27.22         0.95 
TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
       12.56         0.76        26.07        18.41         0.62        15.72 
TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
        0.39         0.23        15.39        39.72         8.48        18.21 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1P0 
       13.25        16.57        15.68        22.82        29.95        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA 
       39.78        29.82        23.11        18.48        30.08        18.90 
TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FS 
       19.99        13.94        10.52        34.55        19.96        52.73 
TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 TCGA-GM-A2D9 TCGA-GM-A2DA 
       22.09        21.27        17.49        10.59        59.57       194.27 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DK 
       53.13        53.52        43.04        42.71        61.91        62.33 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
       76.64        77.33        53.36       110.50        38.20        32.28 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YX 
       69.30        53.95        57.63        13.55        18.12        11.57 
TCGA-LD-A66U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YN 
        8.28         4.60         0.66         3.58         6.90         3.65 
TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ 
        3.25         2.63         4.14         4.50         4.50         5.59 
TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D7 TCGA-OL-A5D8 
        3.22         6.21         2.79         2.10        46.55         7.53 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY 
       44.61        27.65        24.10        26.20        16.87        14.10 
TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L 
       10.29        14.76        23.70        54.51        33.90        31.07 
TCGA-OL-A66O TCGA-OL-A66P TCGA-S3-A6ZG TCGA-W8-A86G 
        7.23         4.44         6.81         5.29 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.03               0.23 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            211.56             234.28 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            19.905             22.965 
[1] "0.0 - 211.6 (19.9)" "0.2 - 234.3 (23.0)"
[1] "hr=" "1.9"
D73V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18Q LOSS MUTATED        24       22        0        1        90        62
  18Q LOSS WILD-TYPE      56       55        9        8       245       162
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18Q LOSS MUTATED           0         48         15         22        4
  18Q LOSS WILD-TYPE         2         90         12         37       13
                    vv
clus                 STAGE TIS STAGE X
  18Q LOSS MUTATED           0       5
  18Q LOSS WILD-TYPE         1      11
D73V3, multiclass
            clus
vv           18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                  24                 56
  STAGE IA                 22                 55
  STAGE IB                  0                  9
  STAGE II                  1                  8
  STAGE IIA                90                245
  STAGE IIB                62                162
  STAGE III                 0                  2
  STAGE IIIA               48                 90
  STAGE IIIB               15                 12
  STAGE IIIC               22                 37
  STAGE IV                  4                 13
  STAGE TIS                 0                  1
  STAGE X                   5                 11
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  18Q LOSS MUTATED    66 177  33  17
  18Q LOSS WILD-TYPE 192 404  84  19
D73V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1               66                192
  T2              177                404
  T3               33                 84
  T4               17                 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                  N0  N1  N2  N3
  18Q LOSS MUTATED   131  91  42  24
  18Q LOSS WILD-TYPE 337 239  69  46
D73V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0              131                337
  N1               91                239
  N2               42                 69
  N3               24                 46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  18Q LOSS MUTATED          1 248   4  41
  18Q LOSS WILD-TYPE        1 597  13  90
D73V6, multiclass
          clus
vv         18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CM0 (I+)                1                  1
  M0                    248                597
  M1                      4                 13
  MX                     41                 90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   291   3
  18Q LOSS WILD-TYPE 693   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    291    3
  18Q LOSS WILD-TYPE  693    8
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE              291                693
  MALE                  3                  8
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  18Q LOSS MUTATED                            1                           235
  18Q LOSS WILD-TYPE                          0                           500
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  18Q LOSS MUTATED                               39                   1
  18Q LOSS WILD-TYPE                            127                   4
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  18Q LOSS MUTATED                                  6                  0
  18Q LOSS WILD-TYPE                               23                 14
                    vv
clus                 OTHER  SPECIFY
  18Q LOSS MUTATED               11
  18Q LOSS WILD-TYPE             33
D73V8, multiclass
                                  clus
vv                                 18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      1                  0
  INFILTRATING DUCTAL CARCINOMA                 235                500
  INFILTRATING LOBULAR CARCINOMA                 39                127
  MEDULLARY CARCINOMA                             1                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                6                 23
  MUCINOUS CARCINOMA                              0                 14
  OTHER  SPECIFY                                 11                 33
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V9, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    89 205
  18Q LOSS WILD-TYPE 193 508
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     89  205
  18Q LOSS WILD-TYPE  193  508
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                89                193
  YES              205                508
[1] 2 2
[1] FALSE
D73V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q LOSS MUTATED                                  0    23
  18Q LOSS WILD-TYPE                                1    33
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED                          42   198
  18Q LOSS WILD-TYPE                        95   510
D73V11, multiclass
                                  clus
vv                                 18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          23                 33
  BLACK OR AFRICAN AMERICAN                      42                 95
  WHITE                                         198                510
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V12, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    13 237
  18Q LOSS WILD-TYPE  23 559
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     13  237
  18Q LOSS WILD-TYPE   23  559
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   13                 23
  NOT HISPANIC OR LATINO              237                559
[1] 2 2
[1] FALSE

Clustering(74) Variable = 19P LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED   150  23
  19P LOSS WILD-TYPE 710  91
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               173                801 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                23                 91 
$`19P LOSS MUTATED`
TCGA-A1-A0SJ TCGA-A1-A0SQ TCGA-A2-A04P TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04X 
       13.68        18.21        18.02        73.84        22.06        55.43 
TCGA-A2-A0CM TCGA-A2-A0CW TCGA-A2-A0D4 TCGA-A2-A0EO TCGA-A2-A0T3 TCGA-A2-A0T7 
       24.79        64.04        25.22        80.28        18.71        20.75 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A3XT TCGA-A2-A3XX 
       21.90        21.67        23.77        17.36        83.01        38.40 
TCGA-A2-A3XZ TCGA-A2-A4S1 TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A26I TCGA-A7-A4SD 
       31.99        12.00        31.73        10.72        21.73        14.50 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A6VX TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T 
       17.92        14.73        10.42         1.02        17.98        41.06 
TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07G TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07W 
       17.03        53.98        18.97        17.03         9.99         9.99 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08S 
       18.05        19.96        12.00        37.05        31.00        19.07 
TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09I TCGA-A8-A09N TCGA-AC-A2BM 
       12.00         9.99         1.02        33.07         1.02        38.20 
TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A62V TCGA-AC-A6IX TCGA-AN-A041 TCGA-AN-A04A 
       26.04         1.02         0.07         0.43         0.23         2.96 
TCGA-AN-A0AS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FZ TCGA-AO-A03M TCGA-AO-A03N 
        0.33         6.02         0.33         0.33        47.84        66.77 
TCGA-AO-A03P TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0JD TCGA-AO-A0JM TCGA-AO-A1KQ 
       84.69        21.40        17.65        72.00        71.80        61.87 
TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TW 
       17.79         5.65         2.56        49.32        37.41        24.30 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AJ TCGA-AR-A1AQ TCGA-AR-A24H TCGA-AR-A24R 
       83.87        76.18        52.77        43.07       109.58        57.40 
TCGA-AR-A24S TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A2LK TCGA-AR-A5QQ TCGA-B6-A0I1 
       62.07        56.15        40.64        42.87        10.59        77.62 
TCGA-B6-A0IB TCGA-B6-A0IO TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A402 TCGA-B6-A408 
      129.57       110.14       101.52       139.17        54.28        49.94 
TCGA-BH-A0AV TCGA-BH-A0B3 TCGA-BH-A0BG TCGA-BH-A0BT TCGA-BH-A0BW TCGA-BH-A0DQ 
       38.79        39.55        24.85        45.57        11.67         3.22 
TCGA-BH-A0E0 TCGA-BH-A0EB TCGA-BH-A0H0 TCGA-BH-A0H7 TCGA-BH-A0HX TCGA-BH-A0HY 
        4.41        24.49        15.16        23.08        27.25        50.79 
TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18I TCGA-BH-A18L TCGA-BH-A18S TCGA-BH-A1EV 
       23.05         8.81         7.23        26.66        66.05        12.00 
TCGA-BH-A1F8 TCGA-BH-A1FN TCGA-BH-A1FU TCGA-BH-A204 TCGA-BH-A209 TCGA-C8-A12M 
       24.66        72.07        72.07        83.31       130.16        11.77 
TCGA-C8-A12P TCGA-C8-A12U TCGA-C8-A12W TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HF 
       11.77        12.66        12.66         0.62         3.75        10.92 
TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A27A 
       12.03        10.42         3.25         0.43         8.28        12.20 
TCGA-D8-A13Y TCGA-D8-A1JC TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JM TCGA-D8-A1XA 
       11.90        15.78        18.97        20.09        19.40        27.58 
TCGA-D8-A1XQ TCGA-D8-A1XT TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y3 TCGA-D8-A27M 
       16.41         6.35        16.54        15.32        14.14        13.48 
TCGA-E2-A109 TCGA-E2-A14O TCGA-E2-A152 TCGA-E2-A159 TCGA-E2-A15H TCGA-E2-A15S 
       46.59        44.68        27.12        25.05        12.92        14.07 
TCGA-E2-A1AZ TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N6 TCGA-E9-A1NI TCGA-E9-A1QZ 
       60.53        22.26        19.89        13.48         9.86        11.90 
TCGA-E9-A1R3 TCGA-E9-A1RC TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A22G TCGA-E9-A2JS 
        2.10        40.24        34.59        34.13        23.51        17.75 
TCGA-E9-A5UO TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1PA 
        0.23        25.94        22.82        29.95        40.41        18.90 
TCGA-EW-A1PC TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A3U0 TCGA-GM-A2DC 
        6.15        19.96        55.00        52.73        17.49        53.52 
TCGA-GM-A2DH TCGA-LL-A7T0 TCGA-MS-A51U TCGA-OL-A5D7 TCGA-OL-A5S0 
       42.28         3.22         2.79        46.55         9.80 

$`19P LOSS WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP 
       20.88        31.79         7.96        39.32        28.01        19.20 
TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04Y 
      104.81        41.95        82.16        63.12        64.04        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
      125.59        64.57       112.08        92.48        88.60       107.93 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D0 
       75.55        75.25         5.19        63.45        56.81        21.14 
TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP 
       34.55        33.76        28.77       101.72        89.36       107.61 
TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV 
       79.76        74.40        37.05        35.05        34.29        31.82 
TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV 
       29.75        24.72        24.16        99.19        54.64        27.12 
TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 
       44.88        50.43        44.28        17.52        17.13         8.38 
TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE 
       20.52        17.46        18.90        32.55        25.28        18.21 
TCGA-A2-A0YF TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       15.42        14.50        18.61        19.33        14.63        31.73 
TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 
       23.47        36.79        22.45        20.25        19.20        19.56 
TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D 
       16.47        52.47       107.70        16.31        17.19        18.15 
TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XU 
       91.92        10.59        20.88        39.65        33.93        29.98 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX 
       14.07        49.48        34.98        38.37         7.30         9.01 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE 
        8.81         8.91         6.74         3.42        38.30        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB 
       34.29        35.47        30.61        37.45        35.67        33.11 
TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G 
       12.72        23.61        29.56        31.36        24.26        23.74 
TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 
       23.80        20.61        22.32        11.34        10.59        10.29 
TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB 
       11.28        13.41        14.70        11.97        14.93        13.74 
TCGA-A7-A4SE TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW 
       21.17        12.10        10.72        11.05        10.29         9.37 
TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y 
        8.75        13.02        13.02        29.03        31.00        26.01 
TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07I 
        1.02         9.01        33.01        19.99        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07Z 
       12.00        10.98         8.98         7.99         9.96        28.04 
TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B 
       18.05        15.06        36.95        13.02         0.99        23.08 
TCGA-A8-A08C TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X 
       19.99         9.99        31.00         0.99        93.04        33.99 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 
       40.01        19.07        16.01        17.95        41.98         9.99 
TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09Q 
       12.00        13.02        31.00        29.98        15.02        25.02 
TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 
        8.98        19.04        15.02         0.99        14.01        12.00 
TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB 
       19.04        13.02        21.04         0.99        13.02        17.03 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 
       38.04         0.95         2.37        10.85         2.66         1.48 
TCGA-AC-A2BK TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO 
       38.53        40.57        55.43        36.99        38.79        50.70 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
        0.92         2.27         0.99         0.69        14.83         9.40 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS 
        1.12         1.81         1.68         1.55         1.32         1.55 
TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A8OP TCGA-AN-A03X 
        1.12         1.81         1.18         0.69         1.74         0.33 
TCGA-AN-A03Y TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ 
        0.33         0.33         0.62         1.78         1.71         8.02 
TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD 
        7.36         6.51         0.16         0.33         0.33         6.44 
TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        4.64         7.96         7.00         7.59         7.17         6.28 
TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO 
        0.36         0.33         0.33         0.33         0.33        12.33 
TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV 
        0.30         0.33         0.33         0.33         0.33         5.33 
TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U 
        5.59        80.28        81.63        68.75        47.87        59.05 
TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 
       29.13        32.78        24.16        37.48        20.32        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF 
       53.03        21.53        50.70        50.86        76.77        21.37 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A125 
       26.24        38.53        62.04        55.33       102.58        99.25 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D 
       93.70        94.59        96.10        90.58        77.56        64.04 
TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       57.30        48.36        41.62        28.37        14.73        82.62 
TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 
       70.39         0.53        24.79        26.93       130.09        15.62 
TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TT 
       13.22        21.86         9.99        82.88         5.26        56.88 
TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 
       29.75        64.83        55.86        76.14        65.36        70.16 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM 
       55.36        75.55        61.84        51.25        48.82        62.56 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU 
       43.73        43.56        39.98        17.23        40.83        46.32 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L 
       42.58        35.24        36.26        20.22        50.89        73.02 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24T 
       65.46        68.19        65.69         0.85        66.05        53.26 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 
       53.36        54.18        50.96        48.16        51.75        45.17 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LL 
       39.85        34.82        93.83       128.65        20.25         7.36 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM 
       40.04        17.10        20.81        16.96        20.38        54.74 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA 
       16.04        20.45       143.38       149.59        12.13       220.90 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK 
       50.70        65.72       146.50       112.37       176.98        18.77 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG 
      126.12        84.59       110.93       140.88       211.56        68.45 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
      189.01       234.28        81.17        78.02       172.96       162.05 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV 
      102.77       140.48       100.70        89.46       131.21       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY 
       97.48       188.68        79.63        17.98        21.47       113.79 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      129.57       129.70       186.48        28.27        68.94        58.88 
TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A40B TCGA-B6-A40C 
       43.59        73.51       170.17        85.35        82.88        55.00 
TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 
       24.53        20.45        25.55        28.50        46.95        40.83 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA 
       39.16        48.36        56.94        56.98        51.68        37.22 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM 
       32.02        18.21        25.71        21.70        44.05        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV 
       35.67        48.69        27.19        53.69        53.95        49.94 
TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD 
       49.05        41.75        44.02        48.13        42.90        45.83 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL 
       31.17        23.44        38.01        22.13        13.91        48.23 
TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       17.26        15.65         2.56        38.47        45.17        47.41 
TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 
       16.27        15.68        14.30         9.63        44.81        46.19 
TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H3 
       32.65        31.00        24.43        30.35        10.78        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI 
       35.51        24.56        41.00        52.96        26.50        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW 
        5.85         2.50        13.61        36.85        12.89        51.32 
TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18G 
        5.59        23.93        24.95        42.35        44.81         2.01 
TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q 
       20.12        90.84        72.56        37.74        30.28        55.63 
TCGA-BH-A18R TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO 
       37.55         7.36        51.39        51.16        69.93        91.99 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY 
      113.82        82.85        42.28        55.69        49.58        17.69 
TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1FB TCGA-BH-A1FC 
       25.81        31.53        89.16        97.48       120.62       114.15 
TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
       33.17        74.73       122.89        36.92        63.35        55.00 
TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 
       45.63       144.59         6.90         0.72        38.60        57.83 
TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V 
       10.65         6.44        20.12         0.99       109.28         8.94 
TCGA-C8-A12L TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12Q TCGA-C8-A12V TCGA-C8-A12X 
       11.93        11.77        12.66         0.07        12.66        12.66 
TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A1HE 
        3.12         1.78         1.45         0.69         3.85        12.33 
TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HM TCGA-C8-A26V TCGA-C8-A26W 
       11.34        11.34         0.16         2.30         0.30         0.23 
TCGA-C8-A26X TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B 
        0.36         9.67         0.03         0.03         0.03         0.99 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 
        0.03         0.23        20.88        13.25        20.58        13.97 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 
       14.17        13.48        21.14        19.20        14.17        17.49 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG 
       16.50        18.71        18.15        18.90        12.03        12.03 
TCGA-D8-A1JH TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS 
       14.01        20.12        20.09        20.38        21.01        12.20 
TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 
       13.32        14.70        18.58        17.79        16.73        25.74 
TCGA-D8-A1X9 TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG 
       23.90        18.15         2.66        17.16        15.22        14.73 
TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR 
       21.83        14.50        19.92        17.69         7.96        15.85 
TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       16.31        12.99        15.16        12.66        15.52         3.81 
TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I 
       14.24        17.42        16.04        13.45        13.05        14.43 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T 
        9.44        16.41         4.80         0.76        10.09        13.08 
TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 
       12.53        12.26        14.50        18.51         7.33        43.00 
TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E 
       34.42        27.52        40.41        37.51        40.11        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S 
       28.87        47.15        40.96        38.24        38.60        33.17 
TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y 
       33.30        43.33        34.26        32.02        31.96        28.60 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 
       17.03        25.41        23.24        19.43        21.04        23.87 
TCGA-E2-A158 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F 
       14.79        23.34        22.82        17.29        20.71        21.63 
TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M 
       18.21        17.42        19.40         9.04        20.58         7.73 
TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 
       13.02        19.56        17.06        14.99        53.62        53.03 
TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE 
       29.95        32.35        28.50        16.47        17.10        38.30 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK 
       37.41        32.78        33.73        33.70        28.44        22.65 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 
        3.88        22.19        20.98        11.08        54.18        27.42 
TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG 
       39.62        19.66        24.59        40.47        28.90        18.87 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 
      106.75       102.61         8.75        43.04        16.93         5.52 
TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 
       15.72         7.20        18.05        19.20        36.82        12.00 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF 
       13.12        36.56        39.55        12.59        35.77        20.05 
TCGA-E9-A1NG TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 
       21.57        14.30         0.62         6.12         1.38         2.76 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF 
       21.21        32.09        20.81         0.66        34.65         6.58 
TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       21.27        35.64         0.79        12.53        13.32        39.09 
TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A245 
       22.75        12.89        24.10        17.06         0.69         0.85 
TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JT 
       27.22         1.94         0.95        12.56         0.72         0.76 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FK 
       26.07        18.41         0.62        15.72         0.23         0.39 
TCGA-E9-A5FL TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
        0.26        15.39        12.20        39.72         8.48        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OY 
       18.90        13.25        16.57        15.68        28.77        29.85 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 
       41.13        39.78        52.96        29.82        23.11        18.48 
TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
       30.08         7.86        19.99        13.94        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A423 TCGA-EW-A424 
       34.55        25.91        22.09        21.27        10.16        10.59 
TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DD 
        7.40       109.87        59.57       194.27        53.13        43.04 
TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       42.71        61.91        62.33        90.84        76.64        77.33 
TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN 
       53.36       110.50        38.20        32.28        69.30        53.95 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U 
       57.63        13.55        18.12        11.84        11.57         8.28 
TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y 
        6.67         4.60         0.66         2.99         3.58         6.90 
TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FQ 
        5.56         4.70         3.65         3.19         3.25         2.63 
TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A8F5 
        3.88         4.14         4.50         4.50         5.59         6.21 
TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
       15.91         2.10        12.66         7.53        44.61        27.65 
TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H 
       24.10        26.20        16.87        14.10        10.29        14.76 
TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O 
       23.70        54.51        33.90        31.07        18.21         7.23 
TCGA-OL-A66P TCGA-S3-A6ZG TCGA-W8-A86G 
        4.44         6.81         5.29 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.07               0.03 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            139.17             234.28 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             20.09              21.57 
[1] "0.1 - 139.2 (20.1)" "0.0 - 234.3 (21.6)"
[1] "hr=" "1.5"
D74V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19P LOSS MUTATED        13       11        1        0        59        41
  19P LOSS WILD-TYPE      67       66        8        9       276       183
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19P LOSS MUTATED           1         27          5         11        5
  19P LOSS WILD-TYPE         1        111         22         48       12
                    vv
clus                 STAGE TIS STAGE X
  19P LOSS MUTATED           0       2
  19P LOSS WILD-TYPE         1      14
D74V3, multiclass
            clus
vv           19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                  13                 67
  STAGE IA                 11                 66
  STAGE IB                  1                  8
  STAGE II                  0                  9
  STAGE IIA                59                276
  STAGE IIB                41                183
  STAGE III                 1                  1
  STAGE IIIA               27                111
  STAGE IIIB                5                 22
  STAGE IIIC               11                 48
  STAGE IV                  5                 12
  STAGE TIS                 0                  1
  STAGE X                   2                 14
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  19P LOSS MUTATED    39 110  20   7
  19P LOSS WILD-TYPE 219 471  97  29
D74V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1               39                219
  T2              110                471
  T3               20                 97
  T4                7                 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                  N0  N1  N2  N3
  19P LOSS MUTATED    75  67  18  14
  19P LOSS WILD-TYPE 393 263  93  56
D74V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0               75                393
  N1               67                263
  N2               18                 93
  N3               14                 56
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  19P LOSS MUTATED          1 151   5  19
  19P LOSS WILD-TYPE        1 694  12 112
D74V6, multiclass
          clus
vv         19P LOSS MUTATED 19P LOSS WILD-TYPE
  CM0 (I+)                1                  1
  M0                    151                694
  M1                      5                 12
  MX                     19                112
[1] 4 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   174   2
  19P LOSS WILD-TYPE 810   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED    174    2
  19P LOSS WILD-TYPE  810    9
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE              174                810
  MALE                  2                  9
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  19P LOSS MUTATED                            0                           157
  19P LOSS WILD-TYPE                          1                           578
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  19P LOSS MUTATED                                6                   1
  19P LOSS WILD-TYPE                            160                   4
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  19P LOSS MUTATED                                  3                  3
  19P LOSS WILD-TYPE                               26                 11
                    vv
clus                 OTHER  SPECIFY
  19P LOSS MUTATED                5
  19P LOSS WILD-TYPE             39
D74V8, multiclass
                                  clus
vv                                 19P LOSS MUTATED 19P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 157                578
  INFILTRATING LOBULAR CARCINOMA                  6                160
  MEDULLARY CARCINOMA                             1                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                3                 26
  MUCINOUS CARCINOMA                              3                 11
  OTHER  SPECIFY                                  5                 39
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V9, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    54 122
  19P LOSS WILD-TYPE 228 591
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     54  122
  19P LOSS WILD-TYPE  228  591
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                54                228
  YES              122                591
[1] 2 2
[1] FALSE
D74V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P LOSS MUTATED                                  0    14
  19P LOSS WILD-TYPE                                1    42
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED                          34   106
  19P LOSS WILD-TYPE                       103   602
D74V11, multiclass
                                  clus
vv                                 19P LOSS MUTATED 19P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          14                 42
  BLACK OR AFRICAN AMERICAN                      34                103
  WHITE                                         106                602
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V12, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     8 134
  19P LOSS WILD-TYPE  28 662
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      8  134
  19P LOSS WILD-TYPE   28  662
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    8                 28
  NOT HISPANIC OR LATINO              134                662
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19Q LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED   127  20
  19Q LOSS WILD-TYPE 733  94
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               147                827 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                20                 94 
$`19Q LOSS MUTATED`
TCGA-A1-A0SQ TCGA-A2-A04U TCGA-A2-A04X TCGA-A2-A0CM TCGA-A2-A0CW TCGA-A2-A0D1 
       18.21        22.06        55.43        24.79        64.04        34.55 
TCGA-A2-A0EO TCGA-A2-A0SV TCGA-A2-A0T7 TCGA-A2-A0YG TCGA-A2-A0YT TCGA-A2-A1FW 
       80.28        27.12        20.75        21.90        23.77        17.36 
TCGA-A2-A1G1 TCGA-A2-A3XT TCGA-A7-A13E TCGA-A7-A2KD TCGA-A7-A56D TCGA-A8-A06Q 
       19.20        83.01        10.72        22.32        14.73         1.02 
TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A076 TCGA-A8-A07G TCGA-A8-A07L TCGA-A8-A07O 
       17.98        41.06        53.98        18.97        17.03         9.99 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08O TCGA-A8-A08S TCGA-A8-A097 
       18.05        19.96        12.00        31.00        19.07        12.00 
TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09N TCGA-AC-A23C 
        9.99         1.02        33.07        15.02         1.02         0.95 
TCGA-AC-A2BM TCGA-AC-A2FM TCGA-AC-A62V TCGA-AN-A041 TCGA-AN-A04A TCGA-AN-A0AS 
       38.20        26.04         0.07         0.23         2.96         0.33 
TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FZ TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03P 
        6.02         0.33         0.33        80.28        66.77        84.69 
TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0JD TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A1KQ 
       21.40        17.65        72.00        55.33        71.80        61.87 
TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A0Y5 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AJ 
       17.79        24.79         5.65        83.87        76.18        52.77 
TCGA-AR-A1AQ TCGA-AR-A24H TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A252 TCGA-AR-A2LK 
       43.07       109.58        57.40        62.07        40.64        42.87 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0IB TCGA-B6-A0WX TCGA-B6-A1KF TCGA-B6-A1KN 
       10.59        77.62       129.57        21.47       101.52       139.17 
TCGA-B6-A402 TCGA-B6-A408 TCGA-BH-A0BT TCGA-BH-A0C0 TCGA-BH-A0C7 TCGA-BH-A0DQ 
       54.28        49.94        45.57        41.75        42.90         3.22 
TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0H0 TCGA-BH-A0H7 TCGA-BH-A0HY TCGA-BH-A0WA 
       24.49        31.00        15.16        23.08        50.79        23.05 
TCGA-BH-A18F TCGA-BH-A18I TCGA-BH-A18S TCGA-BH-A1FU TCGA-BH-A204 TCGA-BH-A209 
        8.81         7.23        66.05        72.07        83.31       130.16 
TCGA-C8-A12M TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A1HF TCGA-C8-A1HL 
       11.77        11.77         0.07        12.66        10.92        10.42 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A278 TCGA-C8-A27A TCGA-D8-A13Y TCGA-D8-A1JC 
        0.36         0.43         0.03        12.20        11.90        15.78 
TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JM TCGA-D8-A1XA TCGA-D8-A1XQ TCGA-D8-A1XT 
       18.97        20.09        19.40        27.58        16.41         6.35 
TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y3 TCGA-D8-A27M TCGA-E2-A109 TCGA-E2-A14O 
       16.54        15.32        14.14        13.48        46.59        44.68 
TCGA-E2-A159 TCGA-E2-A15H TCGA-E2-A15S TCGA-E2-A1AZ TCGA-E2-A573 TCGA-E2-A574 
       25.05        12.92        14.07        60.53        22.26        19.89 
TCGA-E9-A1N6 TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R3 TCGA-E9-A1R7 
       13.48        20.05         9.86        11.90         2.10        21.21 
TCGA-E9-A1RB TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A2JS 
       20.81        34.59        34.13        23.51         0.69        17.75 
TCGA-E9-A5UO TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1PA TCGA-EW-A1PC 
        0.23        22.82        29.95        40.41        18.90         6.15 
TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A3U0 TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH 
       55.00        52.73        17.49        53.52        42.71        42.28 
TCGA-LL-A7T0 TCGA-OL-A5D7 TCGA-OL-A5RY 
        3.22        46.55        14.10 

$`19Q LOSS WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
       20.88        13.68        31.79         7.96        39.32        28.01 
TCGA-A1-A0SP TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T 
       19.20       104.81        18.02        41.95        82.16        73.84 
TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO 
       63.12        64.04        36.13       125.59        64.57       112.08 
TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU 
       92.48        88.60       107.93        75.55        75.25         5.19 
TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 
       63.45        56.81        21.14        33.76        28.77        25.22 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES 
      101.72        89.36       107.61        79.76        74.40        37.05 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY 
       35.05        34.29        31.82        29.75        24.72        24.16 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 
       99.19        54.64        44.88        50.43        44.28        17.52 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.13         8.38        18.71        20.52        17.46        18.90 
TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YH TCGA-A2-A0YI 
       32.55        25.28        18.21        15.42        21.67        14.50 
TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FX 
       18.61        19.33        14.63        31.73        23.47        36.79 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A 
       22.45        20.25        19.56        16.47        52.47       107.70 
TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
       16.31        17.19        18.15        91.92        10.59        20.88 
TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX 
       39.65        33.93        29.98        14.07        49.48        38.40 
TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY 
       34.98        31.99        38.37         7.30         9.01         8.81 
TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE 
        8.91        12.00         6.74         3.42        38.30        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB 
       34.29        35.47        30.61        37.45        35.67        33.11 
TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F 
       31.73        12.72        23.61        29.56        31.36        24.26 
TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ 
       23.74        23.80        21.73        20.61        11.34        10.59 
TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA 
       10.29        11.28        13.41        14.70        11.97        14.93 
TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A5ZW 
       13.74        14.50        21.17        17.92        12.10        10.72 
TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O 
       11.05        10.29         9.37        10.42         8.75        13.02 
TCGA-A8-A06P TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 
       13.02        29.03        31.00        26.01         1.02        17.03 
TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07J 
        9.01        33.01        19.99        18.97        14.01        12.00 
TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z 
       10.98         8.98         7.99         9.96         9.99        28.04 
TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B 
       18.05        15.06        36.95        13.02         0.99        23.08 
TCGA-A8-A08C TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T 
       19.99        37.05         9.99        31.00         0.99        93.04 
TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 
       33.99        40.01        19.07        16.01        17.95        41.98 
TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09Q 
        9.99        12.00        13.02        31.00        29.98        25.02 
TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 
        8.98        19.04        15.02         0.99        14.01        12.00 
TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB 
       19.04        13.02        21.04         0.99        13.02        17.03 
TCGA-A8-A0AD TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK 
       38.04         2.37        10.85         2.66         1.48        38.53 
TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH 
       40.57        55.43        36.99        38.79        50.70         1.02 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
        0.92         2.27         0.99         0.69        14.83         9.40 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS 
        1.12         1.81         1.68         1.55         1.32         1.55 
TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A8OP 
        1.12         1.81         1.18         0.69         0.43         1.74 
TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D 
        0.33         0.33         0.33         0.62         1.78         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AT 
        8.02         7.36         6.51         0.16         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN 
        6.44         4.64         7.96         7.00         7.59         7.17 
TCGA-AN-A0FS TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN 
        6.28         0.36         0.33         0.33         0.33         0.33 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU 
       12.33         0.30         0.33         0.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T 
        5.33         5.59        47.84        81.63        68.75        47.87 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 
       59.05        29.13        32.78        24.16        37.48        20.32 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE 
       22.36        53.03        21.53        50.70        50.86        76.77 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A124 TCGA-AO-A125 
       21.37        26.24        38.53        62.04       102.58        99.25 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D 
       93.70        94.59        96.10        90.58        77.56        64.04 
TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       57.30        48.36        41.62        28.37        14.73        82.62 
TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       70.39         0.53        26.93       130.09        15.62        13.22 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
        2.56        21.86         9.99        82.88        49.32         5.26 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
       37.41        56.88        29.75        24.30        64.83        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
       76.14        65.36        70.16        55.36        75.55        61.84 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP 
       51.25        48.82        62.56        43.73        43.56        39.98 
TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX 
       17.23        40.83        46.32        42.58        35.24        36.26 
TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       20.22        50.89        73.02        65.46        68.19        65.69 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W 
        0.85        66.05        53.26        53.36        54.18        50.96 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A255 
       48.16        51.75        56.15        45.17        39.85        34.82 
TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN 
       93.83       128.65        20.25         7.36        40.04        17.10 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP 
       20.81        16.96        20.38        54.74        16.04        20.45 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IE 
      143.38       149.59        12.13       220.90        50.70        65.72 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
      146.50       112.37       176.98        18.77       126.12        84.59 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH 
      110.14       110.93       140.88       211.56        68.45       189.01 
TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP 
      234.28        81.17        78.02       172.96       162.05       102.77 
TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS 
      140.48       100.70        89.46       131.21       157.41        97.48 
TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 
      188.68        79.63        17.98       113.79       129.57       129.70 
TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KI 
      186.48        28.27        68.94        58.88        43.59        73.51 
TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV 
      170.17        85.35        82.88        55.00        24.53        38.79 
TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 
       20.45        25.55        28.50        46.95        40.83        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA 
       39.16        48.36        56.94        56.98        51.68        37.22 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL 
       32.02        18.21        25.71        24.85        21.70        44.05 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       61.68        35.67        48.69        27.19        53.69        53.95 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0DD 
       49.94        11.67        49.05        44.02        48.13        45.83 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL 
       31.17        23.44        38.01        22.13        13.91        48.23 
TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       17.26        15.65         2.56        38.47        45.17        47.41 
TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 
       16.27         4.41        15.68        14.30         9.63        44.81 
TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H3 
       46.19        32.65        24.43        30.35        10.78        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI 
       35.51        24.56        41.00        52.96        26.50        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW 
        5.85         2.50        13.61        36.85        12.89        51.32 
TCGA-BH-A0HX TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       27.25         5.59        23.93        24.95        42.35        44.81 
TCGA-BH-A18G TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N 
        2.01        20.12        90.84        26.66        72.56        37.74 
TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V 
       30.28        55.63        37.55         7.36        51.39        51.16 
TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV 
       69.93        91.99       113.82        82.85        42.28        12.00 
TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 
       55.69        49.58        17.69        25.81        31.53        89.16 
TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE 
       97.48        24.66       120.62       114.15        33.17        74.73 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN 
