[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/11541508/BRCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/BRCA-TP/11550288/transformed.cor.cli.txt"

nPatients in clinical file=1043, in cluster file=1079, common to both=1025
[1]   80 1025
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              194               831 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              194               831 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              669               356 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              669               356 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              116               909 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              116               909 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               71               954 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               71               954 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              132               893 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              132               893 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              204               821 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              204               821 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               75               950 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               75               950 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               72               953 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               72               953 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              298               727 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              298               727 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              200               825 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              200               825 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              199               826 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              199               826 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              141               884 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              141               884 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              293               732 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              293               732 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              250               775 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              250               775 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              276               749 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              276               749 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              506               519 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              506               519 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
              136               889 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
              136               889 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              112               913 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              112               913 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               209                816 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               209                816 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               122                903 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               122                903 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
               131                894 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
               131                894 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                91                934 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                91                934 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               217                808 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               217                808 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               184                841 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               184                841 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                87                938 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                87                938 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               137                888 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               137                888 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                84                941 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                84                941 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               450                575 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               450                575 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               135                890 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               135                890 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               102                923 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               102                923 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               208                817 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               208                817 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               168                857 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               168                857 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
               143                882 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
               143                882 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               181                844 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               181                844 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               214                811 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               214                811 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               397                628 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               397                628 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               431                594 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               431                594 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               191                834 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               191                834 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                97                928 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                97                928 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              137               888 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              137               888 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              233               792 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              233               792 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               49               976 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               49               976 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
              172               853 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
              172               853 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
              199               826 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
              199               826 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              176               849 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              176               849 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               98               927 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               98               927 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              335               690 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              335               690 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              295               730 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              295               730 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              135               890 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              135               890 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              216               809 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              216               809 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              175               850 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              175               850 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              260               765 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              260               765 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
              108               917 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
              108               917 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
              116               909 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
              116               909 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              377               648 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              377               648 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               85               940 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               85               940 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              298               727 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              298               727 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              272               753 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              272               753 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               162                863 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               162                863 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               219                806 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               219                806 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               266                759 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               266                759 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               353                672 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               353                672 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
               144                881 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
               144                881 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
               123                902 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
               123                902 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               415                610 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               415                610 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               250                775 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               250                775 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               303                722 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               303                722 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               163                862 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               163                862 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               559                466 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               559                466 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               546                479 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               546                479 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
               258                767 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
               258                767 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               304                721 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               304                721 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               304                721 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               304                721 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               182                843 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               182                843 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               152                873 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               152                873 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                90                935 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                90                935 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                52                973 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                52                973 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               170                855 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               170                855 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               454                571 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               454                571 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              171               854 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              171               854 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "HISTOLOGICALTYPE"                      
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "NUMBER.OF.LYMPH.NODES"                 
[18] "RACE"                                  
[19] "ETHNICITY"                             
[20] "BATCHNUMBER"                           

Input Data has 20 rows and 1025 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
          12          259          437         1321         1463          434 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN 
        1437          635          416           NA          242         1196 
TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q 
         852          584          554         3188           NA         1276 
TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X 
        2499         2246          671           NA         1948         1686 
TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
        1099         4159         1964           NA         3409         2813 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV 
        2695         3283         2298         2289           NA         1930 
TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 
        1948         1728          643         1051         1027          875 
TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ 
         767         3094         2718         2442         3273         2426 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW 
        2263         1127         1066         1043          968          905 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW 
         752          735         3017         1662           NA           NA 
TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 
        1534         1347          533          521           NA          569 
TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD 
         624          531          575          631          990          769 
TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ 
         554          469          666          659          441          566 
TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW 
         588         1474          965           NA          714          528 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 
        1119          683          616          584          595          501 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
        1596         3276          496          523          552         2796 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU 
         322          635         1206           NA         2525           NA 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 
         996         1505         1168         1064          973         1167 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 
         222          742          648          706          820          643 
TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ 
         666         1165         1074         1043         1079          931 
TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F 
        1139         1085         1007          965          326          387 
TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H 
         718          899          954          738          722          724 
TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 
         661          627          679          345          322          313 
TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB 
         343          408          447          364          454          418 
TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW 
         441          644          545          448          368          326 
TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06N 
         336          313          285          317          266           NA 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U 
         396          396           31          547         1614           NA 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 
          NA          791           31          518         1642          274 
TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J 
        1308          608          577          577          426          365 
TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U 
         518          304          334          273          243          760 
TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A081 TCGA-A8-A082 TCGA-A8-A083 TCGA-A8-A084 
         304          853           NA          549           NA          458 
TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F 
        1124          396           30         1156          881         1004 
TCGA-A8-A08G TCGA-A8-A08H TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O 
         607           NA          365           NA           NA          943 
TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z 
         943           30         1004         2830         1308         1217 
TCGA-A8-A090 TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A094 TCGA-A8-A095 
          NA         1004          942          546           NA         1277 
TCGA-A8-A096 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C 
          NA          365          304          304          365           31 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09G TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M 
        1522         1492           NA         1371          912         1006 
TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
          31          761          273          579          457           30 
TCGA-A8-A09X TCGA-A8-A09Z TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 
          NA           NA          365          579          396          640 
TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E 
          30          396          518         1157           29           72 
TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB 
         330           81           45         1172         1162         1234 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH 
        1686         1125         1180           NA         1542           31 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
          28           69           30           21          451          675 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS 
          34          504          602          707          754           47 
TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX 
           2           34           55           36           21           13 
TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y 
          51           53           34           40           10           10 
TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D 
           7           10           19           90           54           52 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS 
         244          224          198            5           10           10 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL 
          10          196          141          242          213          231 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX 
         218          191          183           10           11           10 
TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP 
          10           10           10           10          375            9 
TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW 
          10           10           10           10          162          170 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R 
        2442         1455         2031           NA         2576         2091 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 
        1456           NA          886          997          651         1587 
TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA 
         735         1140          618          680         1613          655 
TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG 
        1542         1547         2190         2335          650          798 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 
        1528         1887         1683         2184         3120         3019 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D 
        3307         3248         2923         2755         2359         1948 
TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
        1743         1471         1266          863          448         2513 
TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J 
        1882         2141           16          541          754          819 
TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O 
        3957           NA          475          989           78         1001 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT 
         304         3386         1500           NA         2275         2636 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 
         905         3009         1972           NA         2316         1988 
TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
        3101           NA         3468         2615         2298         1881 
TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO 
        1605         1559         1485         1903         1330         1325 
TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
        1216         1310           NA         1150         2318         1864 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L 
        1935         1890          615         3333         1548         2221 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R 
        2947         2388         2561           26         3088         2653 
TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X 
          NA         2312         1623         2596         1550         2548 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 
        2403         1708         2387         2226         2213         1792 
TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL 
          NA         3913           NA         1912         1304          224 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM 
        1218         1161         1198         1233          620         1665 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 
         488          622           NA           NA         4361         4550 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG 
          NA         6719           NA           NA           NA           NA 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO 
          NA         5383           NA         3836           NA         3350 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
        3374         4285         6435         2082         5749         7126 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ 
          NA           NA         5261         4929           NA           NA 
TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT 
          NA         2721         3991         4788           NA         5739 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 
          NA          547           NA           NA         3941           NA 
TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF 
        5672           NA           NA           NA         1326         3088 
TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 
        2236         4233         5176         2596         1651         1519 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY 
        3152         1673          746         1180          622          777 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 
         867         1428         1242         1203         1191         1471 
TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
        1732         1733         1572         1132          974          554 
TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO 
         782          756          660         1340         1876         1085 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV 
        1481          827         1633         1641         1386         1519 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 
         355         1492         1270         1339         1464         1305 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
        1394          948          713         1156          673          423 
TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT 
        1467          525          476           98           78         1170 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 
        1374         1442          495          134          477          435 
TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE 
         293         1363         1405           NA          745          943 
TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
         743          923          328          461         1149         1080 
TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI 
         747          702         1247         1611          806          620 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW 
         178           76          414         1121          392         1561 
TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 
         829         1545          170          728          759         1288 
TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18H TCGA-BH-A18I 
        1363          701          268           61           NA          220 
TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 
          NA           NA          210           22           NA           NA 
TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T 
          NA           NA          324          196          612           30 
TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12K TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N 
        3324          272           NA          363          358          358 
TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12T TCGA-C8-A12U TCGA-C8-A12V 
         385          358            2           NA          385          385 
TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 
         385          385           NA           NA           95           54 
TCGA-C8-A132 TCGA-C8-A133 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 
          44           NA           21           19          117          114 
TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK 
         375          332          345          345            5          366 
TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W 
         317           70           99           NA            9            7 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
          11           13          252          294            1            1 
TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y 
           1          371           30            1            7          362 
TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 
         635          403          626          425          431          410 
TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
         643          584          431          532          502          569 
TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH 
         480          552          575          366          366          426 
TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN 
         577          611          612          611          590          620 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 
         639          371          405          447          565          541 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC 
         509          783          727          839          552           81 
TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL 
         522          463          448          664          441          606 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT 
         538          242          499          482          496          193 
TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 
         395          461          385          503          466          472 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G 
         116          433          430          530          488          409 
TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N 
         397          439          287          499          410          146 
TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 
          23          307          398          381          373          441 
TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 
         563          223         1308         1047          837         1417 
TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N 
        1229         1141         1220          865          878         1434 
TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T 
        1359         1246         1163         1174         1009         1013 
TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z 
        1318         1042          974          972          870          518 
TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 
         773          825          707          591          640          726 
TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E 
         450          762          710          694          526          630 
TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
         658          554          393          530          590          275 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
         626          235          396          595          519          428 
TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
         456         2329         1631         1613          911          984 
TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
         867          501          520         1165         1138          997 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN 
        1026         1025          865          689          118          675 
TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 
         638          337         1648          834         1205          598 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI 
         748         1231           NA          574         3247         3121 
TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z 
          NA         1309          515          168          478          219 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 
         931         1062          605          578          280           NA 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA 
         584         1120          410          365          399         1112 
TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH 
        1203          383         1088          610          656           NA 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 
         300          362          435           19           64          186 
TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC 
          42           84          645          976          633         1224 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI 
          20         1054          200          647         1052         1084 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
        1038           24          381          405         1189          692 
TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 
          NA          392          715          733          519           21 
TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
          26          828           59           29          747           22 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
         540           23          793          560           19          478 
TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP 
         375            7          447            8          420          438 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 
         468          371         1208          258          554          575 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW 
         403          504          477          875          789          694 
TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 
         911          908         1229         1251         1210         1611 
TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA 
         907          703          562          915           NA          575 
TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
         608          187          424          320          439         1051 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 
         607         1673         1604          788          672          647 
TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 
         532          309          322          225         3342           NA 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH 
        5909         1616         1628         1309         1299         1286 
TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO 
        1883         1896         2763         2331         2352         1623 
TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 
        3361         1162         1330         2108         2019         2191 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U 
         412          551          360          352          646          203 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
         124          140          266          290          348          333 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP 
         231          519          466          447          440          450 
TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 
         352           80          118          126          137          137 
TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
         170           98          189          224          849           85 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
          64          385         1416          973         1783          841 
TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 
        1062         1106          513          752          679          620 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
         812          714         1996         1021          945          792 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PL-A8LV TCGA-PL-A8LX 
         220          428          858          600            7            5 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z 
           8          120          502          207          263          322 
TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 
         241          169          259          218          209          119 
TCGA-W8-A86G TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
         161          292          278         3042         3195 
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=116,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=675,	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=7,	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=31,	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=58,	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 1025 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 
265 594 124  39 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
265 594 124  39 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
265 594 124  39 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
265 594 124  39 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
481 339 113  74 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
481 339 113  74 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2  N3 
481 339 113  74 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
481 339 113  74 
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=31, 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   174  19
  1P GAIN WILD-TYPE 712 100
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              193               812 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               19               100 
$`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-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T7 TCGA-A2-A0YI 
       33.76        44.88        17.13         8.38        20.75        14.50 
TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YM TCGA-A2-A1G0 TCGA-A2-A25B TCGA-A2-A3XS 
       18.61        19.33        31.73        20.25        16.31        33.93 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13F 
       31.99        38.37         7.30        35.67        31.73        12.72 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26I TCGA-A7-A3IZ TCGA-A7-A4SD 
       29.56        31.36        24.26        21.73        10.59        14.50 
TCGA-A7-A4SE TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A8-A06Z TCGA-A8-A07O 
       21.17        11.05        10.29         9.37         1.02         9.99 
TCGA-A8-A07U TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A09M TCGA-A8-A09R TCGA-AC-A2BM 
       24.99         0.99        43.00        33.07         8.98        38.20 
TCGA-AC-A2FG TCGA-AC-A2QJ TCGA-AC-A3W6 TCGA-AC-A5XS TCGA-AC-A62X TCGA-AC-A6IV 
       36.99         2.27        19.79         1.55         1.12         1.18 
TCGA-AC-A6IW TCGA-AC-A8OQ TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK 
        0.69         1.12         1.78         1.71         8.02         7.36 
TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FL TCGA-AN-A0FT TCGA-AN-A0FY TCGA-AO-A03R 
        0.16         0.33         7.59         6.02         0.33        68.75 
TCGA-AO-A0J2 TCGA-AO-A0JB TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A128 
       32.78        50.70        72.00        21.37        26.24       106.78 
TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A12F TCGA-AQ-A04L TCGA-AQ-A54O TCGA-AR-A0TS 
       96.10        64.04        48.36       130.09        32.91        74.79 
TCGA-AR-A0TT TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A24K TCGA-AR-A24X TCGA-AR-A252 
       86.66        61.84        51.25        50.89        83.77        73.18 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IE TCGA-B6-A0IH 
       40.54        20.38       143.38       149.59        65.72       112.37 
TCGA-B6-A0RU TCGA-B6-A0X1 TCGA-B6-A1KC TCGA-B6-A408 TCGA-BH-A0AW TCGA-BH-A0B3 
      131.21       186.48        43.59        49.94        20.45        39.55 
TCGA-BH-A0B7 TCGA-BH-A0BF TCGA-BH-A0BL TCGA-BH-A0BZ TCGA-BH-A0C3 TCGA-BH-A0C7 
       56.98        25.71        44.05        49.05        48.13        42.90 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DS TCGA-BH-A0DV TCGA-BH-A0E6 TCGA-BH-A0EE 
       13.91        48.23         2.56        45.17         9.63        31.00 
TCGA-BH-A0H9 TCGA-BH-A0HI TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1FN 
       41.00        20.38        25.81        31.53        97.48        72.07 
TCGA-BH-A1FU TCGA-BH-A203 TCGA-C8-A12M TCGA-C8-A12V TCGA-C8-A135 TCGA-C8-A1HM 
       72.07        38.60        11.77        12.66         0.62         2.30 
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-LD-A7W5 TCGA-LL-A441 
       43.04        42.71        42.28         6.67         4.08        11.44 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-OL-A5D7 TCGA-OL-A5RW 
       14.47        14.79         3.88         4.14        46.55        36.36 
TCGA-OL-A5S0 TCGA-OL-A6VO TCGA-PL-A8LV TCGA-PL-A8LZ TCGA-S3-A6ZG TCGA-S3-A6ZH 
       20.38        28.21         0.23         3.95         6.81         8.65 
TCGA-Z7-A8R6 
      105.04 

$`1P GAIN WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SH 
        0.39         8.52        14.37        43.43        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ 
       20.88        13.68        31.79        39.32        28.01        18.21 
TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04X 
      104.81        18.02        41.95        82.16        63.12        55.43 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
      136.73        64.57       112.08        92.48        88.60       107.93 
TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0D4 
       75.55        63.45        64.04        34.55        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-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-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC 
       17.52        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        48.46 
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 
       32.75        49.48        38.40        34.98        24.39        21.30 
TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE 
       23.21        26.96        21.14        21.90        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-A26G TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY 
       23.61        23.74        23.80        20.61        22.32        11.34 
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-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VX 
       13.74        17.92        14.73        12.10        10.72        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        53.06 
TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 
       29.03        31.00        26.01        17.03        53.98         9.01 
TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J 
       43.00        19.99        18.97        18.97        14.01        12.00 
TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07W TCGA-A8-A07Z 
       17.03        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        38.01 
TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L 
       28.96        33.01        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        33.01        93.04        40.01        33.01 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A 
       30.97        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        50.04        49.05        45.07        29.98 
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-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-A2FB TCGA-AC-A2FF TCGA-AC-A2FK TCGA-AC-A2FM 
        1.48        38.53        40.57        55.43        38.79        26.04 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD 
       50.70         1.02         0.92         0.99         0.69        14.83 
TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A62V 
       22.19         1.12        16.57        23.24        24.79         0.07 
TCGA-AC-A62Y TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AN-A03X 
        1.81         0.43         1.68         1.74         1.32         0.33 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A0AL 
        0.33         0.23         0.33         0.62         2.96         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-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FZ 
        7.17         6.28         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-A03P TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V 
       66.77        81.63        84.69        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        52.18        24.16        37.48        20.32        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JI TCGA-AO-A0JJ 
       53.03        21.53        50.86        76.77        50.24        62.04 
TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A12A 
       55.33        71.80       102.58        99.25       108.72        90.58 
TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       77.56        57.30        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-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A0TP 
        5.65        15.62        32.52         2.56         9.99       111.32 
TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
       49.32         5.26        29.75        98.93        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       101.95        83.87       114.02        85.97 
TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO 
       75.55        52.77        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        37.81        76.21        61.28 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M 
       63.62        62.14        20.22       109.58        73.02        96.89 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24T 
       78.51        84.20         0.85       101.52        87.22        76.01 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 
       53.36        85.35        50.96        79.00        56.15        78.48 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       72.76        58.92        93.83       128.65        20.25        62.86 
TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A5QM 
       42.87         7.36        40.04        38.17        39.39        54.74 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I9 TCGA-B6-A0IA 
       16.04        20.45        10.59        77.62        12.13       220.90 
TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IG TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM 
      129.57        50.70       146.50       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-A0RV TCGA-B6-A0WS 
      102.77       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-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KI 
      129.70        28.27        68.94        58.88       101.52        73.51 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A40B TCGA-B6-A40C 
      139.17       170.17        85.35        54.28       103.63        55.00 
TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 
       24.53        38.79        25.55        28.50        46.95        40.83 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC 
       39.16        48.36        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-A0BP 
       18.21        24.85        21.70        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-A0C0 TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH 
       41.75        44.02        45.83        31.17        23.44        38.01 
TCGA-BH-A0DI TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DT TCGA-BH-A0DX 
       22.13        17.26        15.65         3.22        38.47        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-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 
       32.65        24.49        24.43        30.35        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0HA TCGA-BH-A0HB 
       37.78        35.51        24.56        23.08        52.96        26.50 
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-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-A18N TCGA-BH-A18P TCGA-BH-A18Q 
       90.84        26.66        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-A1EN 
       37.55        66.05         7.36        51.39        51.16        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-A1F5 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC 
       49.58        17.69        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-A204 TCGA-BH-A208 
       45.63       144.59         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-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-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-A1HF TCGA-C8-A1HG 
        0.69         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-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-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-A147 TCGA-D8-A1J9 
       20.58        13.97        13.48        21.14        19.20        17.49 
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-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS 
       20.09        20.12        19.40        20.38        21.01        12.20 
TCGA-D8-A1JU TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XB 
       14.70        17.79        16.73        25.74        23.90        18.15 
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-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-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-A10B TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q 
       37.51        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-A14Y 
       33.17        33.30        43.33        34.26        32.02        28.60 
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-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R 
       19.40        20.58         7.73        13.02        19.56        17.06 
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-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-A1IN TCGA-E2-A1IO 
       33.73        28.44        22.65         3.88        22.19        20.98 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       11.08        54.18        19.66        24.59        40.47        28.90 
TCGA-E2-A1LG TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX 
       18.87         8.75        43.04        16.93         5.52        15.72 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU 
        7.20        30.61        34.92        19.89        19.00         9.21 
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        24.56         0.72        17.75         0.76        26.07 
TCGA-E9-A3Q9 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO 
       18.41        12.33         0.23        14.70         0.26        13.81 
TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
       14.40        15.39        12.20        39.72         8.48        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OX TCGA-EW-A1OY 
       18.90        13.25        15.68        28.77        29.95        29.85 
TCGA-EW-A1OZ TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 
       40.41        39.78        52.96        29.82        23.11        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-A3U0 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GM-A2DA TCGA-GM-A2DB 
       21.27        17.49        10.59         7.40       194.27        53.13 
TCGA-GM-A2DC TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       53.52        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        43.73        69.30        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U 
       72.03        13.55        18.12        11.84        11.57        21.24 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL 
        4.60         8.75         9.53        10.95         7.59        17.06 
TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Z TCGA-LL-A740 
       15.32        14.70        11.57         2.63         4.50         4.50 
TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
        5.59         3.22         6.21         7.36        27.91         2.79 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
        2.10        12.66        31.99        58.62        27.65        34.92 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J 
       16.87        24.72        22.32        26.70        23.47        65.62 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ 
       33.57        31.07        26.04         7.23        14.07        19.73 
TCGA-PL-A8LX TCGA-PL-A8LY TCGA-S3-A6ZF TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 
        0.16         0.26        16.50        10.59         7.92         5.56 
TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-W8-A86G TCGA-XX-A899 
        8.52         7.17         6.87         3.91         5.29         9.60 
TCGA-XX-A89A TCGA-Z7-A8R5 
        9.14       100.01 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.03              0.03 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           186.48            234.28 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            24.26             22.32 
[1] "0.0 - 186.5 (24.3)" "0.0 - 234.3 (22.3)"
[1] "hr=" "1.2"
D1V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1P GAIN MUTATED        14       15        1        0        70        47
  1P GAIN WILD-TYPE      69       65        8        5       272       187
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1P GAIN MUTATED           0         22          6         12        3
  1P GAIN WILD-TYPE         2        120         23         51       15
                   vv
clus                STAGE TIS STAGE X
  1P GAIN MUTATED           1       2
  1P GAIN WILD-TYPE         0      14
D1V3, multiclass
            clus
vv           1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                 14                69
  STAGE IA                15                65
  STAGE IB                 1                 8
  STAGE II                 0                 5
  STAGE IIA               70               272
  STAGE IIB               47               187
  STAGE III                0                 2
  STAGE IIIA              22               120
  STAGE IIIB               6                23
  STAGE IIIC              12                51
  STAGE IV                 3                15
  STAGE TIS                1                 0
  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
  1P GAIN MUTATED    37 126  21   9
  1P GAIN WILD-TYPE 228 468 103  30
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1              37               228
  T2             126               468
  T3              21               103
  T4               9                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
  1P GAIN MUTATED   101  61  18  13
  1P GAIN WILD-TYPE 380 278  95  61
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0             101               380
  N1              61               278
  N2              18                95
  N3              13                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
  1P GAIN MUTATED          0 160   3  31
  1P GAIN WILD-TYPE        5 694  16 116
D1V6, multiclass
          clus
vv         1P GAIN MUTATED 1P GAIN WILD-TYPE
  CM0 (I+)               0                 5
  M0                   160               694
  M1                     3                16
  MX                    31               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"
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED   192   2
  1P GAIN WILD-TYPE 822   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED    192    2
  1P GAIN WILD-TYPE  822    9
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE             192               822
  MALE                 2                 9
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  1P GAIN MUTATED                            0                           156
  1P GAIN WILD-TYPE                          1                           598
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  1P GAIN MUTATED                               19                   3
  1P GAIN WILD-TYPE                            156                   3
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  1P GAIN MUTATED                                  6                  1
  1P GAIN WILD-TYPE                               23                 14
                   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                156               598
  INFILTRATING LOBULAR CARCINOMA                19               156
  MEDULLARY CARCINOMA                            3                 3
  MIXED HISTOLOGY (PLEASE SPECIFY)               6                23
  MUCINOUS CARCINOMA                             1                14
  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    66 128
  1P GAIN WILD-TYPE 216 615
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     66  128
  1P GAIN WILD-TYPE  216  615
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO               66               216
  YES             128               615
[1] 2 2
[1] FALSE
D1V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P GAIN MUTATED                                  1     6
  1P GAIN WILD-TYPE                                0    50
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED                          39   138
  1P GAIN WILD-TYPE                       119   579
D1V11, multiclass
                                  clus
vv                                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          6                50
  BLACK OR AFRICAN AMERICAN                     39               119
  WHITE                                        138               579
[1] 4 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     5 162
  1P GAIN WILD-TYPE  31 664
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      5  162
  1P GAIN WILD-TYPE   31  664
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                31
  NOT HISPANIC OR LATINO             162               664
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED   589  71
  1Q GAIN WILD-TYPE 297  48
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              660               345 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               71                48 
$`1Q GAIN MUTATED`
TCGA-5T-A9QA TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SM 
        0.39        43.43        48.10        47.24        20.88         7.96 
TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04Q TCGA-A2-A04T TCGA-A2-A04U 
       39.32        19.20        18.21        41.95        73.84        22.06 
TCGA-A2-A04W TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CQ 
       64.04        36.13       136.73        24.79       112.08        88.60 
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-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-A0EQ TCGA-A2-A0ET TCGA-A2-A0EV TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SV 
       79.76        35.05        31.82        24.16        99.19        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-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK 
       25.28        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 
       48.46        31.73        23.77        23.47        22.45        20.25 
TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25E TCGA-A2-A3KC TCGA-A2-A3KD 
      107.70        16.31        17.19        91.92        20.88        39.65 
TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW 
       33.93        83.01        29.98        31.99        38.37         7.30 
TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A0DB 
       21.14        38.30        35.47        30.61        35.67        33.11 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F 
       31.73        10.72        12.72        29.56        31.36        24.26 
TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A3IZ TCGA-A7-A3J0 
       23.74        23.80        21.73        20.61        10.59        10.29 
TCGA-A7-A3J1 TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD 
       11.28        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-A8-A06O TCGA-A8-A06Q TCGA-A8-A06X 
       10.29         9.37        10.42        13.02         1.02        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        43.00        19.99 
TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U 
       18.97        18.97         9.99         8.98         7.99        24.99 
TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C 
        9.99        28.04        15.06         0.99        38.01        28.96 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X 
       33.01        19.96        31.00         0.99        93.04        43.00 
TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 
       40.01        30.97        17.95        41.98        12.00         9.99 
TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K 
        9.99        12.00         1.02        49.05        45.07        29.98 
TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X 
       33.07        25.02         8.98        15.02         0.99        14.01 
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-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK 
        0.95         2.37        10.85         2.66         1.48        38.53 
TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FG TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QI 
       38.20        40.57        36.99        26.04        50.70         0.92 
TCGA-AC-A2QJ TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 
        2.27         0.69        14.83         1.12        16.57        19.79 
TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW 
       24.79         1.55         1.12         1.81         1.18         0.69 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AN-A03X TCGA-AN-A03Y 
        0.43         1.68         1.74         1.12         0.33         0.33 
TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ 
        0.23         0.33         0.62         1.78         1.71         8.02 
TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN 
        7.36         0.16         0.33         7.00         7.59         7.17 
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-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR 
        0.33         0.33         0.33        12.33         0.30         0.33 
TCGA-AN-A0XW TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A0J2 TCGA-AO-A0J5 TCGA-AO-A0J7 
        5.59        81.63        68.75        32.78        24.16        20.32 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JD TCGA-AO-A0JF 
       22.36        53.03        21.53        50.70        72.00        21.37 
TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A128 
       26.24        62.04        55.33        71.80        99.25       106.78 
TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A12G 
       96.10        90.58        77.56        64.04        48.36        41.62 
TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04L TCGA-AQ-A0Y5 
       61.87        70.39        17.79        24.79       130.09         5.65 
TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TS 
       32.52        32.91         9.99       111.32         5.26        74.79 
TCGA-AR-A0TT TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL 
       86.66        75.55        61.84        52.77        51.25        48.82 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AV TCGA-AR-A1AW 
       62.56        43.73        39.98        37.81        61.28        63.62 
TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24P 
       20.22        50.89        73.02        96.89        78.51         0.85 
TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A252 
      101.52        87.22        50.96        83.77        56.15        73.18 
TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL 
       72.76        93.83       128.65        62.86        42.87         7.36 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM 
       40.04        38.17        39.39        40.54        20.38        54.74 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 
       16.04        20.45        77.62       143.38       149.59        12.13 
TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IN 
      220.90       129.57        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-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WT 
      172.96       162.05       102.77       100.70       131.21       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-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A401 
       58.88        43.59       101.52        73.51       170.17        85.35 
TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW 
       54.28        49.94       103.63        55.00        24.53        20.45 
TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B5 
       25.55        28.50        46.95        40.83        39.55        48.36 
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-A0BQ TCGA-BH-A0BS 
       21.70        44.05        61.68        35.67        27.19        53.95 
TCGA-BH-A0BT TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 
       45.57        49.05        41.75        44.02        48.13        42.90 
TCGA-BH-A0DD TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO 
       45.83        23.44        22.13        13.91        48.23        17.26 
TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0E1 
       15.65         2.56        38.47        45.17        47.41        15.68 
TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0H0 
        9.63        46.19        32.65        24.49        31.00        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       37.78        23.08        41.00        20.38         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0RX TCGA-BH-A0W3 
       13.61        36.85        12.89        27.25         5.59        23.93 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18P TCGA-BH-A18Q 
        8.81         2.01        90.84        26.66        30.28        55.63 
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-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F0 
       91.99        42.28        12.00        55.69        49.58        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN 
       31.53        97.48        63.35        55.00        45.63        72.07 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A209 TCGA-BH-A28Q 
       72.07         6.90         0.72        38.60       130.16         6.44 
TCGA-BH-A2L8 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12V 
       20.12        11.93        11.77        12.66        11.77        12.66 
TCGA-C8-A12W TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A135 TCGA-C8-A1HE TCGA-C8-A1HI 
       12.66         3.12         1.78         0.62        12.33        11.34 
TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26X TCGA-C8-A26Z 
       12.03        10.42         2.30         3.25         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-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 
        0.23        20.88        13.25        20.58        13.97        14.17 
TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC 
       21.14        14.17        17.49        16.50        18.71        15.78 
TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK 
       18.15        18.90        12.03        18.97        20.09        20.12 
TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU 
       20.09        19.40        20.38        12.20        13.32        14.70 
TCGA-D8-A1X5 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC 
       18.58        16.73        25.74        27.58        18.15         2.66 
TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR 
       15.22        14.73        21.83        17.69         7.96        15.85 
TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1Y0 
       16.31         6.35        15.16        12.66        16.54        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27G TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27N 
        3.81        14.14        13.45        14.43         9.44         4.80 
TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-E2-A107 
       10.09        13.08        12.53        12.26        14.50        34.42 
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-A14Q TCGA-E2-A14R TCGA-E2-A14T TCGA-E2-A14V 
       47.15        44.68        38.24        38.60        33.30        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-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-A15H TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15T 
       12.92        19.40         9.04        20.58         7.73        14.99 
TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B5 TCGA-E2-A1BD TCGA-E2-A1IF TCGA-E2-A1IG 
       60.53        53.62        32.35        17.10        37.41        32.78 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1L6 
       33.73        33.70        28.44         3.88        22.19        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI 
       27.42        39.62        19.66        18.87       106.75       102.61 
TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A574 
        8.75        16.93         5.52        15.72         7.20        19.89 
TCGA-E2-A9RU TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NE 
        9.21        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-A249 TCGA-E9-A24A 
       24.10        17.06         0.69         0.85         0.95        24.56 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A3HO TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54Y 
        0.72        17.75        26.07         0.62        15.72         0.23 
TCGA-E9-A5FK TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1J2 TCGA-EW-A1J3 
       14.70        14.40        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        72.03        13.55 
TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 
       18.12        11.84        11.57        21.24         6.67         4.08 
TCGA-LD-A7W6 TCGA-LL-A441 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN 
        4.60        11.44         7.59        17.06        15.32        14.70 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y 
       14.47        14.79        11.57         2.63         3.88         4.14 
TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 
        4.50         5.59         7.36        27.91         2.79         2.10 
TCGA-OL-A5D7 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX 
       46.55        58.62        27.65        34.92        36.36        16.87 
TCGA-OL-A5S0 TCGA-OL-A66K TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A6VO TCGA-OL-A6VQ 
       20.38        33.57        26.04         7.23        28.21        19.73 
TCGA-PL-A8LV TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z 
        0.23         3.95        16.50         6.81         8.65        10.59 
TCGA-S3-AA11 TCGA-S3-AA17 TCGA-W8-A86G TCGA-XX-A899 TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        5.56         3.91         5.29         9.60       100.01       105.04 

$`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        32.75        49.48        38.40 
TCGA-A2-A3XY TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S3 
       34.98        24.39        21.30        23.21        26.96        21.90 
TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0D9 TCGA-A7-A13G TCGA-A7-A2KD TCGA-A7-A3IY 
       35.31        34.29        37.45        23.61        22.32        11.34 
TCGA-A7-A3RF TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U 
       13.41         8.75        13.02        17.98        53.06        29.03 
TCGA-A8-A079 TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A082 
        9.01        14.01        12.00        17.03        10.98        18.05 
TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O 
       36.95        13.02        12.00        37.05         9.99        31.00 
TCGA-A8-A08S TCGA-A8-A091 TCGA-A8-A09D TCGA-A8-A09N TCGA-A8-A09T TCGA-A8-A0A7 
       33.01        33.01        50.04         1.02        19.04         0.99 
TCGA-A8-A0AD TCGA-AC-A2FF TCGA-AC-A2FK TCGA-AC-A2QH TCGA-AC-A3BB TCGA-AC-A3QP 
       38.04        55.43        38.79         1.02         0.99        22.19 
TCGA-AC-A3YI TCGA-AC-A62V TCGA-AC-A8OR TCGA-AN-A04A TCGA-AN-A0AL TCGA-AN-A0AR 
       23.24         0.07         1.32         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        52.18        37.48 
TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JI TCGA-AO-A124 TCGA-AO-A126 TCGA-AO-A12E 
       50.86        76.77        50.24       102.58       108.72        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        98.93        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       101.95        83.87       114.02        85.97 
TCGA-AR-A1AO TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AU TCGA-AR-A1AX TCGA-AR-A24H 
       43.56        43.07        17.23        76.21        62.14       109.58 
TCGA-AR-A24O TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24Z TCGA-AR-A251 
       84.20        76.01        53.36        85.35        79.00        78.48 
TCGA-AR-A255 TCGA-AR-A2LH TCGA-AR-A5QQ TCGA-B6-A0IC TCGA-B6-A0IG TCGA-B6-A0IK 
       58.92        20.25        10.59        50.70       146.50        18.77 
TCGA-B6-A0IM TCGA-B6-A0RG TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RQ TCGA-B6-A0RT 
      126.12        68.45        81.17        78.02       140.48        89.46 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WY TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A1KN 
      157.41        97.48       113.79        28.27        68.94       139.17 
TCGA-BH-A0AV TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0B9 TCGA-BH-A0BP TCGA-BH-A0BR 
       38.79        39.16        56.94        51.68        48.69        53.69 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0DE TCGA-BH-A0DH TCGA-BH-A0DQ TCGA-BH-A0DZ 
       49.94        11.67        31.17        38.01         3.22        16.27 
TCGA-BH-A0E0 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ 
        4.41        14.30        44.81        24.43        30.35        10.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HW TCGA-BH-A0HY 
       35.51        24.56        52.96        26.50        51.32        50.79 
TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18I TCGA-BH-A18J 
       24.95        42.35        44.81        23.05         7.23        20.12 
TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EY TCGA-BH-A1F5 
       72.56        37.74       113.82        82.85        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-A1FR TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A28O TCGA-BH-A42T 
       36.92       144.59        83.31        57.83        10.65         0.99 
TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12N TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12X 
      109.28         8.94        11.77         0.07        12.66        12.66 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HG 
        1.45         0.69         3.85         3.75        10.92        11.34 
TCGA-C8-A1HJ TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Y TCGA-C8-A27A TCGA-D8-A13Y 
        0.16         0.30         0.23         0.43        12.20        11.90 
TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JP TCGA-D8-A1X6 
       13.48        19.20        12.03        14.01        21.01        17.79 
TCGA-D8-A1X9 TCGA-D8-A1XD TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XQ TCGA-D8-A1XU 
       23.90        17.16        14.50        19.92        16.41        12.99 
TCGA-D8-A1XZ TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27L 
       15.32        14.24        17.42        16.04        13.05        16.41 
TCGA-D8-A27M TCGA-D8-A27P TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A108 
       13.48         0.76        18.51         7.33        43.00        27.52 
TCGA-E2-A14P TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A155 TCGA-E2-A156 
       40.96        33.17        43.33        32.02        21.04        23.87 
TCGA-E2-A158 TCGA-E2-A15C TCGA-E2-A15F TCGA-E2-A15I TCGA-E2-A15O TCGA-E2-A15P 
       14.79        22.82        21.63        17.42        13.02        19.56 
TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B6 TCGA-E2-A1BC 
       17.06        14.07        53.03        29.95        28.50        16.47 
TCGA-E2-A1IE TCGA-E2-A1IK TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1LA TCGA-E2-A1LB 
       38.30        22.65        20.98        11.08        24.59        40.47 
TCGA-E2-A1LE TCGA-E2-A1LL TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A576 TCGA-E9-A1N4 
       28.90        43.04        30.61        34.92        19.00        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-A247 TCGA-E9-A248 TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A54X 
       22.75        27.22         1.94         0.76        18.41        12.33 
TCGA-E9-A5FL TCGA-E9-A5UO TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 
        0.26        13.81        39.72         8.48        18.21        18.90 
TCGA-EW-A1J6 TCGA-EW-A1OZ TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 
       28.77        40.41        39.78        29.82        18.48        30.08 
TCGA-EW-A1PA TCGA-EW-A1PD TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FW TCGA-EW-A3E8 
       18.90        13.94        14.43        34.55        22.09        21.27 
TCGA-EW-A3U0 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       17.49       194.27        53.13        61.91        62.33        90.84 
TCGA-GM-A2DM TCGA-GM-A2DO TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-LD-A9QF 
       76.64        53.36        43.73        69.30        66.38         8.75 
TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A740 TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-OL-A5D6 
        9.53        10.95         4.50         3.22         6.21        12.66 
TCGA-OL-A5D8 TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J 
       31.99        24.72        22.32        26.70        23.47        65.62 
TCGA-OL-A66L TCGA-OL-A66P TCGA-PL-A8LX TCGA-PL-A8LY TCGA-S3-AA10 TCGA-S3-AA12 
       31.07        14.07         0.16         0.26         7.92         8.52 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-XX-A89A 
        7.17         6.87         9.14 

  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 
           21.225            24.590 
[1] "0.0 - 234.3 (21.2)" "0.1 - 194.3 (24.6)"
[1] "hr=" "1.2"
D2V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1Q GAIN MUTATED        46       41        5        5       235       156
  1Q GAIN WILD-TYPE      37       39        4        0       107        78
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1Q GAIN MUTATED           1         87         23         46       11
  1Q GAIN WILD-TYPE         1         55          6         17        7
                   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                 46                37
  STAGE IA                41                39
  STAGE IB                 5                 4
  STAGE II                 5                 0
  STAGE IIA              235               107
  STAGE IIB              156                78
  STAGE III                1                 1
  STAGE IIIA              87                55
  STAGE IIIB              23                 6
  STAGE IIIC              46                17
  STAGE IV                11                 7
  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   148 412  78  29
  1Q GAIN WILD-TYPE 117 182  46  10
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1             148               117
  T2             412               182
  T3              78                46
  T4              29                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  1Q GAIN MUTATED   311 224  69  53
  1Q GAIN WILD-TYPE 170 115  44  21
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0             311               170
  N1             224               115
  N2              69                44
  N3              53                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          2 552  11 104
  1Q GAIN WILD-TYPE        3 302   8  43
D2V6, multiclass
          clus
vv         1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CM0 (I+)               2                 3
  M0                   552               302
  M1                    11                 8
  MX                   104                43
[1] 4 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   663   6
  1Q GAIN WILD-TYPE 351   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    663    6
  1Q GAIN WILD-TYPE  351    5
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE             663               351
  MALE                 6                 5
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  1Q GAIN MUTATED                            1                           476
  1Q GAIN WILD-TYPE                          0                           278
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  1Q GAIN MUTATED                              138                   4
  1Q GAIN WILD-TYPE                             37                   2
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  1Q GAIN MUTATED                                 17                  7
  1Q GAIN WILD-TYPE                               12                  8
                   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                476               278
  INFILTRATING LOBULAR CARCINOMA               138                37
  MEDULLARY CARCINOMA                            4                 2
  MIXED HISTOLOGY (PLEASE SPECIFY)              17                12
  MUCINOUS CARCINOMA                             7                 8
  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   183 486
  1Q GAIN WILD-TYPE  99 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    183  486
  1Q GAIN WILD-TYPE   99  257
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO              183                99
  YES             486               257
[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                          96   481
  1Q GAIN WILD-TYPE                        62   236
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                     96                62
  WHITE                                        481               236
[1] 4 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    18 539
  1Q GAIN WILD-TYPE  18 287
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     18  539
  1Q GAIN WILD-TYPE   18  287
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                  18                18
  NOT HISPANIC OR LATINO             539               287
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    96  18
  2P GAIN WILD-TYPE 790 101
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              114               891 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               18               101 
$`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        26.96 
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        24.99 
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        74.79        64.83        65.36        83.87 
TCGA-AR-A24Q TCGA-B6-A0I2 TCGA-B6-A0RE TCGA-B6-A0RU TCGA-B6-A0WZ TCGA-B6-A0X1 
      101.52       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-A1PC TCGA-EW-A2FR TCGA-GI-A2C9 TCGA-GM-A2DB 
        0.26         8.48         6.15        55.00       109.87        53.13 
TCGA-GM-A2DD TCGA-GM-A2DF TCGA-LL-A5YN TCGA-LL-A5YP TCGA-LL-A7SZ TCGA-OL-A5RW 
       43.04        42.71        14.70        14.79         5.59        36.36 
TCGA-OL-A66I TCGA-OL-A66P TCGA-OL-A6VO TCGA-PL-A8LV TCGA-PL-A8LZ TCGA-S3-AA10 
       23.47        14.07        28.21         0.23         3.95         7.92 

$`2P GAIN WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        0.39         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN 
       47.24        20.88        13.68        31.79         7.96        39.32 
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 
      136.73        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-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-A0SY TCGA-A2-A0T0 TCGA-A2-A0T3 
       54.64        27.12        44.88        44.28        17.52        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-A0YK TCGA-A2-A0YL 
       15.42        21.90        21.67        14.50        19.33        48.46 
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-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-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       83.01        29.98        32.75        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        24.39        21.30        23.21        21.14 
TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 
       21.90        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-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-A5ZW TCGA-A7-A5ZX 
       13.74        14.50        17.92        14.73        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-A06T TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 
       53.06        29.03        26.01         1.02        53.98         9.01 
TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J 
       43.00        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-A07W 
       17.03         9.99        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 
       38.01        28.96        33.01        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        33.01        93.04        43.00 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 
       40.01        33.01        30.97        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        50.04        49.05        45.07 
TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T 
       29.98        33.07         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        22.19 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS 
        1.12        16.57        19.79        23.24        24.79         1.55 
TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OP 
        0.07         1.12         1.18         0.43         1.68         1.74 
TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 
        1.12         1.32         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-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-A0FS TCGA-AN-A0FT TCGA-AN-A0FV 
        7.00         7.59         7.17         6.28         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-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-A0J3 TCGA-AO-A0J4 
       68.75        47.87        59.05        29.13        21.40        52.18 
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-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI 
       50.70        50.86        76.77        21.37        26.24        50.24 
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       108.72       106.78 
TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H 
       96.10        90.58        77.56        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-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N 
       26.93       130.09         5.65        15.62        32.52         2.56 
TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TT 
       32.91         9.99       111.32        49.32         5.26        86.66 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U3 
       29.75        98.93        55.86        76.14       101.95       114.02 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL 
       85.97        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 
       37.81        76.21        61.28        63.62        62.14        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        96.89        78.51        84.20 
TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W 
        0.85        87.22        76.01        53.36        85.35        50.96 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 
       83.77        79.00        56.15        78.48        73.18        72.76 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK 
       58.92        93.83       128.65        20.25        62.86        42.87 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
        7.36        40.04        38.17        39.39        40.54        20.38 
TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I5 
       54.74        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-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-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL 
      110.93       140.88        68.45       189.01       234.28        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-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW 
       89.46       157.41        97.48       188.68        79.63        17.98 
TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
       21.47       113.79       129.70        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-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AY 
       49.94       103.63        55.00        24.53        38.79        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-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-A0BT TCGA-BH-A0BV TCGA-BH-A0BW 
       27.19        53.69        53.95        45.57        49.94        11.67 
TCGA-BH-A0BZ TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG 
       49.05        48.13        42.90        45.83        31.17        23.44 
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-A0E0 
        2.56        38.47        45.17        47.41        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE 
       15.68        14.30        44.81        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-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-A18N TCGA-BH-A18P TCGA-BH-A18Q 
       90.84        26.66        72.56        37.74        30.28        55.63 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET 
       37.55        66.05        51.39        91.99       113.82        82.85 
TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F5 
       42.28        55.69        49.58        17.69        25.81        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-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-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-A12M 
       20.12         0.99       109.28         8.94        11.93        11.77 
TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12Q TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 
       11.77        12.66         0.07        12.66        12.66         3.12 
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-A1HL TCGA-C8-A1HM 
       10.92        11.34        11.34         0.16        10.42         2.30 
TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 
        3.25         0.30         0.23         0.36         8.28         9.67 
TCGA-C8-A275 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-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J9 
       13.25        20.58        13.97        13.48        21.14        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-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-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-A1XM 
        2.66        17.16        14.73        21.83        14.50        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-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V 
        9.44        16.41         4.80         0.76        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-A14O TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U 
       44.68        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-A15C 
       27.12        23.24        19.43        21.04        23.87        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-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-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-A1LG TCGA-E2-A1LH TCGA-E2-A1LI 
       19.66        24.59        40.47        18.87       106.75       102.61 
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        30.61 
TCGA-E2-A573 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 
       34.92        19.00         9.21        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        24.56         0.72         0.76 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y 
       26.07        18.41         0.62        15.72        12.33         0.23 
TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
       14.70        13.81        14.40        15.39        12.20        39.72 
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-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-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
        7.86        18.90        19.99        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-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       53.52        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        43.73        69.30 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX 
       66.38        72.03        13.55        18.12        11.84        11.57 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 
       21.24         6.67         4.08         4.60         8.75         9.53 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YO 
       11.44        10.95         7.59        17.06        15.32        14.47 
TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 
       11.57         2.63         3.88         4.14         4.50         4.50 
TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 
        3.22         6.21         7.36        27.91         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        31.99        58.62        27.65        34.92 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J 
       16.87        24.72        22.32        20.38        26.70        65.62 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A6VQ TCGA-PL-A8LX 
       33.57        31.07        26.04         7.23        19.73         0.16 
TCGA-PL-A8LY TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA11 
        0.26        16.50         6.81         8.65        10.59         5.56 
TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-W8-A86G TCGA-XX-A899 
        8.52         7.17         6.87         3.91         5.29         9.60 
TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        9.14       100.01       105.04 