      122.89        36.92        63.35        55.00        45.63        72.07 
TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A28O 
      144.59         6.90         0.72        38.60        57.83        10.65 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12L 
        6.44        20.12         0.99       109.28         8.94        11.93 
TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 
       11.77        12.66        12.66        12.66        12.66         3.12 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 
        1.78         1.45         0.69         0.62         3.85         3.75 
TCGA-C8-A1HE TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM 
       12.33        11.34        11.34         0.16        12.03         2.30 
TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 
        3.25         0.30         0.23         8.28         9.67         0.03 
TCGA-C8-A275 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Z TCGA-D8-A140 
        0.03         0.99         0.03         0.23        20.88        13.25 
TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 
       20.58        13.97        14.17        13.48        21.14        19.20 
TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JE 
       14.17        17.49        16.50        18.71        18.15        18.90 
TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JN 
       12.03        12.03        14.01        20.12        20.09        20.38 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 
       21.01        12.20        13.32        14.70        18.58        17.79 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD 
       16.73        25.74        23.90        18.15         2.66        17.16 
TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM 
       15.22        14.73        21.83        14.50        19.92        17.69 
TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW 
        7.96        15.85        16.31        12.99        15.16        12.66 
TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G 
       15.52         3.81        14.24        17.42        16.04        13.45 
TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P 
       13.05        14.43         9.44        16.41         4.80         0.76 
TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 
       10.09        13.08        12.53        12.26        14.50        18.51 
TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B 
        7.33        43.00        34.42        27.52        40.41        37.51 
TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q 
       40.11        28.44        28.87        47.15        40.96        38.24 
TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W 
       38.60        33.17        33.30        43.33        34.26        32.02 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 
       31.96        28.60        17.03        25.41        27.12        23.24 
TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15A TCGA-E2-A15C 
       19.43        21.04        23.87        14.79        23.34        22.82 
TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15J 
       17.29        20.71        21.63        18.21        17.42        19.40 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R 
        9.04        20.58         7.73        13.02        19.56        17.06 
TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       14.99        53.62        53.03        29.95        32.35        28.50 
TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       16.47        17.10        38.30        37.41        32.78        33.73 
TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO 
       33.70        28.44        22.65         3.88        22.19        20.98 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA 
       11.08        54.18        27.42        39.62        19.66        24.59 
TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK 
       40.47        28.90        18.87       106.75       102.61         8.75 
TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
       43.04        16.93         5.52        15.72         7.20        18.05 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC 
       19.20        36.82        12.00        13.12        36.56        39.55 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R4 
       12.59        35.77        21.57        14.30         0.62         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE 
        1.38         2.76        32.09        40.24         0.66        34.65 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
        6.58        21.27        35.64         0.79        12.53        13.32 
TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A245 
       39.09        22.75        12.89        24.10        17.06         0.85 
TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JT 
       27.22         1.94         0.95        12.56         0.72         0.76 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FK 
       26.07        18.41         0.62        15.72         0.23         0.39 
TCGA-E9-A5FL TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
        0.26        15.39        12.20        39.72         8.48        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV 
       18.90        13.25        16.57        15.68        28.77        25.94 
TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 
       29.85        41.13        39.78        52.96        29.82        23.11 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE 
       18.48        30.08         7.86        19.99        13.94        10.52 
TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 
       14.43        34.55        19.96        25.91        22.09        21.27 
TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       10.16        10.59         7.40       109.87        59.57       194.27 
TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       53.13        43.04        61.91        62.33        90.84        76.64 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL 
       77.33        53.36       110.50        38.20        32.28        69.30 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX 
       53.95        57.63        13.55        18.12        11.84        11.57 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
        8.28         6.67         4.60         0.66         2.99         3.58 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP 
        6.90         5.56         4.70         3.65         3.19         3.25 
TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ 
        2.63         3.88         4.14         4.50         4.50         5.59 
TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 
        6.21        15.91         2.79         2.10        12.66         7.53 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RZ 
       44.61        27.65        24.10        26.20        16.87        10.29 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L 
        9.80        14.76        23.70        54.51        33.90        31.07 
TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-S3-A6ZG TCGA-W8-A86G 
       18.21         7.23         4.44         6.81         5.29 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.03               0.03 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            139.17             234.28 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             20.81              21.63 
[1] "0.0 - 139.2 (20.8)" "0.0 - 234.3 (21.6)"
[1] "hr=" "1.4"
D75V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19Q LOSS MUTATED         9        9        1        0        52        34
  19Q LOSS WILD-TYPE      71       68        8        9       283       190
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19Q LOSS MUTATED           1         27          3          7        4
  19Q LOSS WILD-TYPE         1        111         24         52       13
                    vv
clus                 STAGE TIS STAGE X
  19Q LOSS MUTATED           0       2
  19Q LOSS WILD-TYPE         1      14
D75V3, multiclass
            clus
vv           19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                   9                 71
  STAGE IA                  9                 68
  STAGE IB                  1                  8
  STAGE II                  0                  9
  STAGE IIA                52                283
  STAGE IIB                34                190
  STAGE III                 1                  1
  STAGE IIIA               27                111
  STAGE IIIB                3                 24
  STAGE IIIC                7                 52
  STAGE IV                  4                 13
  STAGE TIS                 0                  1
  STAGE X                   2                 14
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  19Q LOSS MUTATED    36  95  15   3
  19Q LOSS WILD-TYPE 222 486 102  33
D75V4, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1               36                222
  T2               95                486
  T3               15                102
  T4                3                 33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  19Q LOSS MUTATED    60  57  22   9
  19Q LOSS WILD-TYPE 408 273  89  61
D75V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0               60                408
  N1               57                273
  N2               22                 89
  N3                9                 61
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  19Q LOSS MUTATED          1 125   4  19
  19Q LOSS WILD-TYPE        1 720  13 112
D75V6, multiclass
          clus
vv         19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CM0 (I+)                1                  1
  M0                    125                720
  M1                      4                 13
  MX                     19                112
[1] 4 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   147   2
  19Q LOSS WILD-TYPE 837   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED    147    2
  19Q LOSS WILD-TYPE  837    9
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE              147                837
  MALE                  2                  9
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  19Q LOSS MUTATED                            0                           133
  19Q LOSS WILD-TYPE                          1                           602
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  19Q LOSS MUTATED                                4                   1
  19Q LOSS WILD-TYPE                            162                   4
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  19Q LOSS MUTATED                                  3                  3
  19Q LOSS WILD-TYPE                               26                 11
                    vv
clus                 OTHER  SPECIFY
  19Q LOSS MUTATED                4
  19Q LOSS WILD-TYPE             40
D75V8, multiclass
                                  clus
vv                                 19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 133                602
  INFILTRATING LOBULAR CARCINOMA                  4                162
  MEDULLARY CARCINOMA                             1                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                3                 26
  MUCINOUS CARCINOMA                              3                 11
  OTHER  SPECIFY                                  4                 40
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V9, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    51  98
  19Q LOSS WILD-TYPE 231 615
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     51   98
  19Q LOSS WILD-TYPE  231  615
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                51                231
  YES               98                615
[1] 2 2
[1] FALSE
D75V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q LOSS MUTATED                                  0    12
  19Q LOSS WILD-TYPE                                1    44
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED                          25    93
  19Q LOSS WILD-TYPE                       112   615
D75V11, multiclass
                                  clus
vv                                 19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          12                 44
  BLACK OR AFRICAN AMERICAN                      25                112
  WHITE                                          93                615
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V12, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     5 116
  19Q LOSS WILD-TYPE  31 680
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      5  116
  19Q LOSS WILD-TYPE   31  680
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                 31
  NOT HISPANIC OR LATINO              116                680
[1] 2 2
[1] FALSE

Clustering(76) Variable = 20P LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    70  13
  20P LOSS WILD-TYPE 790 101
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                83                891 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                13                101 
$`20P LOSS MUTATED`
TCGA-A1-A0SK TCGA-A2-A04T TCGA-A2-A0YE TCGA-A2-A3XU TCGA-A2-A4S3 TCGA-A7-A0CE 
       31.79        73.84        18.21        29.98         3.42        35.31 
TCGA-A7-A26E TCGA-A7-A26I TCGA-A7-A4SE TCGA-A8-A06Q TCGA-A8-A079 TCGA-A8-A07L 
       31.36        21.73        21.17         1.02         9.01        17.03 
TCGA-A8-A08F TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A0AB TCGA-AC-A3W5 TCGA-AC-A62X 
       18.05         9.99        31.00        17.03         1.81         1.12 
TCGA-AN-A0AM TCGA-AN-A0XW TCGA-AO-A0J6 TCGA-AO-A1KT TCGA-AQ-A04J TCGA-AQ-A54N 
        0.16         5.59        37.48        17.79        26.93         2.56 
TCGA-AR-A0TZ TCGA-AR-A0U3 TCGA-AR-A1AR TCGA-AR-A24K TCGA-AR-A251 TCGA-B6-A0I9 
       76.14        76.18        17.23        50.89        45.17        12.13 
TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0RL TCGA-B6-A0RS TCGA-B6-A0X1 TCGA-B6-A1KN 
      176.98        18.77        81.17       100.70       186.48       139.17 
TCGA-BH-A0AV TCGA-BH-A0B4 TCGA-BH-A0B9 TCGA-BH-A0BR TCGA-BH-A0DH TCGA-BH-A0E1 
       38.79        39.16        51.68        53.69        38.01        15.68 
TCGA-BH-A18V TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FM TCGA-C8-A12M TCGA-C8-A134 
       51.16       114.15        33.17        45.63        11.77         0.69 
TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1XA TCGA-D8-A1XJ TCGA-D8-A1XK 
       20.12        20.09        19.40        27.58        21.83        14.50 
TCGA-D8-A1XQ TCGA-D8-A1Y3 TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27R TCGA-E2-A14N 
       16.41        14.14        16.04        13.05        10.09        47.15 
TCGA-E2-A14R TCGA-E2-A15A TCGA-E2-A15E TCGA-E2-A2P5 TCGA-E2-A573 TCGA-E9-A1N5 
       38.60        23.34        20.71        16.93        22.26        36.82 
TCGA-E9-A1NC TCGA-E9-A1R6 TCGA-E9-A1RE TCGA-E9-A22G TCGA-E9-A244 TCGA-EW-A1P4 
       39.55         2.76        34.65        23.51         0.69        29.82 
TCGA-EW-A1P8 TCGA-EW-A2FR TCGA-EW-A2FW TCGA-EW-A423 TCGA-GM-A2DF TCGA-JL-A3YX 
        7.86        55.00        22.09        10.16        42.71        11.57 
TCGA-LL-A5YP TCGA-MS-A51U TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-OL-A66O 
        3.25         2.79        26.20         9.80         7.23 

$`20P LOSS WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP 
       20.88        13.68         7.96        39.32        28.01        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04U 
       18.21       104.81        18.02        41.95        82.16        22.06 
TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL 
       63.12        64.04        55.43        36.13       125.59        64.57 
TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS 
       24.79       112.08        92.48        88.60       107.93        75.55 
TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 
       75.25         5.19        63.45        64.04        56.81        21.14 
TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN 
       34.55        33.76        28.77        25.22       101.72        89.36 
TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET 
       80.28       107.61        79.76        74.40        37.05        35.05 
TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST 
       34.29        31.82        29.75        24.72        24.16        99.19 
TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 
       54.64        27.12        44.88        50.43        44.28        17.52 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.13         8.38        18.71        20.52        17.46        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH 
       20.75        32.55        25.28        15.42        21.90        21.67 
TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT 
       14.50        18.61        19.33        14.63        31.73        23.77 
TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 
       23.47        17.36        36.79        22.45        20.25        19.20 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C 
       19.56        16.47        52.47       107.70        16.31        17.19 
TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS 
       18.15        91.92        10.59        20.88        39.65        33.93 
TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ 
       83.01        14.07        49.48        38.40        34.98        31.99 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 
       38.37         7.30         9.01         8.81         8.91        12.00 
TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 
        6.74        38.30        34.29        35.47        30.61        37.45 
TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G 
       35.67        33.11        31.73        10.72        12.72        23.61 
TCGA-A7-A13H TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD 
       29.56        24.26        23.74        23.80        20.61        22.32 
TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 
       11.34        10.59        10.29        11.28        13.41        14.70 
TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A56D 
       11.97        14.93        13.74        14.50        17.92        14.73 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX 
       12.10        10.72        11.05        10.29         9.37        10.42 
TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U 
        8.75        13.02        13.02        17.98        41.06        29.03 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07B 
       31.00        26.01         1.02        17.03        53.98        33.01 
TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07O 
       19.99        18.97        18.97        14.01        12.00         9.99 
TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z 
       10.98         8.98         7.99         9.96         9.99        28.04 
TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B 
       18.05        15.06        36.95        13.02         0.99        23.08 
TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08R 
       19.99        19.96        12.00        37.05        31.00         0.99 
TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 
       19.07        93.04        33.99        40.01        19.07        16.01 
TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B 
       17.95        41.98        12.00         9.99         9.99        12.00 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M 
        1.02        13.02        31.00        33.07        29.98        15.02 
TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
        1.02        25.02         8.98        19.04        15.02         0.99 
TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 
       14.01        12.00        19.04        13.02        21.04         0.99 
TCGA-A8-A0A9 TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H 
       13.02        38.04         0.95         2.37        10.85         2.66 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG 
        1.48        38.53        38.20        40.57        55.43        36.99 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ 
       38.79        26.04        50.70         1.02         0.92         2.27 
TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W6 
        0.99         0.69        14.83         9.40         1.12         1.68 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV 
        1.55         1.32         1.55         0.07         1.81         1.18 
TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 
        0.69         0.43         1.74         0.33         0.33         0.23 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ 
        0.33         0.62         2.96         1.78         1.71         8.02 
TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD 
        7.36         6.51         0.33         0.33         0.33         6.44 
TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        4.64         7.96         7.00         7.59         7.17         6.28 
TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ 
        6.02         0.33         0.36         0.33         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS 
        0.33         0.33        12.33         0.30         0.33         0.33 
TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N 
        0.33         0.33         5.33        80.28        47.84        66.77 
TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V 
       81.63        84.69        68.75        47.87        59.05        29.13 
TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J7 TCGA-AO-A0J8 
       32.78        21.40        17.65        24.16        20.32        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE 
       53.03        21.53        50.70        50.86        72.00        76.77 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM 
       21.37        26.24        38.53        62.04        55.33        71.80 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A 
      102.58        99.25        93.70        94.59        96.10        90.58 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
       77.56        64.04        57.30        48.36        41.62        28.37 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04H 
       14.73        82.62        61.87        70.39         0.53        24.79 
TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AQ-A7U7 
      130.09         5.65        15.62        13.22        21.86         9.99 
TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV 
       82.88        49.32         5.26        37.41        56.88        29.75 
TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 
       24.30        64.83        55.86        65.36        70.16        83.87 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL 
       55.36        75.55        61.84        52.77        51.25        48.82 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS 
       62.56        43.73        43.56        39.98        43.07        40.83 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H 
       46.32        42.58        35.24        36.26        20.22       109.58 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q 
       73.02        65.46        68.19        65.69         0.85        66.05 
TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W 
       57.40        62.07        53.26        53.36        54.18        50.96 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 
       48.16        51.75        56.15        40.64        39.85        34.82 
TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM 
       93.83       128.65        20.25        42.87         7.36        40.04 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN 
       17.10        20.81        16.96        20.38        54.74        16.04 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IA 
       20.45        10.59        77.62       143.38       149.59       220.90 
TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IM 
      129.57        50.70        65.72       146.50       112.37       126.12 
TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG 
       84.59       110.14       110.93       140.88       211.56        68.45 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP 
      189.01       234.28        78.02       172.96       162.05       102.77 
TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT 
      140.48        89.46       131.21       157.41        97.48       188.68 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 
       79.63        17.98        21.47       113.79       129.57       129.70 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI 
       28.27        68.94        58.88        43.59       101.52        73.51 
TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C 
      170.17        85.35        54.28        49.94        82.88        55.00 
TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 
       24.53        20.45        25.55        28.50        46.95        40.83 
TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BC 
       39.55        48.36        56.94        56.98        37.22        32.02 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM 
       18.21        25.71        24.85        21.70        44.05        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV 
       35.67        48.69        27.19        53.95        45.57        49.94 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 
       11.67        49.05        41.75        44.02        48.13        42.90 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL 
       45.83        31.17        23.44        22.13        13.91        48.23 
TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       17.26        15.65         3.22         2.56        38.47        45.17 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 