  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 
            21.45             22.45 
[1] "0.0 - 211.6 (21.5)" "0.0 - 234.3 (22.4)"
[1] "hr=" "1.3"
D3V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2P GAIN MUTATED         5        9        0        0        44        30
  2P GAIN WILD-TYPE      78       71        9        5       298       204
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2P GAIN MUTATED           0         12          3          7        2
  2P GAIN WILD-TYPE         2        130         26         56       16
                   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                78
  STAGE IA                 9                71
  STAGE IB                 0                 9
  STAGE II                 0                 5
  STAGE IIA               44               298
  STAGE IIB               30               204
  STAGE III                0                 2
  STAGE IIIA              12               130
  STAGE IIIB               3                26
  STAGE IIIC               7                56
  STAGE IV                 2                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
  2P GAIN MUTATED    25  73  12   5
  2P GAIN WILD-TYPE 240 521 112  34
D3V4, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1              25               240
  T2              73               521
  T3              12               112
  T4               5                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
  2P GAIN MUTATED    55  37  14   8
  2P GAIN WILD-TYPE 426 302  99  66
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0              55               426
  N1              37               302
  N2              14                99
  N3               8                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
  2P GAIN MUTATED          0 100   2  14
  2P GAIN WILD-TYPE        5 754  17 133
D3V6, multiclass
          clus
vv         2P GAIN MUTATED 2P GAIN WILD-TYPE
  CM0 (I+)               0                 5
  M0                   100               754
  M1                     2                17
  MX                    14               133
[1] 4 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   116   0
  2P GAIN WILD-TYPE 898  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED    116    0
  2P GAIN WILD-TYPE  898   11
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE             116               898
  MALE                 0                11
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  2P GAIN MUTATED                            1                           104
  2P GAIN WILD-TYPE                          0                           650
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  2P GAIN MUTATED                                4                   2
  2P GAIN WILD-TYPE                            171                   4
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  2P GAIN MUTATED                                  0                  0
  2P GAIN WILD-TYPE                               29                 15
                   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                104               650
  INFILTRATING LOBULAR CARCINOMA                 4               171
  MEDULLARY CARCINOMA                            2                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               0                29
  MUCINOUS CARCINOMA                             0                15
  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  80
  2P GAIN WILD-TYPE 246 663
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     36   80
  2P GAIN WILD-TYPE  246  663
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO               36               246
  YES              80               663
[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                          27    69
  2P GAIN WILD-TYPE                       131   648
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                     27               131
  WHITE                                         69               648
[1] 4 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  99
  2P GAIN WILD-TYPE  36 727
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      0   99
  2P GAIN WILD-TYPE   36  727
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                36
  NOT HISPANIC OR LATINO              99               727
[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 825 111
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               69               936 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                8               111 
$`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        26.96        30.61        35.67        31.73 
TCGA-A7-A26I TCGA-A7-A4SE TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A07U TCGA-A8-A097 
       21.73        21.17        17.98        31.00        24.99        12.00 
TCGA-AC-A23H TCGA-AC-A62Y TCGA-AN-A04C TCGA-AO-A124 TCGA-AO-A12D TCGA-AO-A12F 
        2.66         1.81         1.78       102.58        64.04        48.36 
TCGA-AR-A24Q TCGA-B6-A0WZ TCGA-B6-A0X1 TCGA-B6-A402 TCGA-BH-A0AW TCGA-BH-A0BG 
      101.52       129.57       186.48        54.28        20.45        24.85 
TCGA-BH-A0BL TCGA-BH-A0C1 TCGA-BH-A0DL TCGA-BH-A0E9 TCGA-BH-A18T TCGA-BH-A18V 
       44.05        44.02        48.23        46.19         7.36        51.16 
TCGA-BH-A1EN TCGA-BH-A1F2 TCGA-BH-A203 TCGA-C8-A12P TCGA-C8-A12U TCGA-C8-A12V 
       69.93        31.53        38.60        11.77        12.66        12.66 
TCGA-C8-A131 TCGA-C8-A26Y TCGA-C8-A274 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1XU 
        1.78         0.43         0.03        19.20        14.17        12.99 
TCGA-D8-A27M TCGA-E2-A109 TCGA-E2-A10C TCGA-E2-A14P TCGA-E2-A159 TCGA-E2-A15A 
       13.48        46.59        40.11        40.96        25.05        23.34 
TCGA-E2-A1LE TCGA-E2-A574 TCGA-E9-A5FL TCGA-EW-A1IY TCGA-EW-A1PC TCGA-EW-A2FR 
       28.90        19.89         0.26         8.48         6.15        55.00 
TCGA-GI-A2C9 TCGA-GM-A2DB TCGA-LL-A5YN TCGA-LL-A5YP TCGA-LL-A73Y TCGA-OL-A5RW 
      109.87        53.13        14.70        14.79         4.14        36.36 
TCGA-OL-A66I TCGA-PL-A8LZ TCGA-S3-AA10 
       23.47         3.95         7.92 

$`2Q GAIN WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        0.39         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN 
       47.24        20.88        13.68        31.79         7.96        39.32 
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-A04X TCGA-A2-A04Y TCGA-A2-A0CK 
       73.84        22.06        63.12        55.43        36.13       136.73 
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-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-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-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        48.46        31.73        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-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV 
       20.88        39.65        33.93        83.01        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX 
       49.48        38.40        34.98        38.37         7.30        24.39 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE 
       21.30        23.21        21.14        21.90        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-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-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV 
       17.92        14.73        12.10        10.72        11.05        10.29 
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-A075 TCGA-A8-A076 
       53.06        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        43.00        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-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        38.01        28.96        33.01        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        33.01 
TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 
       93.04        43.00        40.01        33.01        30.97        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        50.04 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q 
       49.05        45.07        29.98        33.07         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-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-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        22.19         1.12        16.57        19.79        23.24 
TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IW 
       24.79         1.55         0.07         1.12         1.18         0.69 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AN-A03X 
        0.43         1.68         1.74         1.12         1.32         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-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        52.18 
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-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 
       50.24        62.04        55.33        71.80        99.25       108.72 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12G 
      106.78        96.10        90.58        77.56        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 
       32.52         2.56        32.91         9.99       111.32        49.32 
TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX 
        5.26        74.79        86.66        29.75        98.93        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       101.95        83.87       114.02 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL 
       85.97        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 
       37.81        76.21        61.28        63.62        62.14        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        96.89        78.51        84.20 
TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W 
        0.85        87.22        76.01        53.36        85.35        50.96 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 
       83.77        79.00        56.15        78.48        73.18        72.76 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK 
       58.92        93.83       128.65        20.25        62.86        42.87 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
        7.36        40.04        38.17        39.39        40.54        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-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-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-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-A408 TCGA-B6-A40B TCGA-B6-A40C 
      139.17       170.17        85.35        49.94       103.63        55.00 
TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 
       24.53        38.79        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-A0BM 
       37.22        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-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-A0C3 TCGA-BH-A0C7 
       49.94        11.67        49.05        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-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-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 
       47.41        16.27         4.41        15.68        14.30         9.63 
TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY 
       44.81        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-A18U TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV 
       51.39        91.99       113.82        82.85        42.28        12.00 
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-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-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-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-A273 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A 
        0.36         8.28         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-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J9 
       20.58        13.97        14.17        13.48        21.14        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-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-A1XJ 
       18.15         2.66        17.16        15.22        14.73        21.83 
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-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-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27N 
       13.45        13.05        14.43         9.44        16.41         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-A10A 
       18.51         7.33        43.00        34.42        27.52        40.41 
TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14Q 
       37.51        28.44        28.87        47.15        44.68        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-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-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-A1LG TCGA-E2-A1LH TCGA-E2-A1LI 
       19.66        24.59        40.47        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-A576 TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1N5 
       30.61        34.92        19.00         9.21        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-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-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 
       24.56         0.72        17.75         0.76        26.07        18.41 
TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UO 
        0.62        15.72        12.33         0.23        14.70        13.81 
TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J1 
       14.40        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-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-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-A2DC TCGA-GM-A2DD 
       10.59         7.40        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        43.73        69.30 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX 
       66.38        72.03        13.55        18.12        11.84        11.57 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 
       21.24         6.67         4.08         4.60         8.75         9.53 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YO 
       11.44        10.95         7.59        17.06        15.32        14.47 
TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ 
       11.57         2.63         3.88         4.50         4.50         5.59 
TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 
        3.22         6.21         7.36        27.91         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        31.99        58.62        27.65        34.92 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J 
       16.87        24.72        22.32        20.38        26.70        65.62 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO 
       33.57        31.07        26.04         7.23        14.07        28.21 
TCGA-OL-A6VQ TCGA-PL-A8LV TCGA-PL-A8LX TCGA-PL-A8LY TCGA-S3-A6ZF TCGA-S3-A6ZG 
       19.73         0.23         0.16         0.26        16.50         6.81 
TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 
        8.65        10.59         5.56         8.52         7.17         6.87 
TCGA-S3-AA17 TCGA-W8-A86G TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        3.91         5.29         9.60         9.14       100.01       105.04 

  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 
            24.99             22.19 
[1] "0.0 - 186.5 (25.0)" "0.0 - 234.3 (22.2)"
[1] "hr=" "1"  
D4V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2Q GAIN MUTATED         4        5        0        0        28        22
  2Q GAIN WILD-TYPE      79       75        9        5       314       212
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2Q GAIN MUTATED           0          4          2          4        1
  2Q GAIN WILD-TYPE         2        138         27         59       17
                   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                79
  STAGE IA                 5                75
  STAGE IB                 0                 9
  STAGE II                 0                 5
  STAGE IIA               28               314
  STAGE IIB               22               212
  STAGE III                0                 2
  STAGE IIIA               4               138
  STAGE IIIB               2                27
  STAGE IIIC               4                59
  STAGE IV                 1                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
  2Q GAIN MUTATED    14  48   7   2
  2Q GAIN WILD-TYPE 251 546 117  37
D4V4, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1              14               251
  T2              48               546
  T3               7               117
  T4               2                37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  2Q GAIN MUTATED    37  22   6   4
  2Q GAIN WILD-TYPE 444 317 107  70
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0              37               444
  N1              22               317
  N2               6               107
  N3               4                70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  2Q GAIN MUTATED          0  62   1   8
  2Q GAIN WILD-TYPE        5 792  18 139
D4V6, multiclass
          clus
vv         2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CM0 (I+)               0                 5
  M0                    62               792
  M1                     1                18
  MX                     8               139
[1] 4 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 943  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     71    0
  2Q GAIN WILD-TYPE  943   11
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              71               943
  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                           691
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  2Q GAIN MUTATED                                3                   0
  2Q GAIN WILD-TYPE                            172                   6
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  2Q GAIN MUTATED                                  0                  0
  2Q GAIN WILD-TYPE                               29                 15
                   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               691
  INFILTRATING LOBULAR CARCINOMA                 3               172
  MEDULLARY CARCINOMA                            0                 6
  MIXED HISTOLOGY (PLEASE SPECIFY)               0                29
  MUCINOUS CARCINOMA                             0                15
  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 261 693
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     21   50
  2Q GAIN WILD-TYPE  261  693
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO               21               261
  YES              50               693
[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                          16    42
  2Q GAIN WILD-TYPE                       142   675
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                     16               142
  WHITE                                         42               675
[1] 4 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  61
  2Q GAIN WILD-TYPE  36 765
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      0   61
  2Q GAIN WILD-TYPE   36  765
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                36
  NOT HISPANIC OR LATINO              61               765
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED   111  19
  3P GAIN WILD-TYPE 775 100
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              130               875 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               19               100 
$`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        24.39        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        38.01        28.96 
TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A091 TCGA-A8-A093 
       33.01        12.00        37.05        31.00        33.01        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        49.05        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        52.18 
TCGA-AO-A0J7 TCGA-AO-A128 TCGA-AO-A12D TCGA-AQ-A04H TCGA-AQ-A54N TCGA-AQ-A54O 
       20.32       106.78        64.04        24.79         2.56        32.91 
TCGA-AR-A0TS TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AS TCGA-AR-A24K TCGA-AR-A24V 
       74.79        61.84        52.77        37.81        50.89        85.35 
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-A147 
        0.07        12.66        11.34         0.99        20.88        19.20 
TCGA-D8-A1XA TCGA-D8-A1XQ TCGA-D8-A1XV TCGA-D8-A1Y2 TCGA-D8-A27R TCGA-E2-A109 
       27.58        16.41        15.16        14.24        10.09        46.59 
TCGA-E2-A10B TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14T TCGA-E2-A14Z TCGA-E2-A154 
       37.51        47.15        44.68        33.30        17.03        19.43 
TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A1AZ TCGA-E2-A1IH TCGA-E2-A1LG TCGA-E2-A1LI 
       20.71        18.21        60.53        33.73        18.87       102.61 
TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RF TCGA-E9-A54Y TCGA-E9-A5UP TCGA-EW-A1J6 
       20.81        40.24         6.58         0.23        14.40        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        15.32        14.79 
TCGA-LL-A6FR TCGA-OL-A5RW TCGA-OL-A6VO TCGA-S3-A6ZF 
        3.88        36.36        28.21        16.50 

$`3P GAIN WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        0.39         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN 
       47.24        20.88        13.68        31.79         7.96        39.32 
TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q 
       28.01        19.20        18.21       104.81        18.02        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-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
       36.13       136.73        64.57       112.08        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 
      107.93        75.25         5.19        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-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T3 
       54.64        44.88        44.28        17.52        17.13        18.71 
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-A0YT TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 
       48.46        23.77        23.47        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-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       83.01        29.98        32.75        49.48        38.40        34.98 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 
       31.99        38.37         7.30        21.30        23.21        26.96 
TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ 
       21.14        21.90        35.31        34.29        35.47        30.61 
TCGA-A7-A0D9 TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       37.45        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-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-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW 
       14.93        13.74        17.92        14.73        12.10        10.72 
TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06R 
       11.05         9.37        10.42         8.75        13.02        17.98 
TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 
       53.06        29.03        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        43.00        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 
       24.99         9.99        28.04        18.05        15.06        36.95 
TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08G TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R 
       13.02         0.99        19.96         9.99        31.00         0.99 
TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A095 
       33.01        93.04        43.00        40.01        30.97        41.98 
TCGA-A8-A099 TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09N 
        9.99         1.02        50.04        45.07        33.07         1.02 
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-A2FO TCGA-AC-A2QH 
       40.57        55.43        36.99        38.79        50.70         1.02 
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        22.19         1.12 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V 
       16.57        19.79        23.24        24.79         1.55         0.07 
TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO 
        1.12         1.81         1.18         0.69         0.43         1.68 
TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 
        1.74         1.12         1.32         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-A0AT TCGA-AN-A0FD TCGA-AN-A0FF 
        6.51         0.16         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-A0FT 
        7.96         7.00         7.59         7.17         6.28         6.02 
TCGA-AN-A0FV TCGA-AN-A0FY 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-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-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 
       29.13        32.78        21.40        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        50.24        62.04        55.33        71.80 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B 
      102.58        99.25       108.72        96.10        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-A04J TCGA-AQ-A04L 
       61.87        70.39         0.53        17.79        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        32.52         9.99       111.32        49.32 
TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
        5.26        86.66        29.75        98.93        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       101.95        83.87       114.02        85.97 
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-A1AQ TCGA-AR-A1AR TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       39.98        43.07        17.23        76.21        61.28        63.62 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       62.14        20.22       109.58        73.02        96.89        78.51 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24U 
       84.20         0.85       101.52        87.22        76.01        53.36 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 
       50.96        83.77        79.00        56.15        78.48        73.18 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       72.76        58.92        93.83       128.65        20.25        62.86 
TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
       42.87        40.04        38.17        39.39        40.54        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-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG 
      149.59        12.13       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-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-A0RO TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS 
      172.96       162.05       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-A402 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV 
      139.17       170.17        54.28       103.63        55.00        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-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC 
       39.16        48.36        56.98        51.68        37.22        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-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ 
       48.69        27.19        53.95        49.94        11.67        49.05 
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-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-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HK 
       24.56        23.08        41.00        52.96        26.50         5.85 
TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0RX 
        2.50        13.61        36.85        12.89        51.32         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-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-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-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-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-A12P TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 
       11.77        11.77        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-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-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 
        0.03         0.23        11.90        13.25        20.58        13.97 
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-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-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM 
       14.01        18.97        20.09        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-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-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-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU 
       17.69         7.96        15.85        16.31         6.35        12.99 
TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y3 
       12.66        16.54        15.32        15.52         3.81        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-A27T TCGA-D8-A27V 
       16.41        13.48         4.80         0.76        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-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14P 
       27.52        40.41        40.11        28.44        28.87        40.96 
TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W 
       38.24        38.60        33.17        43.33        34.26        32.02 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A155 
       31.96        28.60        25.41        27.12        23.24        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-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-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-A1LH TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX 
      106.75         8.75        43.04        16.93         5.52        15.72 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU 
        7.20        30.61        34.92        19.89        19.00         9.21 
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-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-A1RD TCGA-E9-A1RE TCGA-E9-A1RG 
        2.76        21.21        32.09         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-A248 TCGA-E9-A249 TCGA-E9-A24A 
        0.69         0.85        27.22         1.94         0.95        24.56 
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-A54X TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE 
       15.72        12.33        14.70         0.26        13.81        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-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY 
       16.57        15.68        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-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-A2FR TCGA-EW-A2FS TCGA-EW-A2FV 
       10.52        14.43        34.55        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-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        43.73        66.38        72.03 
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        21.24         6.67 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
        4.08         4.60         8.75         9.53        11.44        10.95 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ 
        7.59        17.06        14.70        14.47        11.57         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-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 
        7.36        27.91         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 
       31.99        58.62        27.65        34.92        16.87        24.72 
TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K 
       22.32        20.38        26.70        23.47        65.62        33.57 
TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ TCGA-PL-A8LV 
       31.07        26.04         7.23        14.07        19.73         0.23 
TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z 
        0.16         0.26         3.95         6.81         8.65        10.59 
TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 
        7.92         5.56         8.52         7.17         6.87         3.91 
TCGA-W8-A86G TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        5.29         9.60         9.14       100.01       105.04 

  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 
            26.58             22.06 
[1] "0.1 - 220.9 (26.6)" "0.0 - 234.3 (22.1)"
[1] "hr=" "1.2"
D5V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3P GAIN MUTATED        11        8        0        2        53        19
  3P GAIN WILD-TYPE      72       72        9        3       289       215
                   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        124         22         57       14
                   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                72
  STAGE IA                 8                72
  STAGE IB                 0                 9
  STAGE II                 2                 3
  STAGE IIA               53               289
  STAGE IIB               19               215
  STAGE III                0                 2
  STAGE IIIA              18               124
  STAGE IIIB               7                22
  STAGE IIIC               6                57
  STAGE IV                 4                14
  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    31  82   9   9
  3P GAIN WILD-TYPE 234 512 115  30
D5V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1              31               234
  T2              82               512
  T3               9               115
  T4               9                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
  3P GAIN MUTATED    65  36  18  10
  3P GAIN WILD-TYPE 416 303  95  64
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0              65               416
  N1              36               303
  N2              18                95
  N3              10                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
  3P GAIN MUTATED          0 122   4   6
  3P GAIN WILD-TYPE        5 732  15 141
D5V6, multiclass
          clus
vv         3P GAIN MUTATED 3P GAIN WILD-TYPE
  CM0 (I+)               0                 5
  M0                   122               732
  M1                     4                15
  MX                     6               141
[1] 4 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   131   1
  3P GAIN WILD-TYPE 883  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED    131    1
  3P GAIN WILD-TYPE  883   10
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE             131               883
  MALE                 1                10
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  3P GAIN MUTATED                            0                           112
  3P GAIN WILD-TYPE                          1                           642
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  3P GAIN MUTATED                                7                   2
  3P GAIN WILD-TYPE                            168                   4
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  3P GAIN MUTATED                                  4                  1
  3P GAIN WILD-TYPE                               25                 14
                   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                112               642
  INFILTRATING LOBULAR CARCINOMA                 7               168
  MEDULLARY CARCINOMA                            2                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               4                25
  MUCINOUS CARCINOMA                             1                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"
D5V9, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    40  92
  3P GAIN WILD-TYPE 242 651
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     40   92
  3P GAIN WILD-TYPE  242  651
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO               40               242
  YES              92               651
[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                          23    81
  3P GAIN WILD-TYPE                       135   636
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                     23               135
  WHITE                                         81               636
[1] 4 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  99
  3P GAIN WILD-TYPE  31 727
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      5   99
  3P GAIN WILD-TYPE   31  727
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                31
  NOT HISPANIC OR LATINO              99               727
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED   176  25
  3Q GAIN WILD-TYPE 710  94
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              201               804 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               25                94 
$`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        24.39        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        24.99         9.99        38.01        28.96        33.01 
TCGA-A8-A08I TCGA-A8-A08P TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09A TCGA-A8-A09B 
       12.00        31.00        33.01        17.95         9.99        12.00 
TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R TCGA-AC-A23H 
       49.05        29.98        33.07        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        52.18 
TCGA-AO-A0J7 TCGA-AO-A128 TCGA-AO-A12D TCGA-AO-A1KR TCGA-AQ-A54N TCGA-AQ-A54O 
       20.32       106.78        64.04        70.39         2.56        32.91 
TCGA-AR-A0TS TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AS TCGA-AR-A24K TCGA-AR-A24M 
       74.79        61.84        52.77        37.81        50.89        96.89 
TCGA-AR-A24V TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LL TCGA-AR-A5QP TCGA-B6-A0I2 
       85.35        58.92        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        34.92        12.00        20.05        20.81 
TCGA-E9-A1RC TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A54Y TCGA-E9-A5FL TCGA-E9-A5UP 
       40.24         6.58        34.59         0.23         0.26        14.40 
TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A1PC 
       28.77        22.82        29.82         7.86        19.99         6.15 
TCGA-EW-A1PH TCGA-EW-A2FS TCGA-GI-A2C8 TCGA-GM-A2DB TCGA-GM-A2DF TCGA-GM-A2DH 
       19.96        52.73         7.40        53.13        42.71        42.28 
TCGA-GM-A3XL TCGA-LL-A5YM TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A8F5 
       69.30        15.32        14.79         3.88         4.14         6.21 
TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-OL-A6VO TCGA-PL-A8LV TCGA-PL-A8LZ TCGA-S3-A6ZF 
       36.36        20.38        28.21         0.23         3.95        16.50 
TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 
        8.65        10.59         7.92 