       47.41        16.27         4.41        14.30         9.63        44.81 
TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY 
       46.19        32.65        24.49        31.00        24.43        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 
       10.78        15.16        37.78        35.51        24.56        23.08 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       41.00        52.96        26.50        20.38         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY 
       13.61        36.85        12.89        51.32        27.25        50.79 
TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA 
        5.59        23.93        24.95        42.35        44.81        23.05 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L 
        8.81         2.01         7.23        20.12        90.84        26.66 
TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S 
       72.56        37.74        30.28        55.63        37.55        66.05 
TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET 
        7.36        51.39        69.93        91.99       113.82        82.85 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 
       42.28        12.00        55.69        49.58        17.69        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FE 
       31.53        89.16        97.48        24.66       120.62        74.73 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR 
      122.89        36.92        63.35        55.00        72.07       144.59 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 
       72.07         6.90         0.72        38.60        83.31        57.83 
TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
      130.16        10.65         6.44        20.12         0.99       109.28 
TCGA-BH-A42V TCGA-C8-A12L TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q 
        8.94        11.93        11.77        12.66        11.77         0.07 
TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A131 
       12.66        12.66        12.66        12.66         3.12         1.78 
TCGA-C8-A132 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF 
        1.45         0.62         3.85         3.75        12.33        10.92 
TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM 
       11.34        11.34         0.16        12.03        10.42         2.30 
TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z 
        3.25         0.30         0.23         0.36         0.43         8.28 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B 
        9.67         0.03         0.03         0.03        12.20         0.99 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 
        0.03         0.23        11.90        20.88        13.25        20.58 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 
       13.97        14.17        13.48        21.14        19.20        14.17 
TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE 
       17.49        16.50        18.71        15.78        18.15        18.90 
TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JN 
       12.03        12.03        14.01        18.97        20.09        20.38 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 
       21.01        12.20        13.32        14.70        18.58        17.79 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD 
       16.73        25.74        23.90        18.15         2.66        17.16 
TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR 
       15.22        14.73        19.92        17.69         7.96        15.85 
TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY 
       16.31         6.35        12.99        15.16        12.66        16.54 
TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27G 
       15.32        15.52         3.81        14.24        17.42        13.45 
TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P 
       14.43         9.44        16.41        13.48         4.80         0.76 
TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 
       13.08        12.53        12.26        14.50        18.51         7.33 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B 
       43.00        34.42        27.52        46.59        40.41        37.51 
TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q 
       40.11        28.44        28.87        44.68        40.96        38.24 
TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X 
       33.17        33.30        43.33        34.26        32.02        31.96 
TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 
       28.60        17.03        25.41        27.12        23.24        19.43 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15C TCGA-E2-A15D 
       21.04        23.87        14.79        25.05        22.82        17.29 
TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       21.63        18.21        12.92        17.42        19.40         9.04 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
       20.58         7.73        13.02        19.56        17.06        14.07 
TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       14.99        60.53        53.62        53.03        29.95        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       28.50        16.47        17.10        38.30        37.41        32.78 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN 
       33.73        33.70        28.44        22.65         3.88        22.19 
TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 
       20.98        11.08        54.18        27.42        39.62        19.66 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI 
       24.59        40.47        28.90        18.87       106.75       102.61 
TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
        8.75        43.04         5.52        15.72         7.20        18.05 
TCGA-E2-A574 TCGA-E9-A1N4 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA 
       19.89        19.20        13.48        12.00        13.12        36.56 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ 
       12.59        35.77        20.05        21.57         9.86        11.90 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 
       14.30         0.62         2.10         6.12         1.38        21.21 
TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RF TCGA-E9-A1RG 
       32.09        20.81        40.24         0.66         6.58        21.27 
TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
       34.59        35.64        34.13         0.79        12.53        13.32 
TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A245 
       39.09        22.75        12.89        24.10        17.06         0.85 
TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS 
       27.22         1.94         0.95        12.56         0.72        17.75 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54Y 
        0.76        26.07        18.41         0.62        15.72         0.23 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
        0.39         0.26         0.23        15.39        12.20        39.72 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
        8.48        18.21        18.90        13.25        16.57        15.68 
TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ 
       28.77        25.94        22.82        29.95        29.85        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 
       41.13        39.78        52.96        23.11        18.48        30.08 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
       18.90        19.99         6.15        13.94        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A3E8 TCGA-EW-A3U0 
       34.55        19.96        52.73        25.91        21.27        17.49 
TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       10.59         7.40       109.87        59.57       194.27        53.13 
TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       53.52        43.04        42.28        61.91        62.33        90.84 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
       76.64        77.33        53.36       110.50        38.20        32.28 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW 
       69.30        53.95        57.63        13.55        18.12        11.84 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
        8.28         6.67         4.60         0.66         2.99         3.58 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FQ 
        6.90         5.56         4.70         3.65         3.19         2.63 
TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 
        3.88         4.14         4.50         4.50         5.59         3.22 
TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 
        6.21        15.91         2.10        12.66        46.55         7.53 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       44.61        27.65        24.10        16.87        14.10        10.29 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       14.76        23.70        54.51        33.90        31.07        18.21 
TCGA-OL-A66P TCGA-S3-A6ZG TCGA-W8-A86G 
        4.44         6.81         5.29 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.16               0.03 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            186.48             234.28 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             21.73              21.40 
[1] "0.2 - 186.5 (21.7)" "0.0 - 234.3 (21.4)"
[1] "hr=" "1.4"
D76V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20P LOSS MUTATED         3        4        0        0        36        17
  20P LOSS WILD-TYPE      77       73        9        9       299       207
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20P LOSS MUTATED           0         13          3          6        3
  20P LOSS WILD-TYPE         2        125         24         53       14
                    vv
clus                 STAGE TIS STAGE X
  20P LOSS MUTATED           0       0
  20P LOSS WILD-TYPE         1      16
D76V3, multiclass
            clus
vv           20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                   3                 77
  STAGE IA                  4                 73
  STAGE IB                  0                  9
  STAGE II                  0                  9
  STAGE IIA                36                299
  STAGE IIB                17                207
  STAGE III                 0                  2
  STAGE IIIA               13                125
  STAGE IIIB                3                 24
  STAGE IIIC                6                 53
  STAGE IV                  3                 14
  STAGE TIS                 0                  1
  STAGE X                   0                 16
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  20P LOSS MUTATED    14  61   7   3
  20P LOSS WILD-TYPE 244 520 110  33
D76V4, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1               14                244
  T2               61                520
  T3                7                110
  T4                3                 33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  20P LOSS MUTATED    39  26  11   8
  20P LOSS WILD-TYPE 429 304 100  62
D76V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0               39                429
  N1               26                304
  N2               11                100
  N3                8                 62
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  20P LOSS MUTATED          0  70   3  12
  20P LOSS WILD-TYPE        2 775  14 119
D76V6, multiclass
          clus
vv         20P LOSS MUTATED 20P LOSS WILD-TYPE
  CM0 (I+)                0                  2
  M0                     70                775
  M1                      3                 14
  MX                     12                119
[1] 4 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    84   1
  20P LOSS WILD-TYPE 900  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     84    1
  20P LOSS WILD-TYPE  900   10
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE               84                900
  MALE                  1                 10
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  20P LOSS MUTATED                            0                            71
  20P LOSS WILD-TYPE                          1                           664
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  20P LOSS MUTATED                                7                   2
  20P LOSS WILD-TYPE                            159                   3
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  20P LOSS MUTATED                                  2                  0
  20P LOSS WILD-TYPE                               27                 14
                    vv
clus                 OTHER  SPECIFY
  20P LOSS MUTATED                3
  20P LOSS WILD-TYPE             41
D76V8, multiclass
                                  clus
vv                                 20P LOSS MUTATED 20P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                  71                664
  INFILTRATING LOBULAR CARCINOMA                  7                159
  MEDULLARY CARCINOMA                             2                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)                2                 27
  MUCINOUS CARCINOMA                              0                 14
  OTHER  SPECIFY                                  3                 41
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V9, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    28  57
  20P LOSS WILD-TYPE 254 656
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     28   57
  20P LOSS WILD-TYPE  254  656
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                28                254
  YES               57                656
[1] 2 2
[1] FALSE
D76V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P LOSS MUTATED                                  0     4
  20P LOSS WILD-TYPE                                1    52
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED                          18    55
  20P LOSS WILD-TYPE                       119   653
D76V11, multiclass
                                  clus
vv                                 20P LOSS MUTATED 20P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           4                 52
  BLACK OR AFRICAN AMERICAN                      18                119
  WHITE                                          55                653
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V12, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     5  63
  20P LOSS WILD-TYPE  31 733
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      5   63
  20P LOSS WILD-TYPE   31  733
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                 31
  NOT HISPANIC OR LATINO               63                733
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED    38   8
  20Q LOSS WILD-TYPE 822 106
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                46                928 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 8                106 
$`20Q LOSS MUTATED`
TCGA-A1-A0SK TCGA-A2-A3XU TCGA-A7-A0CE TCGA-A7-A0DA TCGA-A7-A26E TCGA-A7-A26I 
       31.79        29.98        35.31        35.67        31.36        21.73 
TCGA-A7-A6VW TCGA-A8-A06Q TCGA-A8-A07B TCGA-A8-A08O TCGA-A8-A0AB TCGA-AC-A62X 
        9.37         1.02        33.01        31.00        17.03         1.12 
TCGA-AN-A0AR TCGA-AN-A0XW TCGA-AO-A03P TCGA-AO-A0J6 TCGA-AO-A1KS TCGA-AQ-A04J 
        0.33         5.59        84.69        37.48         0.53        26.93 
TCGA-AQ-A54N TCGA-AR-A0U3 TCGA-AR-A1AR TCGA-AR-A24K TCGA-B6-A0RS TCGA-B6-A0X1 
        2.56        76.18        17.23        50.89       100.70       186.48 
TCGA-BH-A0AV TCGA-BH-A18V TCGA-BH-A1FC TCGA-C8-A12M TCGA-C8-A27B TCGA-D8-A1JK 
       38.79        51.16       114.15        11.77         0.99        20.12 
TCGA-D8-A1JL TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-E2-A14N TCGA-E2-A15E TCGA-E2-A2P5 
       20.09        21.83        14.50        47.15        20.71        16.93 
TCGA-E9-A1NC TCGA-E9-A22G TCGA-EW-A1P4 TCGA-EW-A1P8 TCGA-EW-A2FW TCGA-JL-A3YX 
       39.55        23.51        29.82         7.86        22.09        11.57 
TCGA-LL-A5YP TCGA-MS-A51U TCGA-OL-A5RW TCGA-OL-A66O 
        3.25         2.79        26.20         7.23 

$`20Q LOSS WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP 
       20.88        13.68         7.96        39.32        28.01        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T 
       18.21       104.81        18.02        41.95        82.16        73.84 
TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK 
       22.06        63.12        64.04        55.43        36.13       125.59 
TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
       64.57        24.79       112.08        92.48        88.60       107.93 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX 
       75.55        75.25         5.19        63.45        64.04        56.81 
TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM 
       21.14        34.55        33.76        28.77        25.22       101.72 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES 
       89.36        80.28       107.61        79.76        74.40        37.05 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY 
       35.05        34.29        31.82        29.75        24.72        24.16 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY 
       99.19        54.64        27.12        44.88        50.43        44.28 
TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 
       17.52        17.13         8.38        18.71        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF 
       18.90        20.75        32.55        25.28        18.21        15.42 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL 
       21.90        21.67        14.50        18.61        19.33        14.63 
TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ 
       31.73        23.77        23.47        17.36        36.79        22.45 
TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A 
       20.25        19.20        19.56        16.47        52.47       107.70 
TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
       16.31        17.19        18.15        91.92        10.59        20.88 
TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX 
       39.65        33.93        83.01        14.07        49.48        38.40 
TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY 
       34.98        31.99        38.37         7.30         9.01         8.81 
TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CG 
        8.91        12.00         6.74         3.42        38.30        34.29 
TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E 
       35.47        30.61        37.45        33.11        31.73        10.72 
TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H 
       12.72        23.61        29.56        24.26        23.74        23.80 
TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       20.61        22.32        11.34        10.59        10.29        11.28 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD 
       13.41        14.70        11.97        14.93        13.74        14.50 
TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX 
       21.17        17.92        14.73        12.10        10.72        11.05 
TCGA-A7-A6VV TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06R 
       10.29        10.42         8.75        13.02        13.02        17.98 
TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 
       41.06        29.03        31.00        26.01         1.02        17.03 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I 
       53.98         9.01        19.99        18.97        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S 
       12.00        17.03         9.99        10.98         8.98         7.99 
TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 
        9.96         9.99        28.04        18.05        15.06        36.95 
TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G 
       13.02         0.99        23.08        19.99        18.05        19.96 
TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S 
       12.00        37.05         9.99        31.00         0.99        19.07 
TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 
       93.04        33.99        40.01        19.07        16.01        17.95 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C 
       41.98        12.00         9.99         9.99        12.00         1.02 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N 
       13.02        31.00        33.07        29.98        15.02         1.02 
TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X 
       25.02         8.98        19.04        15.02         0.99        14.01 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 
       12.00        19.04        13.02        21.04         0.99        13.02 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 
       38.04         0.95         2.37        10.85         2.66         1.48 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
       38.53        38.20        40.57        55.43        36.99        38.79 
TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB 
       26.04        50.70         1.02         0.92         2.27         0.99 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 
        0.69        14.83         9.40         1.12         1.81         1.68 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV 
        1.55         1.32         1.55         0.07         1.81         1.18 
TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 
        0.69         0.43         1.74         0.33         0.33         0.23 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ 
        0.33         0.62         2.96         1.78         1.71         8.02 
TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD 
        7.36         6.51         0.16         0.33         0.33         6.44 
TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        4.64         7.96         7.00         7.59         7.17         6.28 
TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ 
        6.02         0.33         0.36         0.33         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS 
        0.33         0.33        12.33         0.30         0.33         0.33 
TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N 
        0.33         0.33         5.33        80.28        47.84        66.77 
TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 
       81.63        68.75        47.87        59.05        29.13        32.78 
TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 
       21.40        17.65        24.16        20.32        22.36        53.03 
TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF 
       21.53        50.70        50.86        72.00        76.77        21.37 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 
       26.24        38.53        62.04        55.33        71.80       102.58 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B 
       99.25        93.70        94.59        96.10        90.58        77.56 
TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
       64.04        57.30        48.36        41.62        28.37        14.73 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04L 
       82.62        61.87        70.39        17.79        24.79       130.09 
TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP 
        5.65        15.62        13.22        21.86         9.99        82.88 
TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW 
       49.32         5.26        37.41        56.88        29.75        24.30 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 
       64.83        55.86        76.14        65.36        70.16        83.87 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL 
       55.36        75.55        61.84        52.77        51.25        48.82 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS 
       62.56        43.73        43.56        39.98        43.07        40.83 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H 
       46.32        42.58        35.24        36.26        20.22       109.58 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q 
       73.02        65.46        68.19        65.69         0.85        66.05 
TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W 
       57.40        62.07        53.26        53.36        54.18        50.96 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 
       48.16        51.75        56.15        45.17        40.64        39.85 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LL 
       34.82        93.83       128.65        20.25        42.87         7.36 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM 
       40.04        17.10        20.81        16.96        20.38        54.74 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 
       16.04        20.45        10.59        77.62       143.38       149.59 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG 
       12.13       220.90       129.57        50.70        65.72       146.50 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO 
      112.37       176.98        18.77       126.12        84.59       110.14 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
      110.93       140.88       211.56        68.45       189.01       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ 
       81.17        78.02       172.96       162.05       102.77       140.48 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV 
       89.46       131.21       157.41        97.48       188.68        79.63 
TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 
       17.98        21.47       113.79       129.57       129.70        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN 
       68.94        58.88        43.59       101.52        73.51       139.17 
TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C 
      170.17        85.35        54.28        49.94        82.88        55.00 
TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 
       24.53        20.45        25.55        28.50        46.95        40.83 
TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 
       39.55        39.16        48.36        56.94        56.98        51.68 
TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ 
       37.22        32.02        18.21        25.71        24.85        21.70 
TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR 
       44.05        61.68        35.67        48.69        27.19        53.69 
TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 
       53.95        45.57        49.94        11.67        49.05        41.75 
TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG 
       44.02        48.13        42.90        45.83        31.17        23.44 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP 
       38.01        22.13        13.91        48.23        17.26        15.65 
TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ 
        3.22         2.56        38.47        45.17        47.41        16.27 
TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 
        4.41        15.68        14.30         9.63        44.81        46.19 
TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ 
       32.65        24.49        31.00        24.43        30.35        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 
       15.16        37.78        35.51        24.56        23.08        41.00 
TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       52.96        26.50        20.38         5.85         2.50        13.61 
TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX 
       36.85        12.89        51.32        27.25        50.79         5.59 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F 
       23.93        24.95        42.35        44.81        23.05         8.81 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M 
        2.01         7.23        20.12        90.84        26.66        72.56 
TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T 
       37.74        30.28        55.63        37.55        66.05         7.36 
TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU 
       51.39        69.93        91.99       113.82        82.85        42.28 
TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 
       12.00        55.69        49.58        17.69        25.81        31.53 
TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE 
       89.16        97.48        24.66       120.62        33.17        74.73 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN 
      122.89        36.92        63.35        55.00        45.63        72.07 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 
      144.59        72.07         6.90         0.72        38.60        83.31 
TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T 
       57.83       130.16        10.65         6.44        20.12         0.99 
TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12L TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P 
      109.28         8.94        11.93        11.77        12.66        11.77 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 
        0.07        12.66        12.66        12.66        12.66         3.12 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 
        1.78         1.45         0.69         0.62         3.85         3.75 
TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK 
       12.33        10.92        11.34        11.34         0.16        12.03 
TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X 
       10.42         2.30         3.25         0.30         0.23         0.36 
TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 
        0.43         8.28         9.67         0.03         0.03         0.03 
TCGA-C8-A27A TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 
       12.20         0.03         0.23        11.90        20.88        13.25 
TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 
       20.58        13.97        14.17        13.48        21.14        19.20 
TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD 
       14.17        17.49        16.50        18.71        15.78        18.15 
TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ 
       18.90        12.03        12.03        14.01        18.97        20.09 
TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU 
       19.40        20.38        21.01        12.20        13.32        14.70 
TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA 
       18.58        17.79        16.73        25.74        23.90        27.58 
TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XL 
       18.15         2.66        17.16        15.22        14.73        19.92 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT 
       17.69         7.96        16.41        15.85        16.31         6.35 
TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 
       12.99        15.16        12.66        16.54        15.32        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G 
        3.81        14.24        14.14        17.42        16.04        13.45 
TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N 
       13.05        14.43         9.44        16.41        13.48         4.80 
TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 
        0.76        10.09        13.08        12.53        12.26        14.50 
TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 
       18.51         7.33        43.00        34.42        27.52        46.59 
TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14O 
       40.41        37.51        40.11        28.44        28.87        44.68 
TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U 
       40.96        38.24        38.60        33.17        33.30        43.33 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 
       34.26        32.02        31.96        28.60        17.03        25.41 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 
       27.12        23.24        19.43        21.04        23.87        14.79 
TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15G 
       25.05        23.34        22.82        17.29        21.63        18.21 
TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M 
       12.92        17.42        19.40         9.04        20.58         7.73 
TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ 
       13.02        19.56        17.06        14.07        14.99        60.53 
TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC 
       53.62        53.03        29.95        32.35        28.50        16.47 
TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II 
       17.10        38.30        37.41        32.78        33.73        33.70 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       28.44        22.65         3.88        22.19        20.98        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB 
       54.18        27.42        39.62        19.66        24.59        40.47 
TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL 
       28.90        18.87       106.75       102.61         8.75        43.04 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 
        5.52        15.72         7.20        18.05        22.26        19.89 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA 
       19.20        36.82        13.48        12.00        13.12        36.56 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ 
       12.59        35.77        20.05        21.57         9.86        11.90 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 
       14.30         0.62         2.10         6.12         1.38         2.76 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE 
       21.21        32.09        20.81        40.24         0.66        34.65 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
        6.58        21.27        34.59        35.64        34.13         0.79 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22H 
       12.53        13.32        39.09        22.75        12.89        24.10 
TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 
       17.06         0.69         0.85        27.22         1.94         0.95 
TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 
       12.56         0.72        17.75         0.76        26.07        18.41 
TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO 
        0.62        15.72         0.23         0.39         0.26         0.23 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 
       15.39        12.20        39.72         8.48        18.21        18.90 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW 
       13.25        16.57        15.68        28.77        25.94        22.82 
TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 
       29.95        29.85        40.41        41.13        39.78        52.96 
TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC 
       23.11        18.48        30.08        18.90        19.99         6.15 
TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR 
       13.94        10.52        14.43        34.55        19.96        55.00 
TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 
       52.73        25.91        21.27        17.49        10.16        10.59 
TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC 
        7.40       109.87        59.57       194.27        53.13        53.52 
TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       43.04        42.71        42.28        61.91        62.33        90.84 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
       76.64        77.33        53.36       110.50        38.20        32.28 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW 
       69.30        53.95        57.63        13.55        18.12        11.84 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
        8.28         6.67         4.60         0.66         2.99         3.58 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FQ 
        6.90         5.56         4.70         3.65         3.19         2.63 
TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 
        3.88         4.14         4.50         4.50         5.59         3.22 
TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 
        6.21        15.91         2.10        12.66        46.55         7.53 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       44.61        27.65        24.10        16.87        14.10        10.29 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L 
        9.80        14.76        23.70        54.51        33.90        31.07 
TCGA-OL-A66N TCGA-OL-A66P TCGA-S3-A6ZG TCGA-W8-A86G 
       18.21         4.44         6.81         5.29 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              0.33               0.03 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            186.48             234.28 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             21.96              21.32 
[1] "0.3 - 186.5 (22.0)" "0.0 - 234.3 (21.3)"
[1] "hr=" "1.6"
D77V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20Q LOSS MUTATED         1        0        0        0        27        10
  20Q LOSS WILD-TYPE      79       77        9        9       308       214
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20Q LOSS MUTATED           0          5          0          2        2
  20Q LOSS WILD-TYPE         2        133         27         57       15
                    vv
clus                 STAGE TIS STAGE X
  20Q LOSS MUTATED           0       0
  20Q LOSS WILD-TYPE         1      16
D77V3, multiclass
            clus
vv           20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                   1                 79
  STAGE IA                  0                 77
  STAGE IB                  0                  9
  STAGE II                  0                  9
  STAGE IIA                27                308
  STAGE IIB                10                214
  STAGE III                 0                  2
  STAGE IIIA                5                133
  STAGE IIIB                0                 27
  STAGE IIIC                2                 57
  STAGE IV                  2                 15
  STAGE TIS                 0                  1
  STAGE X                   0                 16
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  20Q LOSS MUTATED     5  38   4   0
  20Q LOSS WILD-TYPE 253 543 113  36
D77V4, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1                5                253
  T2               38                543
  T3                4                113
  T4                0                 36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  20Q LOSS MUTATED    25  15   4   3
  20Q LOSS WILD-TYPE 443 315 107  67
D77V5, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0               25                443
  N1               15                315
  N2                4                107
  N3                3                 67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  20Q LOSS MUTATED          0  38   2   7
  20Q LOSS WILD-TYPE        2 807  15 124
D77V6, multiclass
          clus
vv         20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CM0 (I+)                0                  2
  M0                     38                807
  M1                      2                 15
  MX                      7                124
[1] 4 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    47   0
  20Q LOSS WILD-TYPE 937  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED     47    0
  20Q LOSS WILD-TYPE  937   11
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE               47                937
  MALE                  0                 11
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  20Q LOSS MUTATED                            0                            35
  20Q LOSS WILD-TYPE                          1                           700
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  20Q LOSS MUTATED                                6                   2
  20Q LOSS WILD-TYPE                            160                   3
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  20Q LOSS MUTATED                                  1                  0
  20Q LOSS WILD-TYPE                               28                 14
                    vv
clus                 OTHER  SPECIFY
  20Q LOSS MUTATED                3
  20Q LOSS WILD-TYPE             41
D77V8, multiclass
                                  clus
vv                                 20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                  35                700
  INFILTRATING LOBULAR CARCINOMA                  6                160
  MEDULLARY CARCINOMA                             2                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)                1                 28
  MUCINOUS CARCINOMA                              0                 14
  OTHER  SPECIFY                                  3                 41
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V9, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED    15  32
  20Q LOSS WILD-TYPE 267 681
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED     15   32
  20Q LOSS WILD-TYPE  267  681
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                15                267
  YES               32                681
[1] 2 2
[1] FALSE
D77V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q LOSS MUTATED                                  0     4
  20Q LOSS WILD-TYPE                                1    52
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED                          11    27
  20Q LOSS WILD-TYPE                       126   681
D77V11, multiclass
                                  clus
vv                                 20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           4                 52
  BLACK OR AFRICAN AMERICAN                      11                126
  WHITE                                          27                681
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V12, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     4  35
  20Q LOSS WILD-TYPE  32 761
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      4   35
  20Q LOSS WILD-TYPE   32  761
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 32
  NOT HISPANIC OR LATINO               35                761
[1] 2 2
[1] FALSE

Clustering(78) Variable = 21Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED   142  20
  21Q LOSS WILD-TYPE 718  94
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               162                812 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                20                 94 
$`21Q LOSS MUTATED`
TCGA-A1-A0SN TCGA-A2-A04T TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0EU TCGA-A2-A0SU 
       39.32        73.84        64.04        21.14        34.29        54.64 
TCGA-A2-A0YJ TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A25B TCGA-A2-A3XY 
       18.61        23.77        23.47        17.36        16.31        34.98 
TCGA-A2-A3Y0 TCGA-A7-A0CJ TCGA-A7-A26G TCGA-A7-A4SD TCGA-A8-A06P TCGA-A8-A06U 
       38.37        30.61        23.74        14.50        13.02        29.03 
TCGA-A8-A079 TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08O 
        9.01        18.05        19.96        12.00        37.05        31.00 
TCGA-A8-A08S TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09I TCGA-A8-A09Q TCGA-A8-A09R 
       19.07         9.99        12.00        33.07        25.02         8.98 
TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A9 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A8OP 
       19.04        13.02        13.02        38.53        38.20         1.74 
TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A0AM TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FV 
        2.96         1.78         0.16         4.64         7.96         0.33 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AO-A03L TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A0J3 
        0.33         0.33        80.28        84.69        68.75        21.40 
TCGA-AO-A0J4 TCGA-AO-A0J7 TCGA-AO-A0JD TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AR-A0TP 
       17.65        20.32        72.00       130.09         5.65        82.88 
TCGA-AR-A0TT TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A1AP TCGA-AR-A24S 
       56.88        76.14        70.16        83.87        39.98        62.07 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A256 
       53.36        54.18        50.96        56.15        40.64        93.83 
TCGA-AR-A2LK TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0RP TCGA-B6-A0RS TCGA-B6-A0WW 
       42.87       129.57        65.72       102.77       100.70        17.98 
TCGA-B6-A0X1 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A408 
      186.48        58.88        43.59       139.17       170.17        49.94 
TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0B9 TCGA-BH-A0BG TCGA-BH-A0BP TCGA-BH-A0DE 
       24.53        38.79        51.68        24.85        48.69        31.17 
TCGA-BH-A0DP TCGA-BH-A0E9 TCGA-BH-A0H7 TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0HY 
       15.65        46.19        23.08        12.89        27.25        50.79 
TCGA-BH-A0W3 TCGA-BH-A18L TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1FM TCGA-C8-A12O 
       23.93        26.66        51.39        51.16        45.63        12.66 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12W TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HF 
        0.07        12.66        12.66         3.85         3.75        10.92 
TCGA-C8-A1HK TCGA-C8-A1HN TCGA-C8-A26W TCGA-C8-A27A TCGA-C8-A27B TCGA-D8-A145 
       12.03         3.25         0.23        12.20         0.99        13.48 
TCGA-D8-A1J8 TCGA-D8-A1JD TCGA-D8-A1JF TCGA-D8-A1JM TCGA-D8-A1X6 TCGA-D8-A1XA 
       14.17        18.15        12.03        19.40        17.79        27.58 
TCGA-D8-A1XB TCGA-D8-A1XF TCGA-D8-A1XL TCGA-D8-A1XR TCGA-D8-A1XY TCGA-D8-A1XZ 
       18.15        15.22        19.92        15.85        16.54        15.32 
TCGA-D8-A1Y1 TCGA-D8-A27M TCGA-D8-A27T TCGA-D8-A27W TCGA-E2-A107 TCGA-E2-A109 
        3.81        13.48        13.08        12.26        34.42        46.59 
TCGA-E2-A10C TCGA-E2-A152 TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A1IH 
       40.11        27.12        20.71        18.21        12.92        33.73 
TCGA-E2-A1L8 TCGA-E2-A1LL TCGA-E2-A56Z TCGA-E2-A574 TCGA-E9-A1N8 TCGA-E9-A1NA 
       39.62        43.04         7.20        19.89        12.00        36.56 
TCGA-E9-A1ND TCGA-E9-A1R0 TCGA-E9-A1R4 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RG 
       12.59        14.30         6.12        32.09        20.81        21.27 
TCGA-E9-A226 TCGA-E9-A22G TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A3QA 
       34.13        23.51        17.06        27.22         1.94         0.62 
TCGA-E9-A5FL TCGA-EW-A1IW TCGA-EW-A1J6 TCGA-EW-A2FS TCGA-GI-A2C9 TCGA-GM-A2DL 
        0.26        12.20        28.77        52.73       109.87        90.84 
TCGA-GM-A4E0 TCGA-JL-A3YX TCGA-LL-A5YM TCGA-OL-A5RZ TCGA-OL-A66N TCGA-S3-A6ZG 
       57.63        11.57         4.70        10.29        18.21         6.81 

$`21Q LOSS WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SP 
       20.88        13.68        31.79         7.96        28.01        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04U 
       18.21       104.81        18.02        41.95        82.16        22.06 
TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL 
       63.12        64.04        55.43        36.13       125.59        64.57 
TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS 
       24.79       112.08        92.48        88.60       107.93        75.55 
TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D2 
       75.25         5.19        63.45        56.81        34.55        33.76 
TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP 
       28.77        25.22       101.72        89.36        80.28       107.61 
TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EV TCGA-A2-A0EW 
       79.76        74.40        37.05        35.05        31.82        29.75 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX 
       24.72        24.16        99.19        27.12        44.88        50.43 
TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 
       44.28        17.52        17.13         8.38        18.71        20.52 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE 
       17.46        18.90        20.75        32.55        25.28        18.21 
TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL 
       15.42        21.90        21.67        14.50        19.33        14.63 
TCGA-A2-A0YM TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 
       31.73        36.79        22.45        20.25        19.20        19.56 
TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       16.47        52.47       107.70        17.19        18.15        91.92 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU 
       10.59        20.88        39.65        33.93        83.01        29.98 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XZ TCGA-A2-A4RW TCGA-A2-A4RX 
       14.07        49.48        38.40        31.99         7.30         9.01 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD 
        8.81         8.91        12.00         6.74         3.42        38.30 
TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB 
       35.31        34.29        35.47        37.45        35.67        33.11 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       31.73        10.72        12.72        23.61        29.56        31.36 
TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY 
       24.26        23.80        21.73        20.61        22.32        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 
       10.59        10.29        11.28        13.41        14.70        11.97 
TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV 
       14.93        13.74        21.17        17.92        14.73        12.10 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY 
       10.72        11.05        10.29         9.37        10.42         8.75 
TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06X TCGA-A8-A06Y 
       13.02         1.02        17.98        41.06        31.00        26.01 
TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F 
        1.02        17.03        53.98        33.01        19.99        18.97 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P 
       18.97        14.01        12.00        17.03         9.99        10.98 
TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 
        8.98         7.99         9.96         9.99        28.04        18.05 
TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C 
       15.06        36.95        13.02         0.99        23.08        19.99 
TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z 
        9.99        31.00         0.99        93.04        33.99        40.01 
TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 
       19.07        16.01        17.95        41.98        12.00         9.99 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N 
        1.02        13.02        31.00        29.98        15.02         1.02 
TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A6 
       19.04        15.02         0.99        14.01        12.00        21.04 
TCGA-A8-A0A7 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G 
        0.99        17.03        38.04         0.95         2.37        10.85 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
        2.66         1.48        40.57        55.43        36.99        38.79 
TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB 
       26.04        50.70         1.02         0.92         2.27         0.99 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 
        0.69        14.83         9.40         1.12         1.81         1.68 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y 
        1.55         1.32         1.55         0.07         1.12         1.81 
TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 
        1.18         0.69         0.43         0.33         0.33         0.23 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL 
        0.33         0.62         1.71         8.02         7.36         6.51 
TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FK TCGA-AN-A0FL 
        0.33         0.33         0.33         6.44         7.00         7.59 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY 
        7.17         6.28         6.02         0.36         0.33         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR 
        0.33         0.33         0.33        12.33         0.30         0.33 
TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O 
        0.33         5.33         5.59        47.84        66.77        81.63 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J5 TCGA-AO-A0J6 
       47.87        59.05        29.13        32.78        24.16        37.48 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE 
       22.36        53.03        21.53        50.70        50.86        76.77 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM 
       21.37        26.24        38.53        62.04        55.33        71.80 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A 
      102.58        99.25        93.70        94.59        96.10        90.58 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
       77.56        64.04        57.30        48.36        41.62        28.37 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT 
       14.73        82.62        61.87        70.39         0.53        17.79 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O 
       24.79        26.93        15.62        13.22         2.56        21.86 
TCGA-AQ-A7U7 TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TV TCGA-AR-A0TW 
        9.99        49.32         5.26        37.41        29.75        24.30 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0U0 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH 
       64.83        55.86        65.36        76.18        55.36        75.55 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
       61.84        52.77        51.25        48.82        62.56        43.73 
TCGA-AR-A1AO TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
       43.56        43.07        17.23        40.83        46.32        42.58 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L 
       35.24        36.26        20.22       109.58        50.89        73.02 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R 
       65.46        68.19        65.69         0.85        66.05        57.40 
TCGA-AR-A24T TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A255 
       53.26        48.16        51.75        45.17        39.85        34.82 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
      128.65        20.25         7.36        40.04        17.10        20.81 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       16.96        20.38        54.74        16.04        20.45        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC 
       77.62       143.38       149.59        12.13       220.90        50.70 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
      146.50       112.37       176.98        18.77       126.12        84.59 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH 
      110.14       110.93       140.88       211.56        68.45       189.01 
TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ 
      234.28        81.17        78.02       172.96       162.05       140.48 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV 
       89.46       131.21       157.41        97.48       188.68        79.63 
TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 
       21.47       113.79       129.57       129.70        28.27        68.94 
TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A40B TCGA-B6-A40C 
      101.52        73.51        85.35        54.28        82.88        55.00 
TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 
       20.45        25.55        28.50        46.95        40.83        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BC 
       39.16        48.36        56.94        56.98        37.22        32.02 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO 
       18.21        25.71        21.70        44.05        61.68        35.67 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW 
       27.19        53.69        53.95        45.57        49.94        11.67 
TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD 
       49.05        41.75        44.02        48.13        42.90        45.83 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO 
       23.44        38.01        22.13        13.91        48.23        17.26 
TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ 
        3.22         2.56        38.47        45.17        47.41        16.27 
TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0EA 
        4.41        15.68        14.30         9.63        44.81        32.65 
TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 
       24.49        31.00        24.43        30.35        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB 
       37.78        35.51        24.56        41.00        52.96        26.50 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HW 
       20.38         5.85         2.50        13.61        36.85        51.32 
TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F 
        5.59        24.95        42.35        44.81        23.05         8.81 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18N 
        2.01         7.23        20.12        90.84        72.56        37.74 
TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A1EN 
       30.28        55.63        37.55        66.05         7.36        69.93 
TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW 
       91.99       113.82        82.85        42.28        12.00        55.69 
TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 
       49.58        17.69        25.81        31.53        89.16        97.48 
TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG 
       24.66       120.62       114.15        33.17        74.73       122.89 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU 
       36.92        63.35        55.00        72.07       144.59        72.07 
TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 
        6.90         0.72        38.60        83.31        57.83       130.16 
TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V 
       10.65         6.44        20.12         0.99       109.28         8.94 
TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12P TCGA-C8-A12V TCGA-C8-A12X 
       11.93        11.77        11.77        11.77        12.66        12.66 
TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A1HE 
        3.12         1.78         1.45         0.69         0.62        12.33 
TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A26V 
       11.34        11.34         0.16        10.42         2.30         0.30 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
        0.36         0.43         8.28         9.67         0.03         0.03 
TCGA-C8-A278 TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 
        0.03         0.03         0.23        11.90        20.88        13.25 
TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J9 
       20.58        13.97        14.17        21.14        19.20        17.49 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH 
       16.50        18.71        15.78        18.90        12.03        14.01 
TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JN TCGA-D8-A1JP 
       18.97        20.09        20.12        20.09        20.38        21.01 
TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X7 TCGA-D8-A1X8 
       12.20        13.32        14.70        18.58        16.73        25.74 
TCGA-D8-A1X9 TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK 
       23.90         2.66        17.16        14.73        21.83        14.50 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU 
       17.69         7.96        16.41        16.31         6.35        12.99 
TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E 
       15.16        12.66        15.52        14.24        14.14        17.42 
TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       16.04        13.45        13.05        14.43         9.44        16.41 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 
        4.80         0.76        10.09        12.53        14.50        18.51 
TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E 
        7.33        43.00        27.52        40.41        37.51        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R 
       28.87        47.15        44.68        40.96        38.24        38.60 
TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X 
       33.17        33.30        43.33        34.26        32.02        31.96 
TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 
       28.60        17.03        25.41        23.24        19.43        21.04 
TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D 
       23.87        14.79        25.05        23.34        22.82        17.29 
TCGA-E2-A15F TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M 
       21.63        17.42        19.40         9.04        20.58         7.73 
TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ 
       13.02        19.56        17.06        14.07        14.99        60.53 
TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC 
       53.62        53.03        29.95        32.35        28.50        16.47 
TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1II TCGA-E2-A1IJ 
       17.10        38.30        37.41        32.78        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       22.65         3.88        22.19        20.98        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG 
       27.42        19.66        24.59        40.47        28.90        18.87 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX 
      106.75       102.61         8.75        16.93         5.52        15.72 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 
       18.05        22.26        19.20        36.82        13.48        13.12 
TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ 
       39.55        35.77        20.05        21.57         9.86        11.90 
TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RC 
        0.62         2.10         1.38         2.76        21.21        40.24 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A227 
        0.66        34.65         6.58        34.59        35.64         0.79 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22H 
       12.53        13.32        39.09        22.75        12.89        24.10 
TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS 
        0.69         0.85         0.95        12.56         0.72        17.75 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FK 
        0.76        26.07        18.41        15.72         0.23         0.39 
TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 
        0.23        15.39        39.72         8.48        18.21        18.90 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX 
       13.25        16.57        15.68        25.94        22.82        29.95 
TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 
       29.85        40.41        41.13        39.78        52.96        29.82 
TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB 
       23.11        18.48        30.08         7.86        18.90        19.99 
TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH 
        6.15        13.94        10.52        14.43        34.55        19.96 
TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 
       55.00        25.91        22.09        21.27        17.49        10.16 
TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC 
       10.59         7.40        59.57       194.27        53.13        53.52 
TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DM 
       43.04        42.71        42.28        61.91        62.33        76.64 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL 
       77.33        53.36       110.50        38.20        32.28        69.30 
TCGA-GM-A3XN TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-LD-A66U TCGA-LD-A74U 
       53.95        13.55        18.12        11.84         8.28         6.67 
TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL 
        4.60         0.66         2.99         3.58         6.90         5.56 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y 
        3.65         3.19         3.25         2.63         3.88         4.14 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LQ-A4E4 
        4.50         4.50         5.59         3.22         6.21        15.91 
TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA 
        2.79         2.10        12.66        46.55         7.53        44.61 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5S0 
       27.65        24.10        26.20        16.87        14.10         9.80 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66O 
       14.76        23.70        54.51        33.90        31.07         7.23 
TCGA-OL-A66P TCGA-W8-A86G 
        4.44         5.29 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.07               0.03 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            186.48             234.28 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            21.335             21.500 
[1] "0.1 - 186.5 (21.3)" "0.0 - 234.3 (21.5)"
[1] "hr=" "1.1"
D78V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  21Q LOSS MUTATED        11       12        0        1        49        40
  21Q LOSS WILD-TYPE      69       65        9        8       286       184
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  21Q LOSS MUTATED           1         27          9          5        5
  21Q LOSS WILD-TYPE         1        111         18         54       12
                    vv
clus                 STAGE TIS STAGE X
  21Q LOSS MUTATED           1       3
  21Q LOSS WILD-TYPE         0      13
D78V3, multiclass
            clus
vv           21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                  11                 69
  STAGE IA                 12                 65
  STAGE IB                  0                  9
  STAGE II                  1                  8
  STAGE IIA                49                286
  STAGE IIB                40                184
  STAGE III                 1                  1
  STAGE IIIA               27                111
  STAGE IIIB                9                 18
  STAGE IIIC                5                 54
  STAGE IV                  5                 12
  STAGE TIS                 1                  0
  STAGE X                   3                 13
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  21Q LOSS MUTATED    38  98  18   9
  21Q LOSS WILD-TYPE 220 483  99  27
D78V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1               38                220
  T2               98                483
  T3               18                 99
  T4                9                 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                  N0  N1  N2  N3
  21Q LOSS MUTATED    67  56  29   9
  21Q LOSS WILD-TYPE 401 274  82  61
D78V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0               67                401
  N1               56                274
  N2               29                 82
  N3                9                 61
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  21Q LOSS MUTATED          0 140   5  19
  21Q LOSS WILD-TYPE        2 705  12 112
D78V6, multiclass
          clus
vv         21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CM0 (I+)                0                  2
  M0                    140                705
  M1                      5                 12
  MX                     19                112
[1] 4 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   164   0
  21Q LOSS WILD-TYPE 820  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED    164    0
  21Q LOSS WILD-TYPE  820   11
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE              164                820
  MALE                  0                 11
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  21Q LOSS MUTATED                            0                           137
  21Q LOSS WILD-TYPE                          1                           598
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  21Q LOSS MUTATED                               15                   1
  21Q LOSS WILD-TYPE                            151                   4
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  21Q LOSS MUTATED                                  6                  1
  21Q LOSS WILD-TYPE                               23                 13
                    vv
clus                 OTHER  SPECIFY
  21Q LOSS MUTATED                4
  21Q LOSS WILD-TYPE             40
D78V8, multiclass
                                  clus
vv                                 21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 137                598
  INFILTRATING LOBULAR CARCINOMA                 15                151
  MEDULLARY CARCINOMA                             1                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                6                 23
  MUCINOUS CARCINOMA                              1                 13
  OTHER  SPECIFY                                  4                 40
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V9, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    51 113
  21Q LOSS WILD-TYPE 231 600
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     51  113
  21Q LOSS WILD-TYPE  231  600
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                51                231
  YES              113                600
[1] 2 2
[1] FALSE
D78V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q LOSS MUTATED                                  0    15
  21Q LOSS WILD-TYPE                                1    41
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED                          25   107
  21Q LOSS WILD-TYPE                       112   601
D78V11, multiclass
                                  clus
vv                                 21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          15                 41
  BLACK OR AFRICAN AMERICAN                      25                112
  WHITE                                         107                601
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V12, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     3 130
  21Q LOSS WILD-TYPE  33 666
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      3  130
  21Q LOSS WILD-TYPE   33  666
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 33
  NOT HISPANIC OR LATINO              130                666
[1] 2 2
[1] FALSE

Clustering(79) Variable = 22Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED   378  55
  22Q LOSS WILD-TYPE 482  59
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               433                541 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                55                 59 
$`22Q LOSS MUTATED`
TCGA-A1-A0SD TCGA-A1-A0SG TCGA-A1-A0SJ TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A2-A04N 
       14.37        14.27        13.68        39.32        28.01       104.81 
TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CM TCGA-A2-A0CP 
       18.02        41.95        63.12        36.13        24.79        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW 
       88.60       107.93        75.55         5.19        63.45        64.04 
TCGA-A2-A0D0 TCGA-A2-A0D4 TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0ET TCGA-A2-A0EU 
       21.14        25.22        89.36        80.28        35.05        34.29 
TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SX TCGA-A2-A0T3 
       31.82        29.75        54.64        27.12        50.43        18.71 
TCGA-A2-A0T4 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF 
       20.52        18.90        20.75        25.28        18.21        15.42 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1G0 TCGA-A2-A25A 
       21.90        21.67        23.77        17.36        20.25       107.70 
TCGA-A2-A25B TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XZ TCGA-A2-A3Y0 
       16.31        33.93        83.01        29.98        31.99        38.37 
TCGA-A2-A4RY TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ 
        8.81         3.42        35.31        34.29        35.47        30.61 
TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13H TCGA-A7-A26E 
       35.67        33.11        31.73        10.72        29.56        31.36 
TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A7-A4SB TCGA-A7-A4SD 
       21.73        20.61        11.28        11.97        13.74        14.50 
TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06P 
       21.17        17.92        14.73         9.37         8.75        13.02 
TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y 
        1.02        17.98        41.06        29.03        31.00        26.01 
TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F 
        1.02        17.03        53.98        33.01        19.99        18.97 
TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07R TCGA-A8-A07W TCGA-A8-A084 
       14.01        12.00        17.03         8.98         9.99        15.06 
TCGA-A8-A085 TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08S 
       36.95        19.96        12.00        37.05        31.00        19.07 
TCGA-A8-A08Z TCGA-A8-A097 TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09N 
       40.01        12.00        12.00         1.02        13.02         1.02 
TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09W TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 
        8.98        19.04         0.99        13.02        21.04         0.99 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-AC-A23G TCGA-AC-A2BK TCGA-AC-A2FF TCGA-AC-A2FM 
       13.02        17.03        10.85        38.53        55.43        26.04 
TCGA-AC-A2QH TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3QP TCGA-AC-A5XS TCGA-AC-A62Y 
        1.02         0.99         0.69         9.40         1.55         1.81 
TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A0AJ 
        1.18         0.43         1.74         0.23         0.62         8.02 
TCGA-AN-A0AK TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FW TCGA-AN-A0FY 
        7.36         6.44         4.64         7.00         0.36         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XO TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU 
        0.33        12.33         0.33         0.33         0.33         0.33 
TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A0J3 TCGA-AO-A0J7 TCGA-AO-A0J8 
       80.28        66.77        84.69        21.40        20.32        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JD TCGA-AO-A0JG TCGA-AO-A12A 
       53.03        21.53        50.70        72.00        26.24        90.58 
TCGA-AO-A12E TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AQ-A54N TCGA-AQ-A54O 
       57.30        82.62        61.87         0.53         2.56        21.86 
TCGA-AQ-A7U7 TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0TZ 
        9.99         5.26        56.88        24.30        55.86        76.14 
TCGA-AR-A0U0 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AM 
       65.36        83.87        76.18        75.55        52.77        62.56 
TCGA-AR-A1AN TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AV TCGA-AR-A1AY 
       43.73        39.98        43.07        17.23        42.58        20.22 
TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R 
      109.58        50.89        73.02        65.69         0.85        57.40 
TCGA-AR-A24S TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 
       62.07        50.96        48.16        51.75        56.15        40.64 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LK TCGA-AR-A2LO TCGA-AR-A5QN TCGA-AR-A5QP 
       34.82        93.83        42.87        20.81        16.04        20.45 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IQ TCGA-B6-A0RE 
      146.50       112.37        84.59       110.14       140.88       211.56 
TCGA-B6-A0RG TCGA-B6-A0RL TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0WW 
       68.45        81.17       172.96       162.05       102.77        17.98 
TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A1KN TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C 
       21.47       113.79       139.17        49.94        82.88        55.00 
TCGA-BH-A0AU TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 
       24.53        25.55        46.95        39.55        39.16        48.36 
TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BF TCGA-BH-A0BJ 
       56.94        56.98        51.68        37.22        25.71        21.70 
TCGA-BH-A0BL TCGA-BH-A0BR TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BZ TCGA-BH-A0C3 
       44.05        53.69        45.57        49.94        49.05        48.13 
TCGA-BH-A0C7 TCGA-BH-A0DH TCGA-BH-A0DQ TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0EB 
       42.90        38.01         3.22         4.41         9.63        24.49 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB 
       30.35        10.78        23.08        41.00        52.96        26.50 
TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0W3 TCGA-BH-A0W5 TCGA-BH-A0W7 
       36.85        12.89        27.25        23.93        42.35        44.81 
TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L 