$`3Q GAIN WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        0.39         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
       47.24        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-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK 
       73.84        63.12        64.04        55.43        36.13       136.73 
TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CT 
       64.57       112.08        92.48        88.60       107.93        75.25 
TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 
        5.19        64.04        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-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-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 
       24.72        99.19        54.64        44.88        44.28        17.52 
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-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL 
       15.42        21.67        14.50        18.61        19.33        48.46 
TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 
       23.77        23.47        36.79        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-A3XT TCGA-A2-A3XU TCGA-A2-A3XV 
       10.59        20.88        39.65        83.01        29.98        32.75 
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-A0CE 
       21.30        23.21        26.96        21.14        21.90        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H 
       34.29        35.47        37.45        10.72        23.61        29.56 
TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD 
       31.36        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-A425 
       11.34        10.59        10.29        11.28        13.41        14.70 
TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A5ZW 
       11.97        14.93        13.74        17.92        12.10        10.72 
TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06R TCGA-A8-A06T 
       11.05         9.37         8.75        13.02        17.98        53.06 
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-A07O 
       43.00        19.99        18.97        18.97        14.01         9.99 
TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 
       10.98         8.98         7.99        28.04        18.05        15.06 
TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08L 
       36.95        13.02         0.99        19.96        37.05         9.99 
TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z 
       31.00         0.99        33.01        93.04        43.00        40.01 
TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09C TCGA-A8-A09D 
       30.97        41.98        12.00         9.99         1.02        50.04 
TCGA-A8-A09I TCGA-A8-A09N TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X 
       45.07         1.02        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-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-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD 
       50.70         1.02         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 
       22.19         1.12        16.57        19.79        23.24        24.79 
TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO 
        1.55         0.07         1.81         1.18         0.43         1.68 
TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A046 TCGA-AN-A04A 
        1.74         1.12         1.32         0.33         0.33         2.96 
TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AT 
        1.78         1.71         7.36         6.51         0.33         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-A0FT TCGA-AN-A0FV TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XP 
        6.02         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-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-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 
       29.13        32.78        21.40        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        50.24        62.04        55.33        71.80 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B 
      102.58        99.25       108.72        96.10        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-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-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ 
        5.65        15.62        32.52         9.99       111.32        49.32 
TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
        5.26        86.66        29.75        98.93        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       101.95        83.87       114.02        85.97 
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-A1AQ TCGA-AR-A1AR TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       39.98        43.07        17.23        76.21        61.28        63.62 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24N TCGA-AR-A24O 
       62.14        20.22       109.58        73.02        78.51        84.20 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24W 
        0.85       101.52        87.22        76.01        53.36        50.96 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 
       83.77        79.00        56.15        78.48        73.18        72.76 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN 
      128.65        20.25        62.86        42.87        40.04        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QQ 
       39.39        40.54        20.38        54.74        16.04        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
       77.62       149.59        12.13       129.57        50.70        65.72 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP 
      146.50       112.37       126.12        84.59       110.14       110.93 
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-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS 
      172.96       162.05       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-A1KI TCGA-B6-A1KN 
      186.48        28.27        68.94        58.88        73.51       139.17 
TCGA-B6-A2IU TCGA-B6-A402 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AW 
      170.17        54.28       103.63        55.00        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-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
       48.36        56.98        51.68        37.22        32.02        18.21 
TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP 
       25.71        24.85        21.70        61.68        35.67        48.69 
TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 
       27.19        53.95        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-A0DT 
       22.13        13.91        17.26        15.65         3.22        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-A0EE TCGA-BH-A0EI TCGA-BH-A0GY 
        9.63        44.81        32.65        31.00        24.43        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 
       10.78        15.16        37.78        35.51        24.56        41.00 
TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ 
       52.96        26.50         5.85         2.50        13.61        36.85 
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-A18R TCGA-BH-A18S TCGA-BH-A18T 
       26.66        72.56        30.28        37.55        66.05         7.36 
TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW 
       69.93        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-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-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-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-A12N TCGA-C8-A12O 
        0.99       109.28         8.94        11.93        11.77        12.66 
TCGA-C8-A12P TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 
       11.77        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-A1HG 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-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 
        0.30         0.36         0.43         8.28         9.67         0.03 
TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A3M7 TCGA-D8-A13Y TCGA-D8-A140 
        0.03         0.03        12.20         0.03        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-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-A1XM TCGA-D8-A1XO TCGA-D8-A1XR 
       17.16        15.22        14.73        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-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-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-A10A TCGA-E2-A10C TCGA-E2-A10E 
       43.00        34.42        27.52        40.41        40.11        28.44 
TCGA-E2-A10F TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T 
       28.87        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-A150 
       43.33        34.26        32.02        31.96        28.60        25.41 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15A 
       27.12        23.24        21.04        23.87        14.79        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-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-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-A1BD TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IJ 
       28.50        16.47        17.10        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-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        30.61 
TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 
       19.89        19.00         9.21        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        24.56 
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-A54X TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW 
       15.72        12.33        14.70        13.81        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-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 
       15.68        25.94        29.95        29.85        40.41        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA 
       39.78        52.96        23.11        18.48        30.08        18.90 
TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FR TCGA-EW-A2FV 
       13.94        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-A2C9 
       22.09        21.27        17.49        10.16        10.59       109.87 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DI TCGA-GM-A2DK 
       59.57       194.27        53.52        43.04        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 
       43.73        66.38        72.03        13.55        18.12        11.84 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF 
       11.57        21.24         6.67         4.08         4.60         8.75 
TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN 
        9.53        11.44        10.95         7.59        17.06        14.70 
TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ 
       14.47        11.57         2.63         4.50         4.50         5.59 
TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
        3.22         7.36        27.91         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        31.99        58.62        27.65        34.92        16.87 
TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K 
       24.72        22.32        26.70        23.47        65.62        33.57 
TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ TCGA-PL-A8LX 
       31.07        26.04         7.23        14.07        19.73         0.16 
TCGA-PL-A8LY TCGA-S3-A6ZG TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 
        0.26         6.81         5.56         8.52         7.17         6.87 
TCGA-S3-AA17 TCGA-W8-A86G TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        3.91         5.29         9.60         9.14       100.01       105.04 

  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 
           22.060            22.505 
[1] "0.1 - 220.9 (22.1)" "0.0 - 234.3 (22.5)"
[1] "hr=" "1.1"
D6V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3Q GAIN MUTATED        15       14        1        2        79        39
  3Q GAIN WILD-TYPE      68       66        8        3       263       195
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3Q GAIN MUTATED           0         26         11         10        4
  3Q GAIN WILD-TYPE         2        116         18         53       14
                   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                68
  STAGE IA                14                66
  STAGE IB                 1                 8
  STAGE II                 2                 3
  STAGE IIA               79               263
  STAGE IIB               39               195
  STAGE III                0                 2
  STAGE IIIA              26               116
  STAGE IIIB              11                18
  STAGE IIIC              10                53
  STAGE IV                 4                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
  3Q GAIN MUTATED    44 128  20  12
  3Q GAIN WILD-TYPE 221 466 104  27
D6V4, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1              44               221
  T2             128               466
  T3              20               104
  T4              12                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
  3Q GAIN MUTATED   105  59  23  13
  3Q GAIN WILD-TYPE 376 280  90  61
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0             105               376
  N1              59               280
  N2              23                90
  N3              13                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
  3Q GAIN MUTATED          0 180   4  20
  3Q GAIN WILD-TYPE        5 674  15 127
D6V6, multiclass
          clus
vv         3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CM0 (I+)               0                 5
  M0                   180               674
  M1                     4                15
  MX                    20               127
[1] 4 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   203   1
  3Q GAIN WILD-TYPE 811  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED    203    1
  3Q GAIN WILD-TYPE  811   10
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE             203               811
  MALE                 1                10
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  3Q GAIN MUTATED                            0                           176
  3Q GAIN WILD-TYPE                          1                           578
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  3Q GAIN MUTATED                                8                   4
  3Q GAIN WILD-TYPE                            167                   2
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  3Q GAIN MUTATED                                  6                  1
  3Q GAIN WILD-TYPE                               23                 14
                   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                176               578
  INFILTRATING LOBULAR CARCINOMA                 8               167
  MEDULLARY CARCINOMA                            4                 2
  MIXED HISTOLOGY (PLEASE SPECIFY)               6                23
  MUCINOUS CARCINOMA                             1                14
  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    63 141
  3Q GAIN WILD-TYPE 219 602
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     63  141
  3Q GAIN WILD-TYPE  219  602
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               63               219
  YES             141               602
[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                          43   125
  3Q GAIN WILD-TYPE                       115   592
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                     43               115
  WHITE                                        125               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"
D6V12, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     6 163
  3Q GAIN WILD-TYPE  30 663
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      6  163
  3Q GAIN WILD-TYPE   30  663
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   6                30
  NOT HISPANIC OR LATINO             163               663
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    64   8
  4P GAIN WILD-TYPE 822 111
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               72               933 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                8               111 
$`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        26.96        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        33.01        93.04 
TCGA-A8-A091 TCGA-A8-A09K TCGA-A8-A0A9 TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A3W5 
       33.01        29.98        13.02         1.02         2.27        16.57 
TCGA-AN-A04C TCGA-AN-A0FY TCGA-AO-A0JD TCGA-AQ-A54O TCGA-AR-A0TS TCGA-AR-A0TW 
        1.78         0.33        72.00        32.91        74.79        98.93 
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-E9-A5UP 
       13.12         2.76        40.24        34.65        27.22        14.40 
TCGA-EW-A1P4 TCGA-EW-A2FS TCGA-EW-A2FV TCGA-LL-A5YN TCGA-S3-A6ZG TCGA-Z7-A8R5 
       29.82        52.73        25.91        14.70         6.81       100.01 

$`4P GAIN WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        0.39         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
       47.24        20.88        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 
      136.73        64.57        24.79       112.08        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 
      107.93        75.55        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-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-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-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-A1FW 
       14.50        18.61        19.33        48.46        23.47        17.36 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       36.79        22.45        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        32.75 
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 
       24.39        21.30        23.21        21.14        21.90        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-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A56D 
       14.70        11.97        14.93        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-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U 
        8.75        13.02         1.02        17.98        53.06        29.03 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07E 
       31.00        26.01         1.02        53.98        43.00        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        24.99        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        38.01        28.96        33.01 
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 
       43.00        40.01        30.97        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        50.04        49.05 
TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T 
       45.07        33.07         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-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E 
       21.04         0.99        17.03        38.04         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-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QI 
       55.43        36.99        38.79        26.04        50.70         0.92 
TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W6 
        0.99         0.69        14.83        22.19         1.12        19.79 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y 
       23.24        24.79         1.55         0.07         1.12         1.81 
TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OQ 
        1.18         0.69         0.43         1.68         1.74         1.12 
TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 
        1.32         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-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-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-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-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 
       52.18        24.16        37.48        20.32        22.36        53.03 
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-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 
       50.24        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 
      108.72       106.78        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-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-A7U7 
      130.09         5.65        15.62        32.52         2.56         9.99 
TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TX 
      111.32        49.32         5.26        86.66        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       101.95        83.87       114.02 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL 
       85.97        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 
       37.81        76.21        61.28        63.62        62.14        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        96.89        78.51        84.20 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V 
        0.85       101.52        87.22        76.01        53.36        85.35 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 
       50.96        83.77        79.00        56.15        78.48        73.18 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       72.76        58.92        93.83       128.65        20.25        62.86 
TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
       42.87        40.04        38.17        39.39        40.54        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-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-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-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-A402 TCGA-B6-A408 
       73.51       139.17       170.17        85.35        54.28        49.94 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B0 
      103.63        55.00        38.79        20.45        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-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-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ 
       53.69        53.95        45.57        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-A0DK TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ 
       23.44        38.01        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-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-A0HW TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 
       12.89        51.32        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-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-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-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-A1FN 
       74.73       122.89        36.92        63.35        55.00        72.07 
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-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-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y 
       10.42         2.30         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-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JF 
       17.49        16.50        18.71        15.78        18.90        12.03 
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-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-A1XK TCGA-D8-A1XL TCGA-D8-A1XM 
       15.22        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-A1XU 
        7.96        16.41        15.85        16.31         6.35        12.99 
TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 
       15.16        12.66        16.54        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-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-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-A14T TCGA-E2-A14U 
       44.68        40.96        38.24        38.60        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-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-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-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-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-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-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU 
       15.72        30.61        34.92        19.89        19.00         9.21 
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        24.56         0.72        17.75 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X 
        0.76        26.07        18.41         0.62        15.72        12.33 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW 
        0.23        14.70         0.26        13.81        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-A1P5 TCGA-EW-A1P6 
       40.41        41.13        39.78        52.96        23.11        18.48 
TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD 
       30.08         7.86        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-A2FW 
       10.52        14.43        34.55        19.96        55.00        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-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        43.73        69.30        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U 
       72.03        13.55        18.12        11.84        11.57        21.24 
TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 
        6.67         4.08         4.60         8.75         9.53        11.44 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A5YP 
       10.95         7.59        17.06        15.32        14.47        14.79 
TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 
       11.57         2.63         3.88         4.14         4.50         4.50 
TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
        5.59         3.22         6.21         7.36        27.91         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        31.99        58.62        27.65 
TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 
       34.92        36.36        16.87        24.72        22.32        20.38 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       26.70        23.47        65.62        33.57        31.07        26.04 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PL-A8LV TCGA-PL-A8LX 
        7.23        14.07        28.21        19.73         0.23         0.16 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 
        0.26         3.95        16.50         8.65        10.59         7.92 
TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-W8-A86G 
        5.56         8.52         7.17         6.87         3.91         5.29 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
        9.60         9.14       105.04 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.33              0.03 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           100.01            234.28 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            21.65             22.45 
[1] "0.3 - 100.0 (21.6)" "0.0 - 234.3 (22.4)"
[1] "hr=" "1.4"
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      80       77        8        3       311       220
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4P GAIN MUTATED           0         10          5          4        2
  4P GAIN WILD-TYPE         2        132         24         59       16
                   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                80
  STAGE IA                 3                77
  STAGE IB                 1                 8
  STAGE II                 2                 3
  STAGE IIA               31               311
  STAGE IIB               14               220
  STAGE III                0                 2
  STAGE IIIA              10               132
  STAGE IIIB               5                24
  STAGE IIIC               4                59
  STAGE IV                 2                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
  4P GAIN MUTATED    13  45  11   6
  4P GAIN WILD-TYPE 252 549 113  33
D7V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1              13               252
  T2              45               549
  T3              11               113
  T4               6                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
  4P GAIN MUTATED    37  26   5   5
  4P GAIN WILD-TYPE 444 313 108  69
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0              37               444
  N1              26               313
  N2               5               108
  N3               5                69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  4P GAIN MUTATED          0  67   2   6
  4P GAIN WILD-TYPE        5 787  17 141
D7V6, multiclass
          clus
vv         4P GAIN MUTATED 4P GAIN WILD-TYPE
  CM0 (I+)               0                 5
  M0                    67               787
  M1                     2                17
  MX                     6               141
[1] 4 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    74   1
  4P GAIN WILD-TYPE 940  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     74    1
  4P GAIN WILD-TYPE  940   10
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE              74               940
  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                           694
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  4P GAIN MUTATED                                4                   1
  4P GAIN WILD-TYPE                            171                   5
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  4P GAIN MUTATED                                  2                  1
  4P GAIN WILD-TYPE                               27                 14
                   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               694
  INFILTRATING LOBULAR CARCINOMA                 4               171
  MEDULLARY CARCINOMA                            1                 5
  MIXED HISTOLOGY (PLEASE SPECIFY)               2                27
  MUCINOUS CARCINOMA                             1                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"
D7V9, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    19  56
  4P GAIN WILD-TYPE 263 687
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     19   56
  4P GAIN WILD-TYPE  263  687
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO               19               263
  YES              56               687
[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    51
  4P GAIN WILD-TYPE                       150   666
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               150
  WHITE                                         51               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"
D7V12, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     3  58
  4P GAIN WILD-TYPE  33 768
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      3   58
  4P GAIN WILD-TYPE   33  768
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                33
  NOT HISPANIC OR LATINO              58               768
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    61   9
  4Q GAIN WILD-TYPE 825 110
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               70               935 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                9               110 
$`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        26.96        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        33.01        93.04        33.01 
TCGA-A8-A0A9 TCGA-AC-A2QJ TCGA-AC-A3W5 TCGA-AN-A04C TCGA-AN-A0FY TCGA-AO-A0J3 
       13.02         2.27        16.57         1.78         0.33        21.40 
TCGA-AQ-A54O TCGA-AR-A0TS TCGA-AR-A0TW TCGA-AR-A250 TCGA-AR-A2LL TCGA-B6-A0RG 
       32.91        74.79        98.93        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-E9-A5UP TCGA-EW-A1P4 TCGA-EW-A2FS TCGA-EW-A2FV TCGA-LL-A5YN 
       27.22        14.40        29.82        52.73        25.91        14.70 
TCGA-OL-A66I TCGA-S3-A6ZG TCGA-S3-AA10 TCGA-Z7-A8R5 
       23.47         6.81         7.92       100.01 

$`4Q GAIN WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        0.39         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
       47.24        20.88        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 
      136.73        64.57        24.79       112.08        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 
      107.93        75.55        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-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-A1FW 
       14.50        18.61        19.33        48.46        23.47        17.36 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       36.79        22.45        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        32.75 
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 
       24.39        21.30        23.21        21.14        21.90        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-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF 
       14.70        11.97        14.93        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        53.06 
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        43.00 
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-A07Z TCGA-A8-A082 
       10.98         8.98         7.99        24.99        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        38.01        28.96 
TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P 
       33.01        12.00        37.05         9.99        31.00        31.00 
TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 
        0.99        43.00        40.01        30.97        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        50.04 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q 
       49.05        45.07        29.98        33.07         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-A0AB TCGA-A8-A0AD 
       19.04        13.02        21.04         0.99        17.03        38.04 
TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK 
        0.95         2.37        10.85         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-A3HN TCGA-AC-A3OD 
       50.70         1.02         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-A5XS 
       22.19         1.12        19.79        23.24        24.79         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-A6NO TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y 
        1.68         1.74         1.12         1.32         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-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-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-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-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 
       29.13        32.78        52.18        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        50.24        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       108.72       106.78        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-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-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
       32.52         2.56         9.99       111.32        49.32         5.26 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 
       86.66        29.75        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-A1AI 
      101.95        83.87       114.02        85.97        75.55        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-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
       39.98        43.07        17.23        37.81        76.21        61.28 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L 
       63.62        62.14        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 
       96.89        78.51        84.20         0.85       101.52        87.22 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
       76.01        53.36        85.35        50.96        83.77        79.00 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE 
       78.48        73.18        72.76        58.92        93.83       128.65 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       20.25        62.86        42.87        40.04        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       40.54        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       103.63        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-A0DL 
       45.83        31.17        23.44        38.01        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-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-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-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-A0HY 
        2.50        13.61        36.85        12.89        51.32        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-A18M 
        8.81         2.01         7.23        20.12        90.84        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-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-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 
       12.00        17.69        25.81        31.53        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-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-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-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-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-A1J9 
       13.97        14.17        13.48        21.14        19.20        17.49 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JI 
       16.50        18.71        15.78        18.90        12.03        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-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 
       12.20        14.70        18.58        17.79        16.73        25.74 
TCGA-D8-A1X9 TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ 
       23.90        18.15         2.66        17.16        14.73        21.83 
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-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY 
       16.31         6.35        12.99        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-A27N 
       13.45        13.05        14.43         9.44        16.41         4.80 
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-A14O TCGA-E2-A14P TCGA-E2-A14Q 
       28.44        28.87        47.15        44.68        40.96        38.24 
TCGA-E2-A14R TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X 
       38.60        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-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-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
       20.58         7.73        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-A56Z TCGA-E2-A570 TCGA-E2-A573 
       16.93         5.52        15.72         7.20        30.61        34.92 
TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 
       19.89        19.00         9.21        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        24.56         0.72        17.75         0.76        26.07 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK 
       18.41         0.62        15.72        12.33         0.23        14.70 
TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
        0.26        13.81        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-A1OZ TCGA-EW-A1P0 
       25.94        22.82        29.95        29.85        40.41        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-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-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 
       34.55        19.96        55.00        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-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        43.73        69.30        66.38        72.03        13.55 
TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 
       18.12        11.84        11.57        21.24         6.67         4.08 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y 
        4.60         8.75         9.53        11.44        10.95         7.59 
TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ 
       17.06        15.32        14.47        14.79        11.57         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-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
        6.21         7.36        27.91         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        31.99        58.62        27.65        34.92        36.36 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J 
       16.87        24.72        22.32        20.38        26.70        65.62 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO 
       33.57        31.07        26.04         7.23        14.07        28.21 
TCGA-OL-A6VQ TCGA-PL-A8LV TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF 
       19.73         0.23         0.16         0.26         3.95        16.50 
TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 
        8.65        10.59         5.56         8.52         7.17         6.87 
TCGA-S3-AA17 TCGA-W8-A86G TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
        3.91         5.29         9.60         9.14       105.04 

  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 
            22.80             22.36 
[1] "0.3 - 114.2 (22.8)" "0.0 - 234.3 (22.4)"
[1] "hr=" "1.5"
D8V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4Q GAIN MUTATED         4        4        2        1        29        13
  4Q GAIN WILD-TYPE      79       76        7        4       313       221
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4Q GAIN MUTATED           0          8          5          4        2
  4Q GAIN WILD-TYPE         2        134         24         59       16
                   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                79
  STAGE IA                 4                76
  STAGE IB                 2                 7
  STAGE II                 1                 4
  STAGE IIA               29               313
  STAGE IIB               13               221
  STAGE III                0                 2
  STAGE IIIA               8               134
  STAGE IIIB               5                24
  STAGE IIIC               4                59
  STAGE IV                 2                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
  4Q GAIN MUTATED    17  40   9   6
  4Q GAIN WILD-TYPE 248 554 115  33
D8V4, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1              17               248
  T2              40               554
  T3               9               115
  T4               6                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
  4Q GAIN MUTATED    34  27   4   5
  4Q GAIN WILD-TYPE 447 312 109  69
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0              34               447
  N1              27               312
  N2               4               109
  N3               5                69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  4Q GAIN MUTATED          0  64   2   6
  4Q GAIN WILD-TYPE        5 790  17 141
D8V6, multiclass
          clus
vv         4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CM0 (I+)               0                 5
  M0                    64               790
  M1                     2                17
  MX                     6               141
[1] 4 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    71   1
  4Q GAIN WILD-TYPE 943  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     71    1
  4Q GAIN WILD-TYPE  943   10
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE              71               943
  MALE                 1                10
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  4Q GAIN MUTATED                            0                            58
  4Q GAIN WILD-TYPE                          1                           696
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  4Q GAIN MUTATED                                4                   2
  4Q GAIN WILD-TYPE                            171                   4
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  4Q GAIN MUTATED                                  1                  1
  4Q GAIN WILD-TYPE                               28                 14
                   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                 58               696
  INFILTRATING LOBULAR CARCINOMA                 4               171
  MEDULLARY CARCINOMA                            2                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               1                28
  MUCINOUS CARCINOMA                             1                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"
D8V9, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    20  52
  4Q GAIN WILD-TYPE 262 691
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     20   52
  4Q GAIN WILD-TYPE  262  691
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO               20               262
  YES              52               691
[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                          10    48
  4Q GAIN WILD-TYPE                       148   669
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                     10               148
  WHITE                                         48               669
[1] 4 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  56
  4Q GAIN WILD-TYPE  33 770
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      3   56
  4Q GAIN WILD-TYPE   33  770
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                33
  NOT HISPANIC OR LATINO              56               770
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED   262  32
  5P GAIN WILD-TYPE 624  87
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              294               711 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               32                87 
$`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 
       24.39        26.96        21.14        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        24.99         9.99        28.04        13.02 
TCGA-A8-A08B TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08P TCGA-A8-A08R 
       38.01        33.01        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-AC-A8OQ TCGA-AN-A03Y TCGA-AN-A04C TCGA-AN-A0AJ TCGA-AN-A0AM TCGA-AN-A0AS 
        1.12         0.33         1.78         8.02         0.16         0.33 
TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XO 
        7.96         7.00         0.33         0.33         0.33        12.33 
TCGA-AN-A0XU TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03O TCGA-AO-A0J2 TCGA-AO-A0J3 
        0.33        80.28        47.84        81.63        32.78        21.40 
TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JL TCGA-AO-A0JM 
       20.32        53.03        50.86        76.77        55.33        71.80 
TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A1KR TCGA-AO-A1KS 
      106.78        90.58        77.56        57.30        70.39         0.53 
TCGA-AQ-A04H TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0TR TCGA-AR-A0TV 
       24.79         5.65         2.56        32.91         5.26        29.75 
TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AV TCGA-AR-A1AY TCGA-AR-A24R TCGA-AR-A24U 
       61.84        51.25        61.28        20.22        87.22        53.36 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LK TCGA-AR-A2LL 
       85.35        50.96        72.76        58.92        42.87         7.36 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QP TCGA-B6-A0I1 TCGA-B6-A0IJ TCGA-B6-A0IQ 
       20.38        54.74        20.45        77.62       176.98       140.88 
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       103.63        24.53 
TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0B7 
       38.79        20.45        28.50        39.55        48.36        56.98 
TCGA-BH-A0BA TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0C1 
       37.22        25.71        21.70        44.05        48.69        44.02 
TCGA-BH-A0DI TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI 
       22.13        15.65         2.56        24.49        31.00        24.43 
TCGA-BH-A0H7 TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0W5 
       23.08        13.61        36.85        27.25        50.79        42.35 
TCGA-BH-A0W7 TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18U 
       44.81        90.84        26.66        72.56        37.74        51.39 
TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1F2 
       69.93        91.99        42.28        12.00        55.69        31.53 
TCGA-BH-A1F6 TCGA-BH-A1FM TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A2L8 
       97.48        45.63         0.72        38.60        57.83        20.12 
TCGA-C8-A12L TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A130 TCGA-C8-A135 TCGA-C8-A1HI 
       11.93        11.77         0.07         3.12         0.62        11.34 
TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A27B TCGA-D8-A142 TCGA-D8-A146 TCGA-D8-A1J8 
       12.03         2.30         0.99        13.97        21.14        14.17 
TCGA-D8-A1J9 TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JJ TCGA-D8-A1JK 
       17.49        18.90        12.03        14.01        20.09        20.12 
TCGA-D8-A1JL TCGA-D8-A1JT TCGA-D8-A1X6 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XL 
       20.09        13.32        17.79        27.58        18.15        19.92 
TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y2 
       16.31        12.99        12.66        16.54        15.52        14.24 
TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27V TCGA-D8-A27W TCGA-E2-A107 TCGA-E2-A10B 
       13.05        14.43        12.53        12.26        34.42        37.51 
TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14Y TCGA-E2-A14Z 
       44.68        40.96        33.17        33.30        28.60        17.03 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A158 TCGA-E2-A15E TCGA-E2-A15G 
       27.12        23.24        21.04        14.79        20.71        18.21 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A1B0 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1BD 
       20.58         7.73        53.62        29.95        32.35        17.10 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L9 
       33.73        33.70        22.19        11.08        54.18        19.66 
TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A2P5 TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N6 
       18.87       106.75        16.93        19.89         9.21        13.48 
TCGA-E9-A1NA TCGA-E9-A1NI TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 
       36.56         9.86         2.10         6.12         1.38         2.76 
TCGA-E9-A1R7 TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RG TCGA-E9-A1RH 
       21.21        20.81        40.24         0.66        21.27        34.59 
TCGA-E9-A243 TCGA-E9-A249 TCGA-E9-A295 TCGA-E9-A3HO TCGA-E9-A54X TCGA-E9-A54Y 
       17.06         0.95         0.72        26.07        12.33         0.23 
TCGA-E9-A5FL TCGA-E9-A5UP TCGA-EW-A1IY TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1P4 
        0.26        14.40         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        66.38        13.55        21.24        15.32        14.79 
TCGA-LL-A6FQ TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-MS-A51U TCGA-OL-A5S0 TCGA-OL-A66N 
        2.63         6.21         7.36         2.79        20.38        26.04 
TCGA-PL-A8LX TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-W8-A86G TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        0.16         6.81         8.65         5.29       100.01       105.04 

$`5P GAIN WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        0.39         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SQ 
       47.24        20.88        31.79         7.96        28.01        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-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM 
       63.12        55.43        36.13       136.73        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-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 
        5.19        63.45        64.04        21.14        34.55        33.76 
TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES 
       28.77        25.22       101.72       107.61        74.40        37.05 
TCGA-A2-A0EW TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SX 
       29.75        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-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YH TCGA-A2-A0YI 
       17.46        32.55        25.28        15.42        21.67        14.50 
TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FZ 
       18.61        19.33        48.46        31.73        23.47        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-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-A3Y0 
       83.01        32.75        49.48        38.40        34.98        38.37 
TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG 
        7.30        21.30        23.21        21.90        35.31        34.29 
TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H 
       35.47        37.45        35.67        10.72        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-A4SE 
       10.59        10.29        11.28        13.41        11.97        21.17 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06T TCGA-A8-A06X 
       10.72        11.05         8.75        13.02        53.06        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        43.00        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-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A08A 
        8.98         7.99        18.05        15.06        36.95         0.99 
TCGA-A8-A08C TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08S TCGA-A8-A08T 
       28.96        37.05         9.99        31.00        33.01        93.04 
TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A099 TCGA-A8-A09D 
       43.00        40.01        33.01        30.97         9.99        50.04 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09T 
       49.05        45.07        29.98        33.07         1.02        19.04 
TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A2 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0AB 
       15.02         0.99        19.04        21.04         0.99        17.03 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM 
       38.04         0.95         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-A3OD TCGA-AC-A3QP TCGA-AC-A3TN 
        1.02         0.92         0.99        14.83        22.19         1.12 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62X 
       16.57        19.79        23.24        24.79         1.55         1.12 
TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OR 
        1.81         1.18         0.69         0.43         1.68         1.32 
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-A0AK TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF 
        7.36         6.51         0.33         0.33         6.44         4.64 
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-A0FZ 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-A0XV TCGA-AN-A0XW TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T 
        5.33         5.59        66.77        84.69        68.75        47.87 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 
       59.05        29.13        52.18        24.16        37.48        22.36 
TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI 
       21.53        50.70        72.00        21.37        26.24        50.24 
TCGA-AO-A0JJ TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12D 
       62.04       102.58        99.25       108.72        96.10        64.04 
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-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A7U7 
       17.79        26.93       130.09        15.62        32.52         9.99 
TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0TX 
      111.32        49.32        74.79        86.66        98.93        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       101.95        83.87       114.02 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
       85.97        75.55        52.77        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        37.81        76.21 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M 
       63.62        62.14       109.58        50.89        73.02        96.89 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24T TCGA-AR-A24X 
       78.51        84.20         0.85       101.52        76.01        83.77 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A256 TCGA-AR-A2LE 
       79.00        56.15        78.48        73.18        93.83       128.65 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       20.25        62.86        40.04        38.17        39.39        40.54 
TCGA-AR-A5QN TCGA-AR-A5QQ TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA 
       16.04        10.59       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-A0IK 
      129.57        50.70        65.72       146.50       112.37        18.77 
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-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-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-A1KC TCGA-B6-A1KF 
      186.48        28.27        68.94        58.88        43.59       101.52 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A40C TCGA-BH-A0AY 
      139.17       170.17        85.35        54.28        55.00        25.55 
TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0B9 TCGA-BH-A0BC 
       46.95        40.83        39.16        56.94        51.68        32.02 
TCGA-BH-A0BD TCGA-BH-A0BG TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR 
       18.21        24.85        61.68        35.67        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-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-A0DQ TCGA-BH-A0DT TCGA-BH-A0DV 
       13.91        48.23        17.26         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-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 
       44.81        46.19        32.65        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-A0HU TCGA-BH-A0HW TCGA-BH-A0RX 
       20.38         5.85         2.50        12.89        51.32         5.59 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I 
       23.93        24.95        23.05         8.81         2.01         7.23 
TCGA-BH-A18J TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T 
       20.12        30.28        55.63        37.55        66.05         7.36 
TCGA-BH-A18V TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 
       51.16       113.82        82.85        49.58        17.69        25.81 
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-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-A204 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q 
       72.07         6.90        83.31       130.16        10.65         6.44 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O 
        0.99       109.28         8.94        11.77        11.77        12.66 
TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A131 TCGA-C8-A132 
       12.66        12.66        12.66        12.66         1.78         1.45 
TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG 
        0.69         3.85         3.75        12.33        10.92        11.34 
TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X 
        0.16        10.42         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-A143 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1JA TCGA-D8-A1JB 
       20.58        14.17        13.48        19.20        16.50        18.71 
TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JF TCGA-D8-A1JI TCGA-D8-A1JM TCGA-D8-A1JN 
       15.78        18.15        12.03        18.97        19.40        20.38 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X7 TCGA-D8-A1X8 
       21.01        12.20        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-A1XJ 
       23.90         2.66        17.16        15.22        14.73        21.83 
TCGA-D8-A1XK TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XT 
       14.50        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        30.61        34.92 
TCGA-E2-A576 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NC 
       19.00        19.20        36.82        12.00        13.12        39.55 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1QZ TCGA-E9-A1R0 
       12.59        35.77        20.05        21.57        11.90        14.30 
TCGA-E9-A1R2 TCGA-E9-A1RA TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RI TCGA-E9-A226 
        0.62        32.09        34.65         6.58        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-A244 TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A248 
       23.51        24.10         0.69         0.85        27.22         1.94 
TCGA-E9-A24A TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
       24.56        17.75         0.76        18.41         0.62        15.72 
TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ 
       14.70        13.81        15.39        12.20        39.72        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX 
       18.90        13.25        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-A1P6 
       29.85        40.41        41.13        39.78        52.96        18.48 
TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PE TCGA-EW-A1PF 
       30.08         7.86        18.90        19.99        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-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-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-A2DO TCGA-GM-A3NY TCGA-GM-A3XG 
       90.84        76.64        77.33        53.36        38.20        43.73 
TCGA-GM-A3XL TCGA-GM-A4E0 TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A74U 
       69.30        72.03        18.12        11.84        11.57         6.67 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
        4.08         4.60         8.75         9.53        11.44        10.95 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FR 
        7.59        17.06        14.70        14.47        11.57         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        27.91 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.10        12.66        46.55        31.99        58.62        27.65 
TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H 
       34.92        36.36        16.87        24.72        22.32        26.70 
TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P 
       23.47        65.62        33.57        31.07         7.23        14.07 
TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PL-A8LV TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF 
       28.21        19.73         0.23         0.26         3.95        16.50 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 
       10.59         7.92         5.56         8.52         7.17         6.87 
TCGA-S3-AA17 TCGA-XX-A899 TCGA-XX-A89A 
        3.91         9.60         9.14 

  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 
           20.515            23.870 
[1] "0.1 - 177.0 (20.5)" "0.0 - 234.3 (23.9)"
[1] "hr=" "1.3"
D9V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5P GAIN MUTATED        27       18        1        2       106        62
  5P GAIN WILD-TYPE      56       62        8        3       236       172
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5P GAIN MUTATED           1         48          9         16        5
  5P GAIN WILD-TYPE         1         94         20         47       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                 27                56
  STAGE IA                18                62
  STAGE IB                 1                 8
  STAGE II                 2                 3
  STAGE IIA              106               236
  STAGE IIB               62               172
  STAGE III                1                 1
  STAGE IIIA              48                94
  STAGE IIIB               9                20
  STAGE IIIC              16                47
  STAGE IV                 5                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    71 174  41  12
  5P GAIN WILD-TYPE 194 420  83  27
D9V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1              71               194
  T2             174               420
  T3              41                83
  T4              12                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
  5P GAIN MUTATED   153  82  43  16
  5P GAIN WILD-TYPE 328 257  70  58
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0             153               328
  N1              82               257
  N2              43                70
  N3              16                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
  5P GAIN MUTATED          1 261   5  31
  5P GAIN WILD-TYPE        4 593  14 116
D9V6, multiclass
          clus
vv         5P GAIN MUTATED 5P GAIN WILD-TYPE
  CM0 (I+)               1                 4
  M0                   261               593
  M1                     5                14
  MX                    31               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"
D9V7, binary
                   cls
clus                  0   1
  5P GAIN MUTATED   293   5
  5P GAIN WILD-TYPE 721   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED    293    5
  5P GAIN WILD-TYPE  721    6
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE             293               721
  MALE                 5                 6
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  5P GAIN MUTATED                            1                           225
  5P GAIN WILD-TYPE                          0                           529
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  5P GAIN MUTATED                               50                   2
  5P GAIN WILD-TYPE                            125                   4
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  5P GAIN MUTATED                                  6                  2
  5P GAIN WILD-TYPE                               23                 13
                   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                225               529
  INFILTRATING LOBULAR CARCINOMA                50               125
  MEDULLARY CARCINOMA                            2                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               6                23
  MUCINOUS CARCINOMA                             2                13
  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    89 209
  5P GAIN WILD-TYPE 193 534
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     89  209
  5P GAIN WILD-TYPE  193  534
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               89               193
  YES             209               534
[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                          40   212
  5P GAIN WILD-TYPE                       118   505
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                     40               118
  WHITE                                        212               505
[1] 4 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    10 239
  5P GAIN WILD-TYPE  26 587
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     10  239
  5P GAIN WILD-TYPE   26  587
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                  10                26
  NOT HISPANIC OR LATINO             239               587
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED   179  18
  5Q GAIN WILD-TYPE 707 101
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              197               808 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               18               101 
$`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        24.39        26.96        21.14 
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        61.28        87.22        85.35        50.96 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A5QM TCGA-AR-A5QP 
       72.76        58.92        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       103.63        24.53 
TCGA-BH-A0AZ TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BJ TCGA-BH-A0BL 
       28.50        48.36        56.98        37.22        21.70        44.05 
TCGA-BH-A0C1 TCGA-BH-A0DI TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0EB TCGA-BH-A0EE 
       44.02        22.13        15.65         2.56        24.49        31.00 
TCGA-BH-A0H7 TCGA-BH-A0HQ TCGA-BH-A0HX TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18K 
       23.08        36.85        27.25        42.35        44.81        90.84 
TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO 
       26.66        72.56        37.74        51.39        69.93        91.99 
TCGA-BH-A1EU TCGA-BH-A1F6 TCGA-BH-A202 TCGA-BH-A2L8 TCGA-C8-A12P TCGA-C8-A135 
       42.28        97.48         0.72        20.12        11.77         0.62 
TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1JE 
       11.34        11.34        12.03        21.14        14.17        18.90 
TCGA-D8-A1JH TCGA-D8-A1JJ TCGA-D8-A1JT TCGA-D8-A1X6 TCGA-D8-A1XA TCGA-D8-A1XB 
       14.01        20.09        13.32        17.79        27.58        18.15 
TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A27I 
       16.31        12.99        16.54        15.52        14.24        14.43 
TCGA-D8-A27V TCGA-D8-A27W TCGA-E2-A107 TCGA-E2-A10B TCGA-E2-A14O TCGA-E2-A14S 
       12.53        12.26        34.42        37.51        44.68        33.17 
TCGA-E2-A14T TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A1B4 
       33.30        27.12        23.24        20.71        18.21        29.95 
TCGA-E2-A1B5 TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L6 
       32.35        17.10        33.73        22.19        11.08        54.18 
TCGA-E2-A1L9 TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A56Z TCGA-E2-A9RU TCGA-E9-A1N6 
       19.66        18.87       106.75         7.20         9.21        13.48 
TCGA-E9-A1NI TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1RC 
        9.86         2.10         6.12         1.38         2.76        40.24 
TCGA-E9-A1RD TCGA-E9-A1RG TCGA-E9-A249 TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A54X 
        0.66        21.27         0.95         0.72        17.75        12.33 
TCGA-E9-A5FL TCGA-E9-A5UP TCGA-EW-A1IY TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1P5 
        0.26        14.40         8.48        16.57        28.77        23.11 
TCGA-EW-A1PC TCGA-EW-A423 TCGA-GM-A2DC TCGA-GM-A3NW TCGA-GM-A3XN TCGA-GM-A5PV 
        6.15        10.16        53.52       110.50        66.38        13.55 
TCGA-LD-A66U TCGA-LL-A6FQ TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-MS-A51U TCGA-OL-A66N 
       21.24         2.63         6.21         7.36         2.79        26.04 
TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-W8-A86G TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        6.81         8.65         5.29       100.01       105.04 

$`5Q GAIN WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        0.39         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SP 
       47.24        20.88        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-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       136.73 
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-A0EO 
       34.55        33.76        28.77        25.22       101.72        80.28 
TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EW TCGA-A2-A0EX 
      107.61        79.76        74.40        37.05        29.75        24.72 
TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX 
       24.16        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-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YH TCGA-A2-A0YI 
       17.46        32.55        25.28        15.42        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        48.46        31.73        23.77        23.47 
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-A3XV TCGA-A2-A3XW TCGA-A2-A3XX 
       39.65        33.93        83.01        32.75        49.48        38.40 
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        21.30        23.21 
TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 
       21.90        35.31        34.29        35.47        30.61        37.45 
TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       35.67        31.73        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-A3IY 
       24.26        23.74        23.80        21.73        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-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-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06T TCGA-A8-A06U 
        9.37        10.42         8.75        13.02        53.06        29.03 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B 
       31.00        26.01        17.03        53.98         9.01        43.00 
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-A082 TCGA-A8-A084 
       10.98         8.98         7.99        24.99        18.05        15.06 
TCGA-A8-A085 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08I 
       36.95         0.99        38.01        28.96        33.01        12.00 
TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08T 
       37.05         9.99        31.00        31.00        33.01        93.04 
TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A099 TCGA-A8-A09A 
       43.00        40.01        33.01        30.97         9.99         9.99 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N 
       50.04        49.05        45.07        29.98        33.07         1.02 
TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A2 TCGA-A8-A0A6 
       25.02        19.04        15.02         0.99        19.04        21.04 
TCGA-A8-A0A7 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A2B8 
        0.99        17.03        38.04         0.95         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-A3BB TCGA-AC-A3OD 
       26.04        50.70         1.02         0.92         0.99        14.83 
TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ 
       22.19         1.12        16.57        19.79        23.24        24.79 
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-A6NO TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A041 
        0.43         1.68         1.12         1.32         0.33         0.23 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AK 
        0.33         0.62         2.96         1.78         1.71         7.36 
TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ 
        6.51         0.33         0.33         6.44         4.64         7.96 
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-A0FY 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-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-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0JA 
       21.40        52.18        24.16        37.48        22.36        21.53 
TCGA-AO-A0JB TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ 
       50.70        72.00        21.37        26.24        50.24        62.04 
TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 
       55.33       102.58        99.25       108.72       106.78        96.10 
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-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       61.87        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        32.52         2.56        32.91         9.99       111.32 
TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX 
       49.32        74.79        86.66        29.75        98.93        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       101.95        83.87       114.02 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
       85.97        75.55        52.77        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        37.81        76.21 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L 
       63.62        62.14        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-A24T 
       96.89        78.51        84.20         0.85       101.52        76.01 
TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 
       53.36        83.77        79.00        56.15        78.48        73.18 
TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN 
       93.83       128.65        20.25        62.86        40.04        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QN TCGA-AR-A5QQ TCGA-B6-A0I1 
       39.39        40.54        20.38        16.04        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-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-A1KC TCGA-B6-A1KF 
      186.48        28.27        68.94        58.88        43.59       101.52 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A40C TCGA-BH-A0AV 
      139.17       170.17        85.35        54.28        55.00        38.79 
TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 
       20.45        25.55        46.95        40.83        39.55        39.16 
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-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-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-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-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-A0HU TCGA-BH-A0HW 
       20.38         5.85         2.50        13.61        12.89        51.32 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0WA TCGA-BH-A18F 
       50.79         5.59        23.93        24.95        23.05         8.81 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R 
        2.01         7.23        20.12        30.28        55.63        37.55 
TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EV 
       66.05         7.36        51.16       113.82        82.85        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-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-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 
       72.07         6.90        38.60        83.31        57.83       130.16 
TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12L 
       10.65         6.44         0.99       109.28         8.94        11.93 
TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V 
       11.77        11.77        12.66         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-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HJ TCGA-C8-A1HL 
        3.85         3.75        12.33        10.92         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-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-A147 TCGA-D8-A1J9 
       20.58        13.97        14.17        13.48        19.20        17.49 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JF TCGA-D8-A1JG 
       16.50        18.71        15.78        18.15        12.03        12.03 
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-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-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27E 
       15.16        12.66        15.32         3.81        14.14        17.42 
TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M 
       16.04        13.45        13.05         9.44        16.41        13.48 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A3Z5 TCGA-D8-A3Z6 
        4.80         0.76        10.09        13.08        14.50        18.51 
TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10C 
        7.33        43.00        27.52        46.59        40.41        40.11 
TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R 
       28.44        28.87        47.15        40.96        38.24        38.60 
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-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 
       25.41        19.43        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-A15I 
       23.34        22.82        17.29        21.63        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-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1II 
       28.50        16.47        38.30        37.41        32.78        33.70 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A1L8 
       28.44        22.65         3.88        20.98        27.42        39.62 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL 
       24.59        40.47        28.90       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        30.61        34.92        19.89 
TCGA-E2-A576 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA 
       19.00        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-A1QZ 
       39.55        12.59        35.77        20.05        21.57        11.90 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RE 
       14.30         0.62        21.21        32.09        20.81        34.65 
TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 
        6.58        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-A244 TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A24A 
       17.06         0.69         0.85        27.22         1.94        24.56 
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-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ 
       14.70        13.81        15.39        12.20        39.72        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX 
       18.90        13.25        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-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-A424 TCGA-GI-A2C8 
       25.91        22.09        21.27        17.49        10.59         7.40 
TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DF 
      109.87        59.57       194.27        53.13        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-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A4E0 TCGA-GM-A5PX 
       53.36        38.20        43.73        69.30        72.03        18.12 
TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF 
       11.84        11.57         6.67         4.08         4.60         8.75 
TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM 
        9.53        11.44        10.95         7.59        17.06        15.32 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FR TCGA-LL-A73Y 
       14.70        14.47        14.79        11.57         3.88         4.14 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LQ-A4E4 TCGA-OK-A5Q2 
        4.50         4.50         5.59         3.22        27.91         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
       12.66        46.55        31.99        58.62        27.65        34.92 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H 
       36.36        16.87        24.72        22.32        20.38        26.70 
TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P 
       23.47        65.62        33.57        31.07         7.23        14.07 
TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PL-A8LV TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ 
       28.21        19.73         0.23         0.16         0.26         3.95 
TCGA-S3-A6ZF TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 
       16.50        10.59         7.92         5.56         8.52         7.17 
TCGA-S3-AA15 TCGA-S3-AA17 TCGA-XX-A899 TCGA-XX-A89A 
        6.87         3.91         9.60         9.14 