       23.05         8.81         7.23        20.12        90.84        26.66 
TCGA-BH-A18M TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU 
       72.56         7.36        51.16       113.82        82.85        42.28 
TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F5 TCGA-BH-A1F8 TCGA-BH-A1FC TCGA-BH-A1FD 
       49.58        17.69        89.16        24.66       114.15        33.17 
TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A42T 
       55.00        45.63        72.07        83.31       130.16         0.99 
TCGA-C8-A12M TCGA-C8-A12U TCGA-C8-A132 TCGA-C8-A138 TCGA-C8-A1HI TCGA-C8-A1HK 
       11.77        12.66         1.45         3.75        11.34        12.03 
TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26Z TCGA-C8-A274 TCGA-C8-A27A 
       10.42         2.30         3.25         8.28         0.03        12.20 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J8 
       11.90        20.88        14.17        13.48        21.14        14.17 
TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JG TCGA-D8-A1JJ TCGA-D8-A1JM TCGA-D8-A1JN 
       18.71        18.15        12.03        20.09        19.40        20.38 
TCGA-D8-A1JP TCGA-D8-A1X5 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XD 
       21.01        18.58        23.90        27.58        18.15        17.16 
TCGA-D8-A1XK TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XT TCGA-D8-A1XU 
       14.50        17.69         7.96        15.85         6.35        12.99 
TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27I TCGA-D8-A27L 
       15.52         3.81        14.24        14.14        14.43        16.41 
TCGA-D8-A27T TCGA-D8-A3Z5 TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10A 
       13.08        14.50        43.00        34.42        46.59        40.41 
TCGA-E2-A10C TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14T 
       40.11        28.87        44.68        38.24        38.60        33.30 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A159 
       34.26        32.02        17.03        25.41        23.24        25.05 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H 
       23.34        22.82        20.71        21.63        18.21        12.92 
TCGA-E2-A15I TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15T TCGA-E2-A1AZ 
       17.42         7.73        13.02        19.56        14.99        60.53 
TCGA-E2-A1B1 TCGA-E2-A1B5 TCGA-E2-A1BD TCGA-E2-A1IF TCGA-E2-A1IH TCGA-E2-A1II 
       53.03        32.35        17.10        37.41        33.73        33.70 
TCGA-E2-A1IJ TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1L8 TCGA-E2-A1LE 
       28.44         3.88        22.19        20.98        39.62        28.90 
TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A56Z TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N5 
        8.75        16.93         7.20        22.26        19.89        36.82 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF 
       12.00        13.12        36.56        12.59        35.77        20.05 
TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R6 TCGA-E9-A1RA 
       21.57         9.86         0.62         2.10         2.76        32.09 
TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG 
       20.81        40.24         0.66        34.65         6.58        21.27 
TCGA-E9-A1RI TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A244 
       35.64        13.32        39.09        12.89        24.10         0.69 
TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A3HO TCGA-E9-A3X8 
       27.22         1.94         0.95        12.56        26.07        15.72 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IX 
        0.23         0.39         0.26         0.23        15.39        39.72 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1P3 
       18.90        13.25        28.77        22.82        29.85        52.96 
TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PC TCGA-EW-A1PH 
       23.11        18.48         7.86        18.90         6.15        19.96 
TCGA-EW-A2FV TCGA-EW-A423 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DK 
       25.91        10.16       194.27        53.13        53.52        62.33 
TCGA-GM-A2DL TCGA-GM-A3NY TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-JL-A3YW TCGA-JL-A3YX 
       90.84        38.20        53.95        57.63        11.84        11.57 
TCGA-LD-A66U TCGA-LL-A442 TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A7T0 TCGA-LQ-A4E4 
        8.28         3.58         3.65         3.19         3.22        15.91 
TCGA-OL-A5D7 TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RZ TCGA-OL-A66K TCGA-OL-A66L 
       46.55        24.10        26.20        10.29        33.90        31.07 
TCGA-S3-A6ZG 
        6.81 

$`22Q LOSS WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK 
        8.52        43.43        48.10        47.24        20.88        31.79 
TCGA-A1-A0SM TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U 
        7.96        19.20        18.21        82.16        73.84        22.06 
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CT 
       64.04        55.43       125.59        64.57       112.08        75.25 
TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EP 
       56.81        34.55        33.76        28.77       101.72       107.61 
TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST 
       79.76        74.40        37.05        24.72        24.16        99.19 
TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T5 
       44.88        44.28        17.52        17.13         8.38        17.46 
TCGA-A2-A0YC TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       32.55        14.50        18.61        19.33        14.63        31.73 
TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 
       23.47        36.79        22.45        19.20        19.56        16.47 
TCGA-A2-A259 TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
       52.47        17.19        18.15        91.92        10.59        20.88 
TCGA-A2-A3KD TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A4RW 
       39.65        14.07        49.48        38.40        34.98         7.30 
TCGA-A2-A4RX TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0D9 
        9.01         8.91        12.00         6.74        38.30        37.45 
TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A2KD 
       12.72        23.61        24.26        23.74        23.80        22.32 
TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SA 
       11.34        10.59        10.29        13.41        14.70        14.93 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VX TCGA-A8-A06O 
       12.10        10.72        11.05        10.29        10.42        13.02 
TCGA-A8-A079 TCGA-A8-A07G TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U 
        9.01        18.97         9.99        10.98         7.99         9.96 
TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C 
       28.04        18.05        13.02         0.99        23.08        19.99 
TCGA-A8-A08F TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X 
       18.05         9.99        31.00         0.99        93.04        33.99 
TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A 
       19.07        16.01        17.95        41.98         9.99         9.99 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09V 
       31.00        33.07        29.98        15.02        25.02        15.02 
TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E 
       14.01        12.00        19.04        38.04         0.95         2.37 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FG TCGA-AC-A2FK 
        2.66         1.48        38.20        40.57        36.99        38.79 
TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3OD TCGA-AC-A3TN TCGA-AC-A3W5 
       50.70         0.92         2.27        14.83         1.12         1.81 
TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IW 
        1.68         1.55         1.32         0.07         1.12         0.69 
TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A046 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D 
        0.33         0.33         0.33         2.96         1.78         1.71 
TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FJ 
        6.51         0.16         0.33         0.33         0.33         7.96 
TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FX 
        7.59         7.17         6.28         6.02         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XP TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03M 
        0.33         0.33         0.30         5.33         5.59        47.84 
TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 
       81.63        68.75        47.87        59.05        29.13        32.78 
TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF 
       17.65        24.16        37.48        50.86        76.77        21.37 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 
       38.53        62.04        55.33        71.80       102.58        99.25 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12F 
       93.70        94.59        96.10        77.56        64.04        48.36 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H 
       41.62        28.37        14.73        70.39        17.79        24.79 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AR-A0TP 
       26.93       130.09         5.65        15.62        13.22        82.88 
TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0U1 TCGA-AR-A0U4 
       49.32        37.41        29.75        64.83        70.16        55.36 
TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AO TCGA-AR-A1AS TCGA-AR-A1AU 
       61.84        51.25        48.82        43.56        40.83        46.32 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24Q TCGA-AR-A24T 
       35.24        36.26        65.46        68.19        66.05        53.26 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A2LE TCGA-AR-A2LH 
       53.36        54.18        45.17        39.85       128.65        20.25 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM 
        7.36        40.04        17.10        16.96        20.38        54.74 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA 
       10.59        77.62       143.38       149.59        12.13       220.90 
TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM 
      129.57        50.70        65.72       176.98        18.77       126.12 
TCGA-B6-A0IP TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RQ TCGA-B6-A0RS 
      110.93       189.01       234.28        78.02       140.48       100.70 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV 
       89.46       131.21       157.41        97.48       188.68        79.63 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      129.57       129.70       186.48        28.27        68.94        58.88 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 
       43.59       101.52        73.51       170.17        85.35        54.28 
TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B2 TCGA-BH-A0BC TCGA-BH-A0BD 
       38.79        20.45        28.50        40.83        32.02        18.21 
TCGA-BH-A0BG TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BS 
       24.85        61.68        35.67        48.69        27.19        53.95 
TCGA-BH-A0BW TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG 
       11.67        41.75        44.02        45.83        31.17        23.44 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DS 
       22.13        13.91        48.23        17.26        15.65         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 
       38.47        45.17        47.41        16.27        15.68        14.30 
TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0H0 
       44.81        46.19        32.65        31.00        24.43        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       37.78        35.51        24.56        20.38         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HW TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A18G 
       13.61        51.32        50.79         5.59        24.95         2.01 
TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U 
       37.74        30.28        55.63        37.55        66.05        51.39 
TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1F0 TCGA-BH-A1F2 
       69.93        91.99        12.00        55.69        25.81        31.53 
TCGA-BH-A1F6 TCGA-BH-A1FB TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
       97.48       120.62        74.73       122.89        36.92        63.35 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 
      144.59        72.07         6.90         0.72        38.60        57.83 
TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12L 
       10.65         6.44        20.12       109.28         8.94        11.93 
TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12V TCGA-C8-A12W 
       11.77        12.66        11.77         0.07        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 
       12.66         3.12         1.78         0.69         0.62         3.85 
TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A26V TCGA-C8-A26W 
       12.33        10.92        11.34         0.16         0.30         0.23 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B 
        0.36         0.43         9.67         0.03         0.03         0.99 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A147 
        0.03         0.23        13.25        20.58        13.97        19.20 
TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JH 
       17.49        16.50        15.78        18.90        12.03        14.01 
TCGA-D8-A1JI TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU 
       18.97        20.12        20.09        12.20        13.32        14.70 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1XC TCGA-D8-A1XF TCGA-D8-A1XG 
       17.79        16.73        25.74         2.66        15.22        14.73 
TCGA-D8-A1XJ TCGA-D8-A1XL TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1XV TCGA-D8-A1XW 
       21.83        19.92        16.41        16.31        15.16        12.66 
TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H 
       16.54        15.32        17.42        16.04        13.45        13.05 
TCGA-D8-A27K TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27V 
        9.44        13.48         4.80         0.76        10.09        12.53 
TCGA-D8-A27W TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A108 TCGA-E2-A10B TCGA-E2-A10E 
       12.26        18.51         7.33        27.52        37.51        28.44 
TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14X TCGA-E2-A14Y 
       47.15        40.96        33.17        43.33        31.96        28.60 
TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15D 
       27.12        19.43        21.04        23.87        14.79        17.29 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A1B0 
       19.40         9.04        20.58        17.06        14.07        53.62 
TCGA-E2-A1B4 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IG TCGA-E2-A1IK 
       29.95        28.50        16.47        38.30        32.78        22.65 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB 
       11.08        54.18        27.42        19.66        24.59        40.47 
TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX 
       18.87       106.75       102.61        43.04         5.52        15.72 
TCGA-E2-A570 TCGA-E9-A1N4 TCGA-E9-A1N6 TCGA-E9-A1NC TCGA-E9-A1QZ TCGA-E9-A1R0 
       18.05        19.20        13.48        39.55        11.90        14.30 
TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A227 
        6.12         1.38        21.21        34.59        34.13         0.79 
TCGA-E9-A228 TCGA-E9-A22B TCGA-E9-A22G TCGA-E9-A243 TCGA-E9-A245 TCGA-E9-A295 
       12.53        22.75        23.51        17.06         0.85         0.72 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-EW-A1IW TCGA-EW-A1IY 
       17.75         0.76        18.41         0.62        12.20         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OZ 
       18.21        16.57        15.68        25.94        29.95        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P7 TCGA-EW-A1PB TCGA-EW-A1PD 
       41.13        39.78        29.82        30.08        19.99        13.94 
TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FW 
       10.52        14.43        34.55        55.00        52.73        22.09 
TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 
       21.27        17.49        10.59         7.40       109.87        59.57 
TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DM TCGA-GM-A2DN 
       43.04        42.71        42.28        61.91        76.64        77.33 
TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A5PV TCGA-GM-A5PX 
       53.36       110.50        32.28        69.30        13.55        18.12 
TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A50Y TCGA-LL-A5YL 
        6.67         4.60         0.66         2.99         6.90         5.56 
TCGA-LL-A5YM TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z 
        4.70         3.25         2.63         3.88         4.14         4.50 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
        4.50         5.59         6.21         2.79         2.10        12.66 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5S0 
        7.53        44.61        27.65        16.87        14.10         9.80 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P 
       14.76        23.70        54.51        18.21         7.23         4.44 
TCGA-W8-A86G 
        5.29 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.03               0.03 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            211.56             234.28 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             22.26              20.38 
[1] "0.0 - 211.6 (22.3)" "0.0 - 234.3 (20.4)"
[1] "hr=" "1.3"
D79V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  22Q LOSS MUTATED        34       33        2        3       139       109
  22Q LOSS WILD-TYPE      46       44        7        6       196       115
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  22Q LOSS MUTATED           1         63         11         32        6
  22Q LOSS WILD-TYPE         1         75         16         27       11
                    vv
clus                 STAGE TIS STAGE X
  22Q LOSS MUTATED           0       7
  22Q LOSS WILD-TYPE         1       9
D79V3, multiclass
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                  34                 46
  STAGE IA                 33                 44
  STAGE IB                  2                  7
  STAGE II                  3                  6
  STAGE IIA               139                196
  STAGE IIB               109                115
  STAGE III                 1                  1
  STAGE IIIA               63                 75
  STAGE IIIB               11                 16
  STAGE IIIC               32                 27
  STAGE IV                  6                 11
  STAGE TIS                 0                  1
  STAGE X                   7                  9
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  22Q LOSS MUTATED   109 268  47  15
  22Q LOSS WILD-TYPE 149 313  70  21
D79V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1              109                149
  T2              268                313
  T3               47                 70
  T4               15                 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                  N0  N1  N2  N3
  22Q LOSS MUTATED   199 150  50  38
  22Q LOSS WILD-TYPE 269 180  61  32
D79V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0              199                269
  N1              150                180
  N2               50                 61
  N3               38                 32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  22Q LOSS MUTATED          1 382   6  51
  22Q LOSS WILD-TYPE        1 463  11  80
D79V6, multiclass
          clus
vv         22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CM0 (I+)                1                  1
  M0                    382                463
  M1                      6                 11
  MX                     51                 80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED   434   6
  22Q LOSS WILD-TYPE 550   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED    434    6
  22Q LOSS WILD-TYPE  550    5
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE              434                550
  MALE                  6                  5
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  22Q LOSS MUTATED                            0                           335
  22Q LOSS WILD-TYPE                          1                           400
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  22Q LOSS MUTATED                               73                   2
  22Q LOSS WILD-TYPE                             93                   3
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  22Q LOSS MUTATED                                 17                  1
  22Q LOSS WILD-TYPE                               12                 13
                    vv
clus                 OTHER  SPECIFY
  22Q LOSS MUTATED               11
  22Q LOSS WILD-TYPE             33
D79V8, multiclass
                                  clus
vv                                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 335                400
  INFILTRATING LOBULAR CARCINOMA                 73                 93
  MEDULLARY CARCINOMA                             2                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)               17                 12
  MUCINOUS CARCINOMA                              1                 13
  OTHER  SPECIFY                                 11                 33
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V9, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED   148 292
  22Q LOSS WILD-TYPE 134 421
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED    148  292
  22Q LOSS WILD-TYPE  134  421
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO               148                134
  YES              292                421
[1] 2 2
[1] FALSE
D79V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q LOSS MUTATED                                  0    20
  22Q LOSS WILD-TYPE                                1    36
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED                          58   321
  22Q LOSS WILD-TYPE                        79   387
D79V11, multiclass
                                  clus
vv                                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          20                 36
  BLACK OR AFRICAN AMERICAN                      58                 79
  WHITE                                         321                387
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V12, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    15 347
  22Q LOSS WILD-TYPE  21 449
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     15  347
  22Q LOSS WILD-TYPE   21  449
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   15                 21
  NOT HISPANIC OR LATINO              347                449
[1] 2 2
[1] FALSE

Clustering(80) Variable = XQ LOSS MUTATION ANALYSIS
D80V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED   141  19
  XQ LOSS WILD-TYPE 719  95
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              160               814 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               19                95 
$`XQ LOSS MUTATED`
TCGA-A1-A0SH TCGA-A1-A0SK TCGA-A2-A04R TCGA-A2-A04U TCGA-A2-A0CS TCGA-A2-A0CT 
       47.24        31.79        82.16        22.06        75.55        75.25 
TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D4 TCGA-A2-A0EO TCGA-A2-A0SV 
       64.04        21.14        34.55        25.22        80.28        27.12 
TCGA-A2-A0T0 TCGA-A2-A3XT TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CJ TCGA-A7-A0DA 
       17.52        83.01         3.42        35.31        30.61        35.67 
TCGA-A7-A3IZ TCGA-A7-A3J1 TCGA-A7-A4SA TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A6VW 
       10.59        11.28        14.93        17.92        14.73         9.37 
TCGA-A7-A6VY TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A084 
        8.75        41.06        29.03        26.01        17.03        15.06 
TCGA-A8-A085 TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A099 TCGA-A8-A09N 
       36.95        12.00         9.99        31.00         9.99         1.02 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A2BM TCGA-AN-A041 TCGA-AN-A0AJ TCGA-AN-A0AK 
       17.03        38.04        38.20         0.23         8.02         7.36 
TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0FD TCGA-AN-A0FJ TCGA-AN-A0FV TCGA-AN-A0XL 
        0.16         0.33         6.44         7.96         0.33         0.33 
TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AO-A03R TCGA-AO-A0J3 TCGA-AO-A0JA TCGA-AO-A0JE 
        0.33         0.33        68.75        21.40        21.53        76.77 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A124 TCGA-AO-A1KQ TCGA-AQ-A1H2 TCGA-AQ-A54N 
       38.53        62.04       102.58        61.87        15.62         2.56 
TCGA-AR-A0TR TCGA-AR-A0TV TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U2 TCGA-AR-A0U3 
        5.26        29.75        55.86        76.14        83.87        76.18 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A251 TCGA-AR-A256 
       55.36        75.55        20.22       109.58        45.17        93.83 
TCGA-AR-A2LO TCGA-AR-A2LR TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IQ 
       20.81        20.38        65.72       146.50        18.77       140.88 
TCGA-B6-A0RG TCGA-B6-A0RL TCGA-B6-A0WX TCGA-B6-A1KN TCGA-BH-A0B0 TCGA-BH-A0BV 
       68.45        81.17        21.47       139.17        46.95        49.94 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DX TCGA-BH-A0GZ TCGA-BH-A0HA TCGA-BH-A0HW 