  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 
           20.120            23.675 
[1] "0.2 - 113.8 (20.1)" "0.0 - 234.3 (23.7)"
[1] "hr=" "1"  
D10V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5Q GAIN MUTATED        19       14        0        2        63        45
  5Q GAIN WILD-TYPE      64       66        9        3       279       189
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5Q GAIN MUTATED           1         35          5         13        1
  5Q GAIN WILD-TYPE         1        107         24         50       17
                   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                 19                64
  STAGE IA                14                66
  STAGE IB                 0                 9
  STAGE II                 2                 3
  STAGE IIA               63               279
  STAGE IIB               45               189
  STAGE III                1                 1
  STAGE IIIA              35               107
  STAGE IIIB               5                24
  STAGE IIIC              13                50
  STAGE IV                 1                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
  5Q GAIN MUTATED    52 108  33   7
  5Q GAIN WILD-TYPE 213 486  91  32
D10V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1              52               213
  T2             108               486
  T3              33                91
  T4               7                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
  5Q GAIN MUTATED    99  58  28  13
  5Q GAIN WILD-TYPE 382 281  85  61
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0              99               382
  N1              58               281
  N2              28                85
  N3              13                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
  5Q GAIN MUTATED          1 172   1  26
  5Q GAIN WILD-TYPE        4 682  18 121
D10V6, multiclass
          clus
vv         5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CM0 (I+)               1                 4
  M0                   172               682
  M1                     1                18
  MX                    26               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"
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED   198   2
  5Q GAIN WILD-TYPE 816   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED    198    2
  5Q GAIN WILD-TYPE  816    9
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE             198               816
  MALE                 2                 9
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  5Q GAIN MUTATED                            0                           140
  5Q GAIN WILD-TYPE                          1                           614
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  5Q GAIN MUTATED                               43                   1
  5Q GAIN WILD-TYPE                            132                   5
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  5Q GAIN MUTATED                                  5                  2
  5Q GAIN WILD-TYPE                               24                 13
                   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                140               614
  INFILTRATING LOBULAR CARCINOMA                43               132
  MEDULLARY CARCINOMA                            1                 5
  MIXED HISTOLOGY (PLEASE SPECIFY)               5                24
  MUCINOUS CARCINOMA                             2                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"
D10V9, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    59 141
  5Q GAIN WILD-TYPE 223 602
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     59  141
  5Q GAIN WILD-TYPE  223  602
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO               59               223
  YES             141               602
[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                          17   152
  5Q GAIN WILD-TYPE                       141   565
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                     17               141
  WHITE                                        152               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"
D10V12, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     7 159
  5Q GAIN WILD-TYPE  29 667
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      7  159
  5Q GAIN WILD-TYPE   29  667
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                29
  NOT HISPANIC OR LATINO             159               667
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED   172  27
  6P GAIN WILD-TYPE 714  92
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              199               806 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               27                92 
$`6P GAIN MUTATED`
TCGA-5T-A9QA TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A2-A04T TCGA-A2-A04X TCGA-A2-A0CM 
        0.39        31.79        28.01        73.84        55.43        24.79 
TCGA-A2-A0D2 TCGA-A2-A0EQ TCGA-A2-A0ET TCGA-A2-A0EV TCGA-A2-A0EY TCGA-A2-A0T2 
       33.76        79.76        35.05        31.82        24.16         8.38 
TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FX 
       18.21        21.90        18.61        31.73        23.77        36.79 
TCGA-A2-A25C TCGA-A2-A3XS TCGA-A2-A3XV TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 
       17.19        33.93        32.75        38.40        34.98        38.37 
TCGA-A2-A4S1 TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A13F TCGA-A7-A26I 
       26.96        38.30        30.61        35.67        12.72        21.73 
TCGA-A7-A26J TCGA-A7-A425 TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A6VV 
       20.61        14.70        14.50        21.17        17.92        10.29 
TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07F TCGA-A8-A07R 
       17.98        31.00        17.03        53.98        18.97         8.98 
TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08R TCGA-A8-A08S 
       24.99         9.99        38.01        28.96         0.99        33.01 
TCGA-A8-A092 TCGA-A8-A09B TCGA-A8-A09E TCGA-A8-A09Q TCGA-AC-A23E TCGA-AC-A2QH 
       30.97        12.00        49.05        25.02         2.37         1.02 
TCGA-AC-A3W5 TCGA-AC-A62X TCGA-AC-A8OQ TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A0AJ 
       16.57         1.12         1.12         0.33         0.23         8.02 
TCGA-AN-A0AM TCGA-AN-A0FK TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0XN TCGA-AO-A03L 
        0.16         7.00         0.36         0.33         0.33        80.28 
TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A129 
       66.77        81.63        55.33        71.80       102.58        96.10 
TCGA-AO-A12B TCGA-AO-A12F TCGA-AO-A1KS TCGA-AQ-A0Y5 TCGA-AQ-A7U7 TCGA-AR-A0TR 
       77.56        48.36         0.53         5.65         9.99         5.26 
TCGA-AR-A0TS TCGA-AR-A0TV TCGA-AR-A0U0 TCGA-AR-A1AV TCGA-AR-A24Q TCGA-AR-A24Z 
       74.79        29.75        65.36        61.28       101.52        79.00 
TCGA-AR-A250 TCGA-AR-A255 TCGA-AR-A2LL TCGA-AR-A2LR TCGA-B6-A0I2 TCGA-B6-A0I9 
       56.15        58.92         7.36        20.38       143.38        12.13 
TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0RU TCGA-B6-A0WY TCGA-B6-A0X1 TCGA-B6-A1KC 
       84.59       110.14       131.21       113.79       186.48        43.59 
TCGA-B6-A1KF TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AW 
      101.52        54.28        49.94        55.00        38.79        20.45 
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-A0DH TCGA-BH-A0EB TCGA-BH-A0HQ 
       45.57        49.05        44.02        38.01        24.49        36.85 
TCGA-BH-A0WA TCGA-BH-A18K TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A1EN TCGA-BH-A1EO 
       23.05        90.84        55.63         7.36        69.93        91.99 
TCGA-BH-A1EV TCGA-BH-A1F2 TCGA-BH-A1FC TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A209 
       12.00        31.53       114.15        38.60        57.83       130.16 
TCGA-BH-A42V TCGA-C8-A12L TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A1HJ TCGA-C8-A1HM 
        8.94        11.93        12.66         3.12         0.16         2.30 
TCGA-C8-A26X TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A1J8 TCGA-D8-A1JJ 
        0.36        20.88        13.97        14.17        14.17        20.09 
TCGA-D8-A1JL TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XQ TCGA-D8-A1XY 
       20.09        21.83        14.50        19.92        16.41        16.54 
TCGA-D8-A1XZ TCGA-D8-A1Y3 TCGA-D8-A27F TCGA-D8-A27R TCGA-D8-A27V TCGA-E2-A10C 
       15.32        14.14        16.04        10.09        12.53        40.11 
TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A159 TCGA-E2-A15M TCGA-E2-A15S 
       31.96        17.03        25.41        25.05         7.73        14.07 
TCGA-E2-A1B0 TCGA-E2-A1II TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1LH TCGA-E2-A1LI 
       53.62        33.70         3.88        22.19       106.75       102.61 
TCGA-E2-A2P5 TCGA-E2-A56Z TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N9 TCGA-E9-A1ND 
       16.93         7.20        34.92        19.89        13.12        12.59 
TCGA-E9-A1RF TCGA-E9-A295 TCGA-E9-A3HO TCGA-E9-A3QA TCGA-E9-A54Y TCGA-EW-A1OV 
        6.58         0.72        26.07         0.62         0.23        25.94 
TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A2FV 
       22.82        29.82        18.48        30.08         7.86        25.91 
TCGA-EW-A423 TCGA-GI-A2C9 TCGA-GM-A2DF TCGA-LD-A7W5 TCGA-LL-A441 TCGA-LL-A5YN 
       10.16       109.87        42.71         4.08        11.44        14.70 
TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A740 TCGA-LL-A7T0 TCGA-OL-A5DA TCGA-OL-A5RW 
        3.88         4.14         4.50         3.22        58.62        36.36 
TCGA-OL-A5S0 TCGA-OL-A66I TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-AA0Z TCGA-S3-AA10 
       20.38        23.47         3.95        16.50        10.59         7.92 
TCGA-Z7-A8R5 
      100.01 

$`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       136.73        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        48.46        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        24.39        21.30        23.21        21.14        21.90 
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        53.06        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        43.00        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        33.01        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 
       43.00        40.01        33.01        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        50.04        45.07        29.98 
TCGA-A8-A09M 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-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        22.19         1.12        19.79        23.24 
TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW 
       24.79         1.55         0.07         1.81         1.18         0.69 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A046 
        0.43         1.68         1.74         1.32         0.33         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-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-A0FV TCGA-AN-A0FX 
        7.59         7.17         6.28         6.02         0.33         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XL 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-A03P 
        0.33         0.33         5.33         5.59        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 
       52.18        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-A125 TCGA-AO-A126 TCGA-AO-A128 
       26.24        50.24        62.04        99.25       108.72       106.78 
TCGA-AO-A12A TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
       90.58        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-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0TP 
      130.09        15.62        32.52         2.56        32.91       111.32 
TCGA-AR-A0TQ TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
       49.32        86.66        98.93        64.83        55.86        76.14 
TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
      101.95        83.87       114.02        85.97        75.55        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-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW 
       39.98        43.07        17.23        37.81        76.21        63.62 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M 
       62.14        20.22       109.58        50.89        73.02        96.89 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24U 
       78.51        84.20         0.85        87.22        76.01        53.36 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 
       85.35        50.96        83.77        78.48        73.18        72.76 
TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM 
       93.83       128.65        20.25        62.86        42.87        40.04 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP 
       38.17        39.39        40.54        54.74        16.04        20.45 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC 
       10.59        77.62       149.59       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-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-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 
       17.98        21.47       129.57       129.70        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A40B 
       58.88        73.51       139.17       170.17        85.35       103.63 
TCGA-BH-A0AU TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B5 
       24.53        28.50        46.95        40.83        39.16        48.36 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ 
       56.98        51.68        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-A0BV TCGA-BH-A0BW TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD 
       49.94        11.67        41.75        48.13        42.90        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-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-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ 
       46.19        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-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-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-A18F TCGA-BH-A18G TCGA-BH-A18I 
       24.95        42.35        44.81         8.81         2.01         7.23 
TCGA-BH-A18J TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18R 
       20.12        26.66        72.56        37.74        30.28        37.55 
TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU 
       66.05        51.39        51.16       113.82        82.85        42.28 
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-A202 TCGA-BH-A204 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
        6.90         0.72        83.31        10.65         6.44        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P 
        0.99       109.28        11.77        11.77        12.66        11.77 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A131 TCGA-C8-A132 
        0.07        12.66        12.66        12.66         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-A1HG TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26V 
       11.34        11.34        12.03        10.42         3.25         0.30 
TCGA-C8-A26W TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
        0.23         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-A140 TCGA-D8-A141 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J9 
       13.25        20.58        13.48        21.14        19.20        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-A1JK TCGA-D8-A1JM TCGA-D8-A1JN 
       12.03        14.01        18.97        20.12        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-A1XM TCGA-D8-A1XO TCGA-D8-A1XR 
       17.16        15.22        14.73        17.69         7.96        15.85 
TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1Y0 
       16.31         6.35        12.99        15.16        12.66        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I 
        3.81        14.24        17.42        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-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-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-A152 
       33.30        43.33        34.26        32.02        28.60        27.12 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15A 
       23.24        19.43        21.04        23.87        14.79        23.34 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H 
       22.82        17.29        20.71        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-A15T TCGA-E2-A1AZ TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       17.06        14.99        60.53        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-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       33.73        28.44        22.65        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-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 
       18.87         8.75        43.04         5.52        15.72        30.61 
TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 
       19.00         9.21        19.20        36.82        13.48        12.00 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI 
       36.56        39.55        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-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-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-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3X8 
        0.95        24.56        17.75         0.76        18.41        15.72 
TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE 
       12.33        14.70         0.26        13.81        14.40        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-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ 
       16.57        15.68        28.77        29.95        29.85        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1PA TCGA-EW-A1PB 
       41.13        39.78        52.96        23.11        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-A2FS TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 
       55.00        52.73        22.09        21.27        17.49        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-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        43.73        69.30        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U 
       72.03        13.55        18.12        11.84        11.57        21.24 
TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y 
        6.67         4.60         8.75         9.53        10.95         7.59 
TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ 
       17.06        15.32        14.47        14.79        11.57         2.63 
TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
        4.50         5.59         6.21         7.36        27.91         2.79 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5RU TCGA-OL-A5RV 
        2.10        12.66        46.55        31.99        27.65        34.92 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K 
       16.87        24.72        22.32        26.70        65.62        33.57 
TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ 
       31.07        26.04         7.23        14.07        28.21        19.73 
TCGA-PL-A8LV TCGA-PL-A8LX TCGA-PL-A8LY TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA11 
        0.23         0.16         0.26         6.81         8.65         5.56 
TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-W8-A86G TCGA-XX-A899 
        8.52         7.17         6.87         3.91         5.29         9.60 
TCGA-XX-A89A TCGA-Z7-A8R6 
        9.14       105.04 

  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 
            23.77             22.16 
[1] "0.2 - 186.5 (23.8)" "0.0 - 234.3 (22.2)"
[1] "hr=" "1.2"
D11V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6P GAIN MUTATED        15        8        3        1        76        47
  6P GAIN WILD-TYPE      68       72        6        4       266       187
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6P GAIN MUTATED           0         26          7         10        4
  6P GAIN WILD-TYPE         2        116         22         53       14
                   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                68
  STAGE IA                 8                72
  STAGE IB                 3                 6
  STAGE II                 1                 4
  STAGE IIA               76               266
  STAGE IIB               47               187
  STAGE III                0                 2
  STAGE IIIA              26               116
  STAGE IIIB               7                22
  STAGE IIIC              10                53
  STAGE IV                 4                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 GAIN MUTATED    38 130  24   7
  6P GAIN WILD-TYPE 227 464 100  32
D11V4, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1              38               227
  T2             130               464
  T3              24               100
  T4               7                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
  6P GAIN MUTATED    97  61  25  11
  6P GAIN WILD-TYPE 384 278  88  63
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0              97               384
  N1              61               278
  N2              25                88
  N3              11                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
  6P GAIN MUTATED          0 166   4  29
  6P GAIN WILD-TYPE        5 688  15 118
D11V6, multiclass
          clus
vv         6P GAIN MUTATED 6P GAIN WILD-TYPE
  CM0 (I+)               0                 5
  M0                   166               688
  M1                     4                15
  MX                    29               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"
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED   198   1
  6P GAIN WILD-TYPE 816  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED    198    1
  6P GAIN WILD-TYPE  816   10
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE             198               816
  MALE                 1                10
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  6P GAIN MUTATED                            0                           163
  6P GAIN WILD-TYPE                          1                           591
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  6P GAIN MUTATED                               17                   4
  6P GAIN WILD-TYPE                            158                   2
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  6P GAIN MUTATED                                  3                  1
  6P GAIN WILD-TYPE                               26                 14
                   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                163               591
  INFILTRATING LOBULAR CARCINOMA                17               158
  MEDULLARY CARCINOMA                            4                 2
  MIXED HISTOLOGY (PLEASE SPECIFY)               3                26
  MUCINOUS CARCINOMA                             1                14
  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    62 137
  6P GAIN WILD-TYPE 220 606
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     62  137
  6P GAIN WILD-TYPE  220  606
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO               62               220
  YES             137               606
[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                          44   129
  6P GAIN WILD-TYPE                       114   588
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                     44               114
  WHITE                                        129               588
[1] 4 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     9 157
  6P GAIN WILD-TYPE  27 669
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      9  157
  6P GAIN WILD-TYPE   27  669
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   9                27
  NOT HISPANIC OR LATINO             157               669
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED   122  19
  6Q GAIN WILD-TYPE 764 100
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              141               864 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               19               100 
$`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        26.96        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 
       38.01        28.96         0.99        33.01        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        74.79        86.66        29.75 
TCGA-AR-A0U0 TCGA-AR-A1AI TCGA-AR-A1AV TCGA-AR-A24Q TCGA-AR-A24Z TCGA-AR-A2LL 
       65.36        61.84        61.28       101.52        79.00         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-A1F2 TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A209 
       91.99        12.00        31.53        38.60        57.83       130.16 
TCGA-BH-A42V TCGA-C8-A12L TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A1HJ TCGA-C8-A1HM 
        8.94        11.93        12.66         3.12         0.16         2.30 
TCGA-C8-A26X TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A1J8 TCGA-D8-A1JJ 
        0.36        20.88        13.97        14.17        14.17        20.09 
TCGA-D8-A1JL TCGA-D8-A1JP TCGA-D8-A1X5 TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XQ 
       20.09        21.01        18.58        21.83        14.50        16.41 
TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y3 TCGA-D8-A27F TCGA-D8-A27V TCGA-E2-A10C 
       16.54        15.32        14.14        16.04        12.53        40.11 
TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A159 TCGA-E2-A15M TCGA-E2-A1B0 
       31.96        17.03        25.41        25.05         7.73        53.62 
TCGA-E2-A1II TCGA-E2-A1LH TCGA-E2-A2P5 TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N9 
       33.70       106.75        16.93        34.92        19.89        13.12 
TCGA-E9-A1NF TCGA-E9-A3QA TCGA-E9-A54Y TCGA-EW-A1OV TCGA-EW-A1P4 TCGA-EW-A1P6 
       20.05         0.62         0.23        25.94        29.82        18.48 
TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A423 TCGA-GI-A2C9 TCGA-GM-A2DH TCGA-LD-A7W5 
       30.08         7.86        10.16       109.87        42.28         4.08 
TCGA-LL-A5YN TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A7T0 TCGA-OL-A5DA TCGA-PL-A8LZ 
       14.70         3.88         4.14         3.22        58.62         3.95 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-Z7-A8R5 
       10.59         7.92       100.01 

$`6Q GAIN WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        0.39         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ 
       47.24        20.88         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-A04U 
      104.81        18.02        41.95        82.16        73.84        22.06 
TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO 
       63.12        64.04        36.13       136.73        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-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D3 
       63.45        64.04        56.81        21.14        34.55        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-A0SX TCGA-A2-A0SY 
       99.19        54.64        27.12        44.88        50.43        44.28 
TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.52        17.13        18.71        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-A1FW 
       19.33        48.46        31.73        23.77        23.47        17.36 
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        32.75        49.48 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       31.99        38.37         7.30        24.39        21.30        23.21 
TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 
       21.14        21.90        35.31        34.29        35.47        37.45 
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-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW 
       11.97        14.93        13.74        14.73        12.10        10.72 
TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P 
       11.05         9.37        10.42         8.75        13.02        13.02 
TCGA-A8-A06Q TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 
        1.02        53.06        29.03        26.01         1.02        53.98 
TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J 
        9.01        43.00        19.99        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        24.99         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-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O 
       33.01        19.96        12.00        37.05         9.99        31.00 
TCGA-A8-A08P TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 
       31.00        93.04        43.00        40.01        33.01        30.97 
TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09C 
       17.95        41.98        12.00         9.99         9.99         1.02 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N 
       50.04        49.05        45.07        29.98        33.07         1.02 
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-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK 
       38.04         0.95        10.85         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-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-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ 
       22.19         1.12        16.57        19.79        23.24        24.79 
TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX 
        1.55         0.07         1.81         1.18         0.69         0.43 
TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A041 
        1.68         1.74         1.12         1.32         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-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-A0FX TCGA-AN-A0FZ 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-A03P 
        5.33         5.59        80.28        47.84        66.77        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 
       52.18        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        50.24        62.04        55.33        71.80        99.25 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G 
      108.72       106.78        90.58        64.04        57.30        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-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N 
       24.79        26.93       130.09        15.62        32.52         2.56 
TCGA-AQ-A54O TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TW TCGA-AR-A0TX 
       32.91       111.32        49.32         5.26        98.93        64.83 
TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 
       55.86        76.14       101.95        83.87       114.02        85.97 
TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
       75.55        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        37.81        76.21 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L 
       63.62        62.14        20.22       109.58        50.89        73.02 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24T 
       96.89        78.51        84.20         0.85        87.22        76.01 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A251 
       53.36        85.35        50.96        83.77        56.15        78.48 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH 
       73.18        72.76        58.92        93.83       128.65        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       62.86        42.87        40.04        38.17        39.39        40.54 
TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I5 
       54.74        16.04        20.45        10.59        77.62       149.59 
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-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-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
      170.17        85.35        49.94       103.63        55.00        24.53 
TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B5 
       20.45        28.50        46.95        40.83        39.16        48.36 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ 
       56.98        51.68        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-A0BV TCGA-BH-A0BW TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD 
       49.94        11.67        41.75        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-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-A0EE TCGA-BH-A0EI TCGA-BH-A0GY 
       44.81        46.19        32.65        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-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-A1EN TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW 
       51.16        69.93       113.82        82.85        42.28        55.69 
TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 
       49.58        17.69        25.81        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-A204 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
        6.90         0.72        83.31        10.65         6.44        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P 
        0.99       109.28        11.77        11.77        12.66        11.77 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A131 TCGA-C8-A132 
        0.07        12.66        12.66        12.66         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-A1HG TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26V 
       11.34        11.34        12.03        10.42         3.25         0.30 
TCGA-C8-A26W TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
        0.23         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-A140 TCGA-D8-A141 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J9 
       13.25        20.58        13.48        21.14        19.20        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-A1JK TCGA-D8-A1JM TCGA-D8-A1JN 
       12.03        14.01        18.97        20.12        19.40        20.38 
TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 
       12.20        13.32        14.70        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-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS 
       14.73        19.92        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-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-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-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-A152 
       33.30        43.33        34.26        32.02        28.60        27.12 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15A 
       23.24        19.43        21.04        23.87        14.79        23.34 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H 
       22.82        17.29        20.71        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-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-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-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-A1LI TCGA-E2-A1LK 
       24.59        40.47        28.90        18.87       102.61         8.75 
TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A576 
       43.04         5.52        15.72         7.20        30.61        19.00 
TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1NA 
        9.21        19.20        36.82        13.48        12.00        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-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-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        24.56         0.72        17.75         0.76        26.07 
TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO 
       18.41        15.72        12.33        14.70         0.26        13.81 
TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
       14.40        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-A1OW 
       18.90        13.25        16.57        15.68        28.77        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-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE 
       23.11        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-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-A2DD TCGA-GM-A2DF TCGA-GM-A2DI 
      194.27        53.13        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        43.73        69.30        66.38        72.03        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        21.24         6.67         4.60 
TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL 
        8.75         9.53        11.44        10.95         7.59        17.06 
TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Z 
       15.32        14.47        14.79        11.57         2.63         4.50 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
        4.50         5.59         6.21         7.36        27.91         2.79 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5RU TCGA-OL-A5RV 
        2.10        12.66        46.55        31.99        27.65        34.92 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H 
       36.36        16.87        24.72        22.32        20.38        26.70 
TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O 
       23.47        65.62        33.57        31.07        26.04         7.23 
TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PL-A8LV TCGA-PL-A8LX TCGA-PL-A8LY 
       14.07        28.21        19.73         0.23         0.16         0.26 
TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 
       16.50         6.81         8.65         5.56         8.52         7.17 
TCGA-S3-AA15 TCGA-S3-AA17 TCGA-W8-A86G TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
        6.87         3.91         5.29         9.60         9.14       105.04 

  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 
           21.010            22.785 
[1] "0.2 - 143.4 (21.0)" "0.0 - 234.3 (22.8)"
[1] "hr=" "1.4"
D12V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6Q GAIN MUTATED        12        5        2        1        58        30
  6Q GAIN WILD-TYPE      71       75        7        4       284       204
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6Q GAIN MUTATED           0         17          5          8        2
  6Q GAIN WILD-TYPE         2        125         24         55       16
                   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                71
  STAGE IA                 5                75
  STAGE IB                 2                 7
  STAGE II                 1                 4
  STAGE IIA               58               284
  STAGE IIB               30               204
  STAGE III                0                 2
  STAGE IIIA              17               125
  STAGE IIIB               5                24
  STAGE IIIC               8                55
  STAGE IV                 2                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
  6Q GAIN MUTATED    24  93  19   5
  6Q GAIN WILD-TYPE 241 501 105  34
D12V4, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1              24               241
  T2              93               501
  T3              19               105
  T4               5                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
  6Q GAIN MUTATED    79  37  15   9
  6Q GAIN WILD-TYPE 402 302  98  65
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0              79               402
  N1              37               302
  N2              15                98
  N3               9                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
  6Q GAIN MUTATED          0 121   2  18
  6Q GAIN WILD-TYPE        5 733  17 129
D12V6, multiclass
          clus
vv         6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CM0 (I+)               0                 5
  M0                   121               733
  M1                     2                17
  MX                    18               129
[1] 4 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   140   1
  6Q GAIN WILD-TYPE 874  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED    140    1
  6Q GAIN WILD-TYPE  874   10
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE             140               874
  MALE                 1                10
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  6Q GAIN MUTATED                            0                           114
  6Q GAIN WILD-TYPE                          1                           640
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  6Q GAIN MUTATED                               12                   4
  6Q GAIN WILD-TYPE                            163                   2
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  6Q GAIN MUTATED                                  3                  1
  6Q GAIN WILD-TYPE                               26                 14
                   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                114               640
  INFILTRATING LOBULAR CARCINOMA                12               163
  MEDULLARY CARCINOMA                            4                 2
  MIXED HISTOLOGY (PLEASE SPECIFY)               3                26
  MUCINOUS CARCINOMA                             1                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"
D12V9, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    43  98
  6Q GAIN WILD-TYPE 239 645
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     43   98
  6Q GAIN WILD-TYPE  239  645
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO               43               239
  YES              98               645
[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                          29    92
  6Q GAIN WILD-TYPE                       129   625
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                     29               129
  WHITE                                         92               625
[1] 4 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     7 110
  6Q GAIN WILD-TYPE  29 716
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      7  110
  6Q GAIN WILD-TYPE   29  716
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                29
  NOT HISPANIC OR LATINO             110               716
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED   254  36
  7P GAIN WILD-TYPE 632  83
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              290               715 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               36                83 
$`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        26.96 
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-A07U TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08P TCGA-A8-A08X TCGA-A8-A093 
       24.99        28.96        19.96        31.00        43.00        17.95 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09K TCGA-A8-A09M 
       41.98        12.00         9.99        12.00        29.98        33.07 
TCGA-A8-A09X TCGA-A8-A0A1 TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2FM TCGA-AC-A2QJ 
       14.01        12.00        10.85         2.66        26.04         2.27 
TCGA-AC-A3W5 TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OQ 
       16.57         0.07         1.81         1.68         1.74         1.12 
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       106.78        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        32.52        32.91         5.26 
TCGA-AR-A0U0 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AR TCGA-AR-A1AV TCGA-AR-A24H 
       65.36        83.87       114.02        17.23        61.28       109.58 
TCGA-AR-A24K TCGA-AR-A24Q TCGA-AR-A24W TCGA-AR-A250 TCGA-AR-A2LR TCGA-AR-A5QM 
       50.89       101.52        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-A1JD TCGA-D8-A1JF 
        0.03        14.17        21.14        14.17        18.15        12.03 
TCGA-D8-A1JG TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1X9 TCGA-D8-A1XF TCGA-D8-A1XL 
       12.03        20.12        20.09        23.90        15.22        19.92 
TCGA-D8-A1XR TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A27K 
       15.85        12.99        16.54        15.32         3.81         9.44 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-E2-A107 TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A14P 
       14.50        18.51        34.42        37.51        40.11        40.96 
TCGA-E2-A14R TCGA-E2-A14T TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A152 TCGA-E2-A153 
       38.60        33.30        34.26        32.02        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-A15M TCGA-E2-A15R TCGA-E2-A1AZ TCGA-E2-A1B5 TCGA-E2-A1BD 
       17.42         7.73        17.06        60.53        32.35        17.10 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IO TCGA-E2-A1L9 TCGA-E2-A1LE TCGA-E2-A1LI 
       33.73        33.70        20.98        19.66        28.90       102.61 
TCGA-E2-A1LL TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A9RU TCGA-E9-A1N8 
       43.04         7.20        30.61        34.92         9.21        12.00 
TCGA-E9-A1N9 TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1QZ TCGA-E9-A1R3 TCGA-E9-A1R4 
       13.12        12.59        20.05        11.90         2.10         6.12 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A226 TCGA-E9-A22E 
       21.21        32.09        20.81        40.24        34.13        12.89 
TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A3HO TCGA-E9-A3X8 
       27.22         0.95        24.56         0.72        26.07        15.72 
TCGA-E9-A54X TCGA-EW-A1IY TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1P0 TCGA-EW-A1P3 
       12.33         8.48        28.77        22.82        41.13        52.96 
TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A423 
       29.82        23.11         7.86        18.90        19.99        10.16 
TCGA-GI-A2C8 TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DL 
        7.40        53.13        53.52        43.04        42.71        90.84 
TCGA-GM-A3XN TCGA-JL-A3YW TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A5YM 
       66.38        11.84         8.75         9.53        11.44        15.32 
TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A740 TCGA-LL-A9Q3 TCGA-OL-A5D7 
       11.57         2.63         3.88         4.50         7.36        46.55 
TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66K 
       34.92        36.36        16.87        22.32        26.70        33.57 
TCGA-OL-A66N TCGA-OL-A66P TCGA-OL-A6VO TCGA-PL-A8LX TCGA-S3-A6ZF TCGA-S3-A6ZH 
       26.04        14.07        28.21         0.16        16.50         8.65 
TCGA-S3-AA17 TCGA-W8-A86G 
        3.91         5.29 

$`7P GAIN WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SH 
        0.39         8.52        14.37        43.43        14.27        47.24 
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       136.73        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-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-A0EW TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU 
       35.05        34.29        29.75        24.72        99.19        54.64 
TCGA-A2-A0SV TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T3 TCGA-A2-A0T4 
       27.12        50.43        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-A0YH TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT 
       21.67        14.50        19.33        48.46        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        32.75        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        24.39        21.30        23.21        21.14 
TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A13H 
       21.90        38.30        34.29        35.47        30.61        29.56 
TCGA-A7-A26E TCGA-A7-A26G TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY 
       31.36        23.74        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-A56D TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY 
       14.73        10.72        11.05         9.37        10.42         8.75 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A075 TCGA-A8-A079 
       13.02        13.02        53.06        29.03        17.03         9.01 
TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
       43.00        19.99        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        38.01 
TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R 
       33.01        12.00        37.05         9.99        31.00         0.99 
TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A099 
       33.01        93.04        40.01        33.01        30.97         9.99 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09N TCGA-A8-A09Q 
        1.02        50.04        49.05        45.07         1.02        25.02 
TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A2 TCGA-A8-A0A4 
        8.98        19.04        15.02         0.99        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-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-A3W6 TCGA-AC-A3YI 
        0.69        14.83        22.19         1.12        19.79        23.24 
TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX 
       24.79         1.55         1.12         1.18         0.69         0.43 
TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A04A 
        1.32         0.33         0.33         0.23         0.33         2.96 
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-A0FS TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0FZ 
        7.59         7.17         6.28         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-A0J2 
       84.69        68.75        47.87        59.05        29.13        32.78 
TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA 
       52.18        24.16        20.32        22.36        53.03        21.53 
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        50.24        62.04 
TCGA-AO-A0JM TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12F TCGA-AO-A12G 
       71.80       108.72        96.10        90.58        48.36        41.62 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H 
       28.37        14.73        82.62         0.53        17.79        24.79 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A0TP 
       26.93       130.09         5.65         2.56         9.99       111.32 
TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX 
       49.32        74.79        86.66        29.75        98.93        64.83 
TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
       55.86        76.14       101.95        85.97        75.55        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-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX 
       39.98        43.07        37.81        76.21        63.62        62.14 
TCGA-AR-A1AY TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
       20.22        73.02        96.89        78.51        84.20         0.85 
TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24X TCGA-AR-A24Z 
       87.22        76.01        53.36        85.35        83.77        79.00 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE 
       78.48        73.18        72.76        58.92        93.83       128.65 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN 
       20.25        62.86        42.87         7.36        40.04        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0IA 
       39.39        40.54        16.04        10.59        77.62       220.90 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IO TCGA-B6-A0IP 
       65.72       146.50       176.98        18.77       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-A402 TCGA-B6-A408 TCGA-B6-A40B 
       73.51       139.17       170.17        54.28        49.94       103.63 
TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B5 
       55.00        38.79        46.95        40.83        39.55        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-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       24.85        61.68        35.67        27.19        53.69        53.95 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DE 
       49.94        11.67        41.75        48.13        42.90        31.17 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DQ TCGA-BH-A0DV 
       23.44        38.01        22.13        13.91         3.22        45.17 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0EE 
       47.41        16.27        15.68        14.30        44.81        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-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 
       12.89        51.32        27.25        23.93        24.95        42.35 
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-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-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW 
        7.36        51.39       113.82        82.85        42.28        55.69 
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-A1FC TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
      114.15        74.73       122.89        36.92        63.35        55.00 
TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A204 
       45.63       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-A42T 
       57.83       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-A12U 
      109.28         8.94        11.77        11.77        12.66        12.66 
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-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HK 
        3.85        12.33        10.92        11.34         0.16        12.03 
TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A274 
       10.42         2.30         3.25         0.30         0.23         0.03 
TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M8 TCGA-D8-A13Y 
        0.03         0.03        12.20         0.99         0.23        11.90 
TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A145 TCGA-D8-A147 
       20.88        13.25        20.58        13.97        13.48        19.20 
TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JH 
       17.49        16.50        18.71        15.78        18.90        14.01 
TCGA-D8-A1JI TCGA-D8-A1JJ 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-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 
       13.32        14.70        18.58        17.79        16.73        25.74 
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-A1XS TCGA-D8-A1XT 
       14.50        17.69         7.96        16.41        16.31         6.35 
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-A27L TCGA-D8-A27M 
       16.04        13.45        13.05        14.43        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-A4Z1 TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10E 
        7.33        43.00        27.52        46.59        40.41        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14U 
       28.87        47.15        44.68        38.24        33.17        43.33 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A155 TCGA-E2-A156 
       31.96        28.60        17.03        25.41        21.04        23.87 
TCGA-E2-A158 TCGA-E2-A15C TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15J TCGA-E2-A15K 
       14.79        22.82        21.63        12.92        19.40         9.04 
TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 
       20.58        13.02        19.56        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-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IU 
       32.78        28.44        22.65         3.88        22.19        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LG 
       54.18        27.42        39.62        24.59        40.47        18.87 
TCGA-E2-A1LH TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A574 
      106.75         8.75        16.93         5.52        15.72        19.89 
TCGA-E2-A576 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1NA TCGA-E9-A1NC 
       19.00        19.20        36.82        13.48        36.56        39.55 
TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R5 
       35.77        21.57         9.86        14.30         0.62         1.38 
TCGA-E9-A1R6 TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH 
        2.76         0.66        34.65         6.58        21.27        34.59 
TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       35.64         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-A248 
       23.51        24.10        17.06         0.69         0.85         1.94 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54Y TCGA-E9-A5FK 
       17.75         0.76        18.41         0.62         0.23        14.70 
TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
        0.26        13.81        14.40        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-A1P1 TCGA-EW-A1P6 TCGA-EW-A1P7 
       29.95        29.85        40.41        39.78        18.48        30.08 
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-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DH TCGA-GM-A2DI 
       10.59       109.87        59.57       194.27        42.28        61.91 
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-A3XL TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YX 
       43.73        69.30        72.03        13.55        18.12        11.57 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LL-A442 TCGA-LL-A50Y 
       21.24         6.67         4.08         4.60        10.95         7.59 
TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A73Y TCGA-LL-A73Z 
       17.06        14.70        14.47        14.79         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        27.91         2.79         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RY TCGA-OL-A5S0 
       12.66        31.99        58.62        27.65        24.72        20.38 
TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A6VQ TCGA-PL-A8LV 
       23.47        65.62        31.07         7.23        19.73         0.23 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 
        0.26         3.95         6.81        10.59         7.92         5.56 
TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
        8.52         7.17         6.87         9.60         9.14       100.01 
TCGA-Z7-A8R6 
      105.04 

  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 
            22.95             22.32 
[1] "0.0 - 234.3 (22.9)" "0.0 - 220.9 (22.3)"
[1] "hr=" "1.2"
D13V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7P GAIN MUTATED        18       20        3        1       105        64
  7P GAIN WILD-TYPE      65       60        6        4       237       170
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7P GAIN MUTATED           0         41          8         22        6
  7P GAIN WILD-TYPE         2        101         21         41       12
                   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                65
  STAGE IA                20                60
  STAGE IB                 3                 6
  STAGE II                 1                 4
  STAGE IIA              105               237
  STAGE IIB               64               170
  STAGE III                0                 2
  STAGE IIIA              41               101
  STAGE IIIB               8                21
  STAGE IIIC              22                41
  STAGE IV                 6                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
  7P GAIN MUTATED    70 173  37  12
  7P GAIN WILD-TYPE 195 421  87  27
D13V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1              70               195
  T2             173               421
  T3              37                87
  T4              12                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
  7P GAIN MUTATED   134  96  31  24
  7P GAIN WILD-TYPE 347 243  82  50
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0             134               347
  N1              96               243
  N2              31                82
  N3              24                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
  7P GAIN MUTATED          2 237   6  48
  7P GAIN WILD-TYPE        3 617  13  99
D13V6, multiclass
          clus
vv         7P GAIN MUTATED 7P GAIN WILD-TYPE
  CM0 (I+)               2                 3
  M0                   237               617
  M1                     6                13
  MX                    48                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   286   7
  7P GAIN WILD-TYPE 728   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    286    7
  7P GAIN WILD-TYPE  728    4
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE             286               728
  MALE                 7                 4
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  7P GAIN MUTATED                            1                           231
  7P GAIN WILD-TYPE                          0                           523
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  7P GAIN MUTATED                               37                   1
  7P GAIN WILD-TYPE                            138                   5
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  7P GAIN MUTATED                                  8                  2
  7P GAIN WILD-TYPE                               21                 13
                   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                231               523
  INFILTRATING LOBULAR CARCINOMA                37               138
  MEDULLARY CARCINOMA                            1                 5
  MIXED HISTOLOGY (PLEASE SPECIFY)               8                21
  MUCINOUS CARCINOMA                             2                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"
D13V9, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    89 204
  7P GAIN WILD-TYPE 193 539
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     89  204
  7P GAIN WILD-TYPE  193  539
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO               89               193
  YES             204               539
[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                          49   204
  7P GAIN WILD-TYPE                       109   513
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                     49               109
  WHITE                                        204               513
[1] 4 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     9 235
  7P GAIN WILD-TYPE  27 591
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      9  235
  7P GAIN WILD-TYPE   27  591
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   9                27
  NOT HISPANIC OR LATINO             235               591
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED   222  26
  7Q GAIN WILD-TYPE 664  93
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              248               757 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               26                93 
$`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        26.96        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-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A08C TCGA-A8-A08F 
       18.97        24.99         9.99        28.04        28.96        33.01 
TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A091 
       19.96        37.05        31.00         0.99        43.00        33.01 
TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09M TCGA-A8-A09Q 
       17.95        41.98         9.99        12.00        33.07        25.02 
TCGA-A8-A09X TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2FM TCGA-AC-A2QJ TCGA-AC-A3W5 
       14.01        10.85         2.66        26.04         2.27        16.57 
TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AN-A0FL 
        1.12         1.81         1.68         1.74         1.12         7.59 
TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AO-A03N TCGA-AO-A0J2 TCGA-AO-A0J4 
        0.36         0.33         0.33        66.77        32.78        52.18 
TCGA-AO-A0J6 TCGA-AO-A0JD TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A12B TCGA-AO-A12D 
       37.48        72.00       102.58        99.25        77.56        64.04 
TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       57.30        48.36        61.87        70.39        15.62        32.52 
TCGA-AQ-A54O TCGA-AR-A0TR TCGA-AR-A1AI TCGA-AR-A1AR TCGA-AR-A1AV TCGA-AR-A24K 
       32.91         5.26        61.84        17.23        61.28        50.89 
TCGA-AR-A24Q TCGA-AR-A256 TCGA-AR-A2LO TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QP 
      101.52        93.83        39.39        20.38        54.74        20.45 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IM 
      143.38       149.59        12.13       112.37       176.98       126.12 
TCGA-B6-A0RE TCGA-B6-A0RI TCGA-B6-A0RV TCGA-B6-A0WV TCGA-B6-A0WZ TCGA-B6-A401 
      211.56       234.28       157.41        79.63       129.57        85.35 
TCGA-B6-A402 TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0B4 TCGA-BH-A0BA TCGA-BH-A0BJ 
       54.28        24.53        20.45        39.16        37.22        21.70 
TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0BT TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0DD 
       44.05        48.69        45.57        49.05        44.02        45.83 
TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0E0 
       48.23        17.26        15.65         2.56        38.47         4.41 
TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0HQ TCGA-BH-A0RX 
        9.63        46.19        32.65        24.49        36.85         5.59 
TCGA-BH-A18K TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1EX TCGA-BH-A1F6 
       90.84        51.16        69.93        91.99        49.58        97.48 
TCGA-C8-A12Q TCGA-C8-A12V TCGA-C8-A134 TCGA-C8-A1HI TCGA-C8-A1HN TCGA-C8-A26X 
        0.07        12.66         0.69        11.34         3.25         0.36 
TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A3M7 TCGA-D8-A146 TCGA-D8-A1J8 
        0.43         8.28         9.67         0.03        21.14        14.17 
TCGA-D8-A1JD TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1XF 
       18.15        12.03        12.03        20.12        20.09        15.22 
TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A27K TCGA-D8-A3Z5 TCGA-D8-A3Z6 
       16.54        15.32         3.81         9.44        14.50        18.51 
TCGA-E2-A107 TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A14P TCGA-E2-A14R TCGA-E2-A14T 
       34.42        37.51        40.11        40.96        38.60        33.30 
TCGA-E2-A14V TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A159 TCGA-E2-A15A 
       34.26        27.12        23.24        19.43        25.05        23.34 
TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15R TCGA-E2-A1AZ 
       17.29        20.71        18.21        17.42        17.06        60.53 
TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1L9 TCGA-E2-A56Z TCGA-E2-A570 
       17.10        33.73        33.70        19.66         7.20        30.61 
TCGA-E2-A573 TCGA-E2-A9RU TCGA-E9-A1N8 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1QZ 
       34.92         9.21        12.00        39.55        12.59        11.90 
TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A226 TCGA-E9-A22E TCGA-E9-A247 
       32.09        20.81        40.24        34.13        12.89        27.22 
TCGA-E9-A249 TCGA-E9-A295 TCGA-E9-A3X8 TCGA-E9-A54X TCGA-EW-A1IY TCGA-EW-A1J6 
        0.95         0.72        15.72        12.33         8.48        28.77 
TCGA-EW-A1OW TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB 
       22.82        52.96        23.11         7.86        18.90        19.99 
TCGA-EW-A423 TCGA-GI-A2C8 TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF 
       10.16         7.40        53.13        53.52        43.04        42.71 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-JL-A3YW TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 
       69.30        66.38        11.84         8.75         9.53        11.44 
TCGA-LL-A5YM TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A740 TCGA-LL-A9Q3 
       15.32        11.57         2.63         3.88         4.50         7.36 
TCGA-OL-A5D7 TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RZ TCGA-OL-A66H 
       46.55        34.92        36.36        16.87        22.32        26.70 
TCGA-OL-A66K TCGA-OL-A66N TCGA-OL-A6VO TCGA-PL-A8LV TCGA-PL-A8LX TCGA-S3-A6ZF 
       33.57        26.04        28.21         0.23         0.16        16.50 
TCGA-S3-A6ZH TCGA-W8-A86G 
        8.65         5.29 