       23.44        38.01        47.41        10.78        52.96        51.32 
TCGA-BH-A0W3 TCGA-BH-A1ES TCGA-BH-A1EY TCGA-BH-A1F8 TCGA-BH-A1FD TCGA-BH-A1FM 
       23.93       113.82        17.69        24.66        33.17        45.63 
TCGA-BH-A42T TCGA-C8-A12Q TCGA-C8-A12X TCGA-C8-A135 TCGA-C8-A1HF TCGA-C8-A1HJ 
        0.99         0.07        12.66         0.62        10.92         0.16 
TCGA-C8-A1HL TCGA-C8-A26V TCGA-C8-A26W TCGA-D8-A13Y TCGA-D8-A147 TCGA-D8-A1J9 
       10.42         0.30         0.23        11.90        19.20        17.49 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JL TCGA-D8-A1JM 
       16.50        18.71        18.97        20.09        20.09        19.40 
TCGA-D8-A1JP TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XJ TCGA-D8-A1XO TCGA-D8-A1Y3 
       21.01        23.90        27.58        21.83         7.96        14.14 
TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27T TCGA-E2-A152 TCGA-E2-A155 TCGA-E2-A158 
       16.04        13.05        13.08        27.12        21.04        14.79 
TCGA-E2-A15H TCGA-E2-A15K TCGA-E2-A15P TCGA-E2-A15S TCGA-E2-A1IE TCGA-E2-A1L7 
       12.92         9.04        19.56        14.07        38.30        27.42 
TCGA-E2-A1L8 TCGA-E2-A1LH TCGA-E9-A1N4 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA 
       39.62       106.75        19.20        12.00        13.12        36.56 
TCGA-E9-A1NC TCGA-E9-A1NF TCGA-E9-A1R4 TCGA-E9-A1RG TCGA-E9-A22G TCGA-E9-A247 
       39.55        20.05         6.12        21.27        23.51        27.22 
TCGA-E9-A5UO TCGA-EW-A1J1 TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1OZ TCGA-EW-A1PA 
        0.23        18.90        28.77        22.82        40.41        18.90 
TCGA-EW-A1PD TCGA-GM-A2DH TCGA-GM-A3XL TCGA-JL-A3YX TCGA-LL-A6FR TCGA-LL-A7T0 
       13.94        42.28        69.30        11.57         3.88         3.22 
TCGA-LQ-A4E4 TCGA-OL-A5DA TCGA-OL-A5RW TCGA-OL-A5RZ 
       15.91        44.61        26.20        10.29 

$`XQ LOSS WILD-TYPE`
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SI 
        8.52        14.37        43.43        48.10        14.27        20.88 
TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ 
       13.68         7.96        39.32        28.01        19.20        18.21 
TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04T TCGA-A2-A04V TCGA-A2-A04W 
      104.81        18.02        41.95        73.84        63.12        64.04 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO 
       55.43        36.13       125.59        64.57        24.79       112.08 
TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CX 
       92.48        88.60       107.93         5.19        63.45        56.81 
TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0EQ 
       33.76        28.77       101.72        89.36       107.61        79.76 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW 
       74.40        37.05        35.05        34.29        31.82        29.75 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SX 
       24.72        24.16        99.19        54.64        44.88        50.43 
TCGA-A2-A0SY TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 
       44.28        17.13         8.38        18.71        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF 
       18.90        20.75        32.55        25.28        18.21        15.42 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL 
       21.90        21.67        14.50        18.61        19.33        14.63 
TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ 
       31.73        23.77        23.47        17.36        36.79        22.45 
TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A 
       20.25        19.20        19.56        16.47        52.47       107.70 
TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
       16.31        17.19        18.15        91.92        10.59        20.88 
TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX 
       39.65        33.93        29.98        14.07        49.48        38.40 
TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY 
       34.98        31.99        38.37         7.30         9.01         8.81 
TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH 
        8.91        12.00         6.74        38.30        34.29        35.47 
TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G 
       37.45        33.11        31.73        10.72        12.72        23.61 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I 
       29.56        31.36        24.26        23.74        23.80        21.73 
TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 
       20.61        22.32        11.34        10.29        13.41        14.70 
TCGA-A7-A426 TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A5ZV TCGA-A7-A5ZW 
       11.97        13.74        14.50        21.17        12.10        10.72 
TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q 
       11.05        10.29        10.42        13.02        13.02         1.02 
TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B 
       17.98        31.00         1.02        53.98         9.01        33.01 
TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
       19.99        18.97        18.97        14.01        12.00        17.03 
TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W 
        9.99        10.98         8.98         7.99         9.96         9.99 
TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C 
       28.04        18.05        13.02         0.99        23.08        19.99 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S 
       18.05        19.96        37.05        31.00         0.99        19.07 
TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 
       93.04        33.99        40.01        19.07        16.01        17.95 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D 
       41.98        12.00         9.99        12.00         1.02        13.02 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R 
       31.00        33.07        29.98        15.02        25.02         8.98 
TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 
       19.04        15.02         0.99        14.01        12.00        19.04 
TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-AC-A23C TCGA-AC-A23E 
       13.02        21.04         0.99        13.02         0.95         2.37 
TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2FB TCGA-AC-A2FF 
       10.85         2.66         1.48        38.53        40.57        55.43 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI 
       36.99        38.79        26.04        50.70         1.02         0.92 
TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN 
        2.27         0.99         0.69        14.83         9.40         1.12 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V 
        1.81         1.68         1.55         1.32         1.55         0.07 
TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A8OP 
        1.12         1.81         1.18         0.69         0.43         1.74 
TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C 
        0.33         0.33         0.33         0.62         2.96         1.78 
TCGA-AN-A04D TCGA-AN-A0AL TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FF TCGA-AN-A0FK 
        1.71         6.51         0.33         0.33         4.64         7.00 
TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FX 
        7.59         7.17         6.28         6.02         0.36         0.33 
TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR 
        0.33         0.33         0.33        12.33         0.30         0.33 
TCGA-AN-A0XS TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N 
        0.33         5.33         5.59        80.28        47.84        66.77 
TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 
       81.63        84.69        47.87        59.05        29.13        32.78 
TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 
       17.65        24.16        37.48        20.32        22.36        53.03 
TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JL 
       50.70        50.86        72.00        21.37        26.24        55.33 
TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A 
       71.80        99.25        93.70        94.59        96.10        90.58 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
       77.56        64.04        57.30        48.36        41.62        28.37 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H 
       14.73        82.62        70.39         0.53        17.79        24.79 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AQ-A7U7 
       26.93       130.09         5.65        13.22        21.86         9.99 
TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0TX 
       82.88        49.32        37.41        56.88        24.30        64.83 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL 
       65.36        70.16        61.84        52.77        51.25        48.82 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR 
       62.56        43.73        43.56        39.98        43.07        17.23 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24K 
       40.83        46.32        42.58        35.24        36.26        50.89 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q 
       73.02        65.46        68.19        65.69         0.85        66.05 
TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W 
       57.40        62.07        53.26        53.36        54.18        50.96 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 
       48.16        51.75        56.15        40.64        39.85        34.82 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN 
      128.65        20.25        42.87         7.36        40.04        17.10 
TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       16.96        54.74        16.04        20.45        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC 
      143.38       149.59        12.13       220.90       129.57        50.70 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP 
      112.37       176.98       126.12        84.59       110.14       110.93 
TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
      211.56       189.01       234.28        78.02       172.96       162.05 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV 
      102.77       140.48       100.70        89.46       131.21       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WY TCGA-B6-A0WZ 
       97.48       188.68        79.63        17.98       113.79       129.57 
TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC 
      129.70       186.48        28.27        68.94        58.88        43.59 
TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 
      101.52        73.51       170.17        85.35        54.28        49.94 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY 
       82.88        55.00        24.53        38.79        20.45        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 
       28.50        40.83        39.55        39.16        48.36        56.94 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       56.98        51.68        37.22        32.02        18.21        25.71 
TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP 
       24.85        21.70        44.05        61.68        35.67        48.69 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BW TCGA-BH-A0BZ 
       27.19        53.69        53.95        45.57        11.67        49.05 
TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE 
       41.75        44.02        48.13        42.90        45.83        31.17 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ 
       22.13        13.91        48.23        17.26        15.65         3.22 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 
        2.56        38.47        45.17        16.27         4.41        15.68 
TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB 
       14.30         9.63        44.81        46.19        32.65        24.49 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       31.00        24.43        30.35        15.16        37.78        35.51 
TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK 
       24.56        23.08        41.00        26.50        20.38         5.85 
TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0HY 
        2.50        13.61        36.85        12.89        27.25        50.79 
TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F 
        5.59        24.95        42.35        44.81        23.05         8.81 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M 
        2.01         7.23        20.12        90.84        26.66        72.56 
TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T 
       37.74        30.28        55.63        37.55        66.05         7.36 
TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1EU 
       51.39        51.16        69.93        91.99        82.85        42.28 
TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 
       12.00        55.69        49.58        25.81        31.53        89.16 
TCGA-BH-A1F6 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH 
       97.48       120.62       114.15        74.73       122.89        36.92 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 
       63.35        55.00        72.07       144.59        72.07         6.90 
TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O 
        0.72        38.60        83.31        57.83       130.16        10.65 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12L TCGA-C8-A12M 
        6.44        20.12       109.28         8.94        11.93        11.77 
TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W 
       11.77        12.66        11.77        12.66        12.66        12.66 
TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A138 
        3.12         1.78         1.45         0.69         3.85         3.75 
TCGA-C8-A1HE TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN 
       12.33        11.34        11.34        12.03         2.30         3.25 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
        0.36         0.43         8.28         9.67         0.03         0.03 
TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Z 
        0.03        12.20         0.99         0.03         0.23        20.88 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 
       13.25        20.58        13.97        14.17        13.48        21.14 
TCGA-D8-A1J8 TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG 
       14.17        15.78        18.15        18.90        12.03        12.03 
TCGA-D8-A1JH TCGA-D8-A1JK TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU 
       14.01        20.12        20.38        12.20        13.32        14.70 
TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1XB TCGA-D8-A1XC 
       18.58        17.79        16.73        25.74        18.15         2.66 
TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM 
       17.16        15.22        14.73        14.50        19.92        17.69 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV 
       16.41        15.85        16.31         6.35        12.99        15.16 
TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 
       12.66        16.54        15.32        15.52         3.81        14.24 
TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M 
       17.42        13.45        14.43         9.44        16.41        13.48 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 
        4.80         0.76        10.09        12.53        12.26        14.50 
TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 
       18.51         7.33        43.00        34.42        27.52        46.59 
TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N 
       40.41        37.51        40.11        28.44        28.87        47.15 
TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T 
       44.68        40.96        38.24        38.60        33.17        33.30 
TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z 
       43.33        34.26        32.02        31.96        28.60        17.03 
TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A156 TCGA-E2-A159 TCGA-E2-A15A 
       25.41        23.24        19.43        23.87        25.05        23.34 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15I 
       22.82        17.29        20.71        21.63        18.21        17.42 
TCGA-E2-A15J TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15R TCGA-E2-A15T 
       19.40        20.58         7.73        13.02        17.06        14.99 
TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       60.53        53.62        53.03        29.95        32.35        28.50 
TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II 
       16.47        17.10        37.41        32.78        33.73        33.70 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       28.44        22.65         3.88        22.19        20.98        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG 
       54.18        19.66        24.59        40.47        28.90        18.87 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX 
      102.61         8.75        43.04        16.93         5.52        15.72 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N5 TCGA-E9-A1N6 
        7.20        18.05        22.26        19.89        36.82        13.48 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 
       12.59        35.77        21.57         9.86        11.90        14.30 
TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA 
        0.62         2.10         1.38         2.76        21.21        32.09 
TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RH 
       20.81        40.24         0.66        34.65         6.58        34.59 
TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       35.64        34.13         0.79        12.53        13.32        39.09 
TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A245 
       22.75        12.89        24.10        17.06         0.69         0.85 
TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT 
        1.94         0.95        12.56         0.72        17.75         0.76 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FK 
       26.07        18.41         0.62        15.72         0.23         0.39 
TCGA-E9-A5FL TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
        0.26        15.39        12.20        39.72         8.48        18.21 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY 
       13.25        16.57        15.68        25.94        29.95        29.85 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 
       41.13        39.78        52.96        29.82        23.11        18.48 
TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PE TCGA-EW-A1PF 
       30.08         7.86        19.99         6.15        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW 
       34.55        19.96        55.00        52.73        25.91        22.09 
TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 
       21.27        17.49        10.16        10.59         7.40       109.87 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF 
       59.57       194.27        53.13        53.52        43.04        42.71 
TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO 
       61.91        62.33        90.84        76.64        77.33        53.36 
TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV 
      110.50        38.20        32.28        53.95        57.63        13.55 
TCGA-GM-A5PX TCGA-JL-A3YW TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 
       18.12        11.84         8.28         6.67         4.60         0.66 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN 
        2.99         3.58         6.90         5.56         4.70         3.65 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 
        3.19         3.25         2.63         4.14         4.50         4.50 
TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 
        5.59         6.21         2.79         2.10        12.66        46.55 
TCGA-OL-A5D8 TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5S0 
        7.53        27.65        24.10        16.87        14.10         9.80 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       14.76        23.70        54.51        33.90        31.07        18.21 
TCGA-OL-A66O TCGA-OL-A66P TCGA-S3-A6ZG TCGA-W8-A86G 
        7.23         4.44         6.81         5.29 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.07              0.03 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           146.50            234.28 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           21.090            21.685 
[1] "0.1 - 146.5 (21.1)" "0.0 - 234.3 (21.7)"
[1] "hr=" "1.1"
D80V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XQ LOSS MUTATED        11       12        0        1        63        40
  XQ LOSS WILD-TYPE      69       65        9        8       272       184
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XQ LOSS MUTATED           0         20          4          5        4
  XQ LOSS WILD-TYPE         2        118         23         54       13
                   vv
clus                STAGE TIS STAGE X
  XQ LOSS MUTATED           1       3
  XQ LOSS WILD-TYPE         0      13
D80V3, multiclass
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                 11                69
  STAGE IA                12                65
  STAGE IB                 0                 9
  STAGE II                 1                 8
  STAGE IIA               63               272
  STAGE IIB               40               184
  STAGE III                0                 2
  STAGE IIIA              20               118
  STAGE IIIB               4                23
  STAGE IIIC               5                54
  STAGE IV                 4                13
  STAGE TIS                1                 0
  STAGE X                  3                13
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  XQ LOSS MUTATED    33 111  12   7
  XQ LOSS WILD-TYPE 225 470 105  29
D80V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1              33               225
  T2             111               470
  T3              12               105
  T4               7                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                 N0  N1  N2  N3
  XQ LOSS MUTATED    79  59  17   8
  XQ LOSS WILD-TYPE 389 271  94  62
D80V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0              79               389
  N1              59               271
  N2              17                94
  N3               8                62
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  XQ LOSS MUTATED          0 147   4  13
  XQ LOSS WILD-TYPE        2 698  13 118
D80V6, multiclass
          clus
vv         XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CM0 (I+)               0                 2
  M0                   147               698
  M1                     4                13
  MX                    13               118
[1] 4 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   161   3
  XQ LOSS WILD-TYPE 823   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED    161    3
  XQ LOSS WILD-TYPE  823    8
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE             161               823
  MALE                 3                 8
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  XQ LOSS MUTATED                            0                           134
  XQ LOSS WILD-TYPE                          1                           601
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  XQ LOSS MUTATED                               14                   0
  XQ LOSS WILD-TYPE                            152                   5
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  XQ LOSS MUTATED                                  7                  2
  XQ LOSS WILD-TYPE                               22                 12
                   vv
clus                OTHER  SPECIFY
  XQ LOSS MUTATED                7
  XQ LOSS WILD-TYPE             37
D80V8, multiclass
                                  clus
vv                                 XQ LOSS MUTATED XQ LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                134               601
  INFILTRATING LOBULAR CARCINOMA                14               152
  MEDULLARY CARCINOMA                            0                 5
  MIXED HISTOLOGY (PLEASE SPECIFY)               7                22
  MUCINOUS CARCINOMA                             2                12
  OTHER  SPECIFY                                 7                37
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V9, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    48 116
  XQ LOSS WILD-TYPE 234 597
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     48  116
  XQ LOSS WILD-TYPE  234  597
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               48               234
  YES             116               597
[1] 2 2
[1] FALSE
D80V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ LOSS MUTATED                                  0    12
  XQ LOSS WILD-TYPE                                1    44
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED                          27   109
  XQ LOSS WILD-TYPE                       110   599
D80V11, multiclass
                                  clus
vv                                 XQ LOSS MUTATED XQ LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         12                44
  BLACK OR AFRICAN AMERICAN                     27               110
  WHITE                                        109               599
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V12, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     6 133
  XQ LOSS WILD-TYPE  30 663
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      6  133
  XQ LOSS WILD-TYPE   30  663
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                30
  NOT HISPANIC OR LATINO             133               663
[1] 2 2
[1] FALSE