$`7Q GAIN WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SH 
        0.39         8.52        14.37        43.43        14.27        47.24 
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-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM 
       63.12        55.43        36.13       136.73        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-A0CU TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM 
        5.19        56.81        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-A0EW TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU 
       35.05        34.29        29.75        24.72        99.19        54.64 
TCGA-A2-A0SV TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T3 
       27.12        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-A0YM 
       15.42        21.67        14.50        19.33        48.46        31.73 
TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G1 TCGA-A2-A1G6 
       23.77        17.36        36.79        22.45        19.20        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
       52.47       107.70        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-A3XX 
       20.88        39.65        29.98        32.75        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        24.39        21.30        23.21 
TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ 
       21.14        21.90        38.30        34.29        35.47        30.61 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J 
       29.56        31.36        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-A56D TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VW 
       11.97        14.93        14.73        10.72        11.05         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        53.06        29.03 
TCGA-A8-A06X TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B 
       31.00         1.02        17.03        53.98         9.01        43.00 
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-A07R TCGA-A8-A07S TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 
       10.98         8.98         7.99        18.05        15.06        36.95 
TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O 
       13.02         0.99        38.01        12.00         9.99        31.00 
TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A097 TCGA-A8-A099 
       33.01        93.04        40.01        30.97        12.00         9.99 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09N 
        1.02        50.04        49.05        45.07        29.98         1.02 
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-A23E TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB 
        0.95         2.37         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-A3W6 
        0.99         0.69        14.83        22.19         1.12        19.79 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A6IV TCGA-AC-A6IW 
       23.24        24.79         1.55         0.07         1.18         0.69 
TCGA-AC-A6IX TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 
        0.43         1.32         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-A0FK TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT 
        4.64         7.96         7.00         7.17         6.28         6.02 
TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0FZ 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-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T 
       80.28        47.84        81.63        84.69        68.75        47.87 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J7 TCGA-AO-A0J8 
       59.05        29.13        21.40        24.16        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-A126 
       26.24        50.24        62.04        55.33        71.80       108.72 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
      106.78        96.10        90.58        41.62        28.37        14.73 
TCGA-AO-A1KP TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       82.62         0.53        17.79        24.79        26.93       130.09 
TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS 
        5.65         2.56         9.99       111.32        49.32        74.79 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
       86.66        29.75        98.93        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       101.95        83.87       114.02        85.97        75.55 
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-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX 
       39.98        43.07        37.81        76.21        63.62        62.14 
TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       20.22       109.58        73.02        96.89        78.51        84.20 
TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W 
        0.85        87.22        76.01        53.36        85.35        50.96 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 
       83.77        79.00        56.15        78.48        73.18        72.76 
TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL 
       58.92       128.65        20.25        62.86        42.87         7.36 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QQ TCGA-B6-A0I1 
       40.04        38.17        40.54        16.04        10.59        77.62 
TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IK 
      220.90       129.57        50.70        65.72       146.50        18.77 
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-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-A0WS TCGA-B6-A0WT TCGA-B6-A0WW 
      100.70        89.46       131.21        97.48       188.68        17.98 
TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
       21.47       113.79       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-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0AZ 
       49.94       103.63        55.00        38.79        25.55        28.50 
TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 
       46.95        40.83        39.55        48.36        56.94        56.98 
TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BM 
       51.68        32.02        18.21        25.71        24.85        61.68 
TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW 
       35.67        27.19        53.69        53.95        49.94        11.67 
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-A0DQ TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ 
       22.13        13.91         3.22        45.17        47.41        16.27 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY 
       15.68        14.30        44.81        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-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0W3 
       13.61        12.89        51.32        27.25        50.79        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-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P 
        7.23        20.12        26.66        72.56        37.74        30.28 
TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1ES 
       55.63        37.55        66.05         7.36        51.39       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-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD 
       31.53        89.16        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-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-A12O TCGA-C8-A12P TCGA-C8-A12U TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 
       12.66        11.77        12.66        12.66        12.66         3.12 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE 
        1.78         1.45         0.62         3.85         3.75        12.33 
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-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A 
        0.30         0.23         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-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA 
       13.97        14.17        13.48        19.20        17.49        16.50 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ 
       18.71        15.78        18.90        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-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-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-A1Y0 TCGA-D8-A1Y2 
        6.35        12.99        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-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-A4Z1 TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A109 
       12.53        12.26         7.33        43.00        27.52        46.59 
TCGA-E2-A10A TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14Q 
       40.41        28.44        28.87        47.15        44.68        38.24 
TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z 
       33.17        43.33        32.02        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-A15M TCGA-E2-A15O 
       12.92        19.40         9.04        20.58         7.73        13.02 
TCGA-E2-A15P TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 
       19.56        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-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-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       54.18        27.42        39.62        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-A574 TCGA-E2-A576 TCGA-E9-A1N4 TCGA-E9-A1N5 
        5.52        15.72        19.89        19.00        19.20        36.82 
TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG 
       13.48        13.12        36.56        35.77        20.05        21.57 
TCGA-E9-A1NI TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 
        9.86        14.30         0.62         2.10         6.12         1.38 
TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG 
        2.76        21.21         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-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A245 
       22.75        23.51        24.10        17.06         0.69         0.85 
TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 
        1.94        24.56        17.75         0.76        26.07        18.41 
TCGA-E9-A3QA TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP 
        0.62         0.23        14.70         0.26        13.81        14.40 
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-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ 
       16.57        15.68        25.94        29.95        29.85        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PC 
       41.13        39.78        29.82        18.48        30.08         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-A424 
       52.73        25.91        22.09        21.27        17.49        10.59 
TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK 
      109.87        59.57       194.27        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-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YX TCGA-LD-A66U 
       43.73        72.03        13.55        18.12        11.57        21.24 
TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL 
        6.67         4.08         4.60        10.95         7.59        17.06 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A7SZ 
       14.70        14.47        14.79         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        27.91         2.79         2.10        12.66 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66I 
       31.99        58.62        27.65        24.72        20.38        23.47 
TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ TCGA-PL-A8LY 
       65.62        31.07         7.23        14.07        19.73         0.26 
TCGA-PL-A8LZ TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 
        3.95         6.81        10.59         7.92         5.56         8.52 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
        7.17         6.87         3.91         9.60         9.14       100.01 
TCGA-Z7-A8R6 
      105.04 

  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 
            23.29             22.19 
[1] "0.0 - 234.3 (23.3)" "0.0 - 220.9 (22.2)"
[1] "hr=" "1.1"
D14V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7Q GAIN MUTATED        14       20        3        0        92        53
  7Q GAIN WILD-TYPE      69       60        6        5       250       181
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7Q GAIN MUTATED           0         30          9         20        6
  7Q GAIN WILD-TYPE         2        112         20         43       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                69
  STAGE IA                20                60
  STAGE IB                 3                 6
  STAGE II                 0                 5
  STAGE IIA               92               250
  STAGE IIB               53               181
  STAGE III                0                 2
  STAGE IIIA              30               112
  STAGE IIIB               9                20
  STAGE IIIC              20                43
  STAGE IV                 6                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    61 146  28  14
  7Q GAIN WILD-TYPE 204 448  96  25
D14V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1              61               204
  T2             146               448
  T3              28                96
  T4              14                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
  7Q GAIN MUTATED   119  77  25  22
  7Q GAIN WILD-TYPE 362 262  88  52
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0             119               362
  N1              77               262
  N2              25                88
  N3              22                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
  7Q GAIN MUTATED          0 201   6  43
  7Q GAIN WILD-TYPE        5 653  13 104
D14V6, multiclass
          clus
vv         7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CM0 (I+)               0                 5
  M0                   201               653
  M1                     6                13
  MX                    43               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"
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   245   5
  7Q GAIN WILD-TYPE 769   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    245    5
  7Q GAIN WILD-TYPE  769    6
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE             245               769
  MALE                 5                 6
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  7Q GAIN MUTATED                            1                           197
  7Q GAIN WILD-TYPE                          0                           557
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  7Q GAIN MUTATED                               32                   2
  7Q GAIN WILD-TYPE                            143                   4
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  7Q GAIN MUTATED                                  6                  2
  7Q GAIN WILD-TYPE                               23                 13
                   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                197               557
  INFILTRATING LOBULAR CARCINOMA                32               143
  MEDULLARY CARCINOMA                            2                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               6                23
  MUCINOUS CARCINOMA                             2                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"
D14V9, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    68 182
  7Q GAIN WILD-TYPE 214 561
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     68  182
  7Q GAIN WILD-TYPE  214  561
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO               68               214
  YES             182               561
[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                          50   163
  7Q GAIN WILD-TYPE                       108   554
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                     50               108
  WHITE                                        163               554
[1] 4 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     7 199
  7Q GAIN WILD-TYPE  29 627
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      7  199
  7Q GAIN WILD-TYPE   29  627
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                29
  NOT HISPANIC OR LATINO             199               627
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED   239  33
  8P GAIN WILD-TYPE 647  86
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              272               733 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               33                86 
$`8P GAIN MUTATED`
TCGA-5T-A9QA TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SJ TCGA-A2-A04N TCGA-A2-A04R 
        0.39        43.43        14.27        13.68       104.81        82.16 
TCGA-A2-A0CM TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D2 
       24.79        75.25        63.45        56.81        21.14        33.76 
TCGA-A2-A0D3 TCGA-A2-A0EO TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0SV TCGA-A2-A0SW 
       28.77        80.28        79.76        74.40        27.12        44.88 
TCGA-A2-A0T2 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YE TCGA-A2-A0YJ 
        8.38        17.46        18.90        20.75        18.21        18.61 
TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A259 TCGA-A2-A3XS TCGA-A2-A3XX TCGA-A2-A3XY 
       20.25        19.20        52.47        33.93        38.40        34.98 
TCGA-A2-A3Y0 TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CJ 
       38.37        24.39        26.96        21.14        38.30        30.61 
TCGA-A7-A0DA TCGA-A7-A13F TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A3J0 
       35.67        12.72        24.26        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-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B 
        8.75        26.01         1.02        53.98         9.01        43.00 
TCGA-A8-A07F TCGA-A8-A082 TCGA-A8-A086 TCGA-A8-A08C TCGA-A8-A08R TCGA-A8-A08T 
       18.97        18.05        13.02        28.96         0.99        93.04 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09E 
       30.97        17.95         9.99        12.00         1.02        49.05 
TCGA-A8-A09M TCGA-A8-A09X TCGA-A8-A0A2 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-AC-A23E 
       33.07        14.01        19.04        13.02        17.03         2.37 
TCGA-AC-A23G TCGA-AC-A2BM TCGA-AC-A2FM TCGA-AC-A2QJ TCGA-AC-A3YI TCGA-AC-A62V 
       10.85        38.20        26.04         2.27        23.24         0.07 
TCGA-AC-A62X TCGA-AC-A6IW TCGA-AC-A6NO TCGA-AN-A03X TCGA-AN-A0AJ TCGA-AN-A0FK 
        1.12         0.69         1.68         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        50.24        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        32.52         2.56        32.91 
TCGA-AR-A0U0 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AQ TCGA-AR-A1AY 
       65.36        85.97        75.55        61.84        43.07        20.22 
TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24W TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A255 
      101.52        87.22        50.96        78.48        72.76        58.92 
TCGA-AR-A256 TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LR TCGA-AR-A5QN 
       93.83        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-A0W7 
       24.56        26.50        36.85        12.89         5.59        44.81 
TCGA-BH-A18L TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EX 
       26.66        91.99       113.82        42.28        12.00        49.58 
TCGA-BH-A1F5 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FM 
       89.16       120.62       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-E2-A576 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1NE TCGA-E9-A1R2 
       34.92        19.00        36.82        13.48        35.77         0.62 
TCGA-E9-A1R3 TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A228 
        2.10         2.76        32.09        20.81        40.24        12.53 
TCGA-E9-A22B TCGA-E9-A22G TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A295 TCGA-E9-A2JS 
       22.75        23.51        17.06        27.22         0.72        17.75 
TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5UP TCGA-EW-A1IY TCGA-EW-A1J1 
       15.72        12.33        14.70        14.40         8.48        18.90 
TCGA-EW-A1J6 TCGA-EW-A1P0 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1PB TCGA-EW-A1PC 
       28.77        41.13        23.11        18.48        19.99         6.15 
TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DO TCGA-LL-A5YO TCGA-LL-A73Y 
       53.52        43.04        42.71        53.36        14.47         4.14 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA 
        4.50         4.50         5.59        46.55        31.99        58.62 
TCGA-OL-A66I TCGA-OL-A66N TCGA-OL-A6VO TCGA-PL-A8LV TCGA-S3-A6ZG TCGA-S3-AA10 
       23.47        26.04        28.21         0.23         6.81         7.92 
TCGA-S3-AA12 TCGA-W8-A86G 
        8.52         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       136.73        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        48.46        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        32.75        49.48        31.99         7.30 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH 
       21.30        23.21        21.90        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-A26G TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ 
       31.36        23.74        20.61        22.32        11.34        10.59 
TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A4SF 
       11.28        13.41        14.70        13.74        21.17        17.92 
TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A8-A06O TCGA-A8-A06P 
       14.73        12.10        11.05         9.37        13.02        13.02 
TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A075 
        1.02        17.98        53.06        29.03        31.00        17.03 
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-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z 
       10.98         8.98         7.99        24.99         9.99        28.04 
TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08F TCGA-A8-A08G 
       15.06        36.95         0.99        38.01        33.01        19.96 
TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08S 
       12.00        37.05         9.99        31.00        31.00        33.01 
TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 
       43.00        40.01        33.01        41.98        12.00         9.99 
TCGA-A8-A09D TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R 
       50.04        45.07        29.98         1.02        25.02         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-A0AD TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK 
        0.99        38.04         0.95         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-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN 
        0.92         0.99         0.69        14.83        22.19         1.12 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62Y TCGA-AC-A6IV 
       16.57        19.79        24.79         1.55         1.81         1.18 
TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AN-A03Y TCGA-AN-A041 
        0.43         1.74         1.12         1.32         0.33         0.23 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AK 
        0.33         0.62         2.96         1.78         1.71         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-A0FV 
        4.64         7.96         7.59         7.17         6.28         0.33 
TCGA-AN-A0FX 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-A03O TCGA-AO-A03P TCGA-AO-A03U TCGA-AO-A03V 
       47.84        66.77        81.63        84.69        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        52.18        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-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 
       21.37        26.24        62.04        55.33        71.80       102.58 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12D TCGA-AO-A12G 
       99.25       108.72       106.78        90.58        64.04        41.62 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J 
       28.37        14.73        70.39        17.79        24.79        26.93 
TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ 
      130.09         5.65        15.62         9.99       111.32        49.32 
TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX 
        5.26        74.79        86.66        29.75        98.93        64.83 
TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AJ 
       55.86        76.14       101.95        83.87       114.02        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        37.81        76.21        61.28        63.62        62.14 
TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
      109.58        50.89        73.02        96.89        78.51        84.20 
TCGA-AR-A24P TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24X TCGA-AR-A24Z 
        0.85        76.01        53.36        85.35        83.77        79.00 
TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A2LE TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN 
       56.15        73.18       128.65        62.86        40.04        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 
       39.39        40.54        54.74        10.59        77.62       143.38 
TCGA-B6-A0I9 TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IJ TCGA-B6-A0IK 
       12.13        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-A0RG 
      126.12        84.59       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-A0RU TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WY 
      131.21        97.48       188.68        79.63        17.98       113.79 
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-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AY 
      139.17        49.94       103.63        55.00        38.79        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 
       28.50        46.95        40.83        48.36        56.94        56.98 
TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM 
       51.68        32.02        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-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD 
       49.94        11.67        41.75        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-A0DQ TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
       17.26         3.22        45.17        47.41        16.27         4.41 
TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI 
        9.63        46.19        32.65        24.49        31.00        24.43 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HI 
       37.78        35.51        23.08        41.00        52.96        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY 
        5.85         2.50        13.61        51.32        27.25        50.79 
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-A18K TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P 
        7.23        20.12        90.84        72.56        37.74        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-A1ET TCGA-BH-A1EW TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 
       69.93        82.85        55.69        17.69        25.81        31.53 
TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FD TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
       97.48        24.66        33.17        36.92        63.35        55.00 
TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A208 
       72.07       144.59        72.07         6.90        38.60        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-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-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-A274 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-A143 TCGA-D8-A145 TCGA-D8-A146 
       11.90        20.88        13.25        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-A1JG TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK 
       18.15        18.90        12.03        18.97        20.09        20.12 
TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1X5 
       20.09        19.40        20.38        12.20        13.32        18.58 
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-A1XQ TCGA-D8-A1XR 
       14.73        21.83        17.69         7.96        16.41        15.85 
TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A27E 
       16.31         6.35        15.16        15.52        14.24        17.42 
TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M 
       16.04        13.45        13.05         9.44        16.41        13.48 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27W TCGA-D8-A3Z5 
        4.80         0.76        10.09        13.08        12.26        14.50 
TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B 
       18.51         7.33        43.00        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-A14V TCGA-E2-A14W TCGA-E2-A14X 
       38.60        33.17        33.30        34.26        32.02        31.96 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15A 
       17.03        25.41        23.24        21.04        23.87        23.34 
TCGA-E2-A15C TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J 
       22.82        20.71        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-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1BC 
       14.99        53.62        53.03        29.95        32.35        16.47 
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-A1L7 
       22.65         3.88        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-A2P6 TCGA-E2-A3DX 
      106.75       102.61         8.75        43.04         5.52        15.72 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1N8 
        7.20        30.61        19.89         9.21        19.20        12.00 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1NG 
       13.12        36.56        39.55        12.59        20.05        21.57 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 
        9.86        11.90        14.30         6.12         1.38        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-A226 TCGA-E9-A227 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22E TCGA-E9-A22H 
       34.13         0.79        13.32        39.09        12.89        24.10 
TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JT 
        0.69         0.85         1.94         0.95        24.56         0.76 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54Y TCGA-E9-A5FL TCGA-E9-A5UO 
       26.07        18.41         0.62         0.23         0.26        13.81 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1J3 
       15.39        12.20        39.72        18.21        13.25        16.57 
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-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA 
       39.78        52.96        29.82        30.08         7.86        18.90 
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-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-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-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 
      110.50        38.20        43.73        69.30        66.38        72.03 
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        21.24         6.67 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
        4.08         4.60         8.75         9.53        11.44        10.95 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YP TCGA-LL-A6FP 
        7.59        17.06        15.32        14.70        14.79        11.57 
TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
        2.63         3.88         3.22         6.21         7.36        27.91 
TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW 
        2.79         2.10        12.66        27.65        34.92        36.36 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J 
       16.87        24.72        22.32        20.38        26.70        65.62 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ TCGA-PL-A8LX 
       33.57        31.07         7.23        14.07        19.73         0.16 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA11 
        0.26         3.95        16.50         8.65        10.59         5.56 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
        7.17         6.87         3.91         9.60         9.14       100.01 
TCGA-Z7-A8R6 
      105.04 

  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 
            21.55             22.82 
[1] "0.0 - 220.9 (21.5)" "0.0 - 234.3 (22.8)"
[1] "hr=" "1"  
D15V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8P GAIN MUTATED        21       23        3        2        92        65
  8P GAIN WILD-TYPE      62       57        6        3       250       169
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8P GAIN MUTATED           2         33          9         13        8
  8P GAIN WILD-TYPE         0        109         20         50       10
                   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                62
  STAGE IA                23                57
  STAGE IB                 3                 6
  STAGE II                 2                 3
  STAGE IIA               92               250
  STAGE IIB               65               169
  STAGE III                2                 0
  STAGE IIIA              33               109
  STAGE IIIB               9                20
  STAGE IIIC              13                50
  STAGE IV                 8                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
  8P GAIN MUTATED    74 156  35   9
  8P GAIN WILD-TYPE 191 438  89  30
D15V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1              74               191
  T2             156               438
  T3              35                89
  T4               9                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
  8P GAIN MUTATED   129  98  26  17
  8P GAIN WILD-TYPE 352 241  87  57
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0             129               352
  N1              98               241
  N2              26                87
  N3              17                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
  8P GAIN MUTATED          0 231   8  37
  8P GAIN WILD-TYPE        5 623  11 110
D15V6, multiclass
          clus
vv         8P GAIN MUTATED 8P GAIN WILD-TYPE
  CM0 (I+)               0                 5
  M0                   231               623
  M1                     8                11
  MX                    37               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"
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED   272   4
  8P GAIN WILD-TYPE 742   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED    272    4
  8P GAIN WILD-TYPE  742    7
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE             272               742
  MALE                 4                 7
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  8P GAIN MUTATED                            0                           216
  8P GAIN WILD-TYPE                          1                           538
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  8P GAIN MUTATED                               35                   3
  8P GAIN WILD-TYPE                            140                   3
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  8P GAIN MUTATED                                  8                  3
  8P GAIN WILD-TYPE                               21                 12
                   vv
clus                OTHER  SPECIFY
  8P GAIN MUTATED               11
  8P GAIN WILD-TYPE             33
D15V8, multiclass
                                  clus
vv                                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                216               538
  INFILTRATING LOBULAR CARCINOMA                35               140
  MEDULLARY CARCINOMA                            3                 3
  MIXED HISTOLOGY (PLEASE SPECIFY)               8                21
  MUCINOUS CARCINOMA                             3                12
  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"
D15V9, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    77 199
  8P GAIN WILD-TYPE 205 544
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     77  199
  8P GAIN WILD-TYPE  205  544
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO               77               205
  YES             199               544
[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                          53   185
  8P GAIN WILD-TYPE                       105   532
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                     53               105
  WHITE                                        185               532
[1] 4 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     9 217
  8P GAIN WILD-TYPE  27 609
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      9  217
  8P GAIN WILD-TYPE   27  609
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   9                27
  NOT HISPANIC OR LATINO             217               609
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED   437  59
  8Q GAIN WILD-TYPE 449  60
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              496               509 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               59                60 
$`8Q GAIN MUTATED`
TCGA-5T-A9QA TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SJ 
        0.39        14.37        43.43        48.10        14.27        13.68 
TCGA-A1-A0SK TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R 
       31.79        39.32        19.20       104.81        41.95        82.16 
TCGA-A2-A04Y TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CP TCGA-A2-A0CT TCGA-A2-A0CV 
       36.13        64.57        24.79        92.48        75.25        63.45 
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-A0EO TCGA-A2-A0EQ TCGA-A2-A0EU TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0SV 
       80.28        79.76        34.29        24.72        24.16        27.12 
TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 
       44.88        50.43        17.52        17.13         8.38        18.71 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YH 
       17.46        18.90        20.75        18.21        21.90        21.67 
TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX 
       18.61        31.73        23.77        23.47        17.36        36.79 
TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25D 
       20.25        19.20        19.56        52.47        16.31        18.15 
TCGA-A2-A25E TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XX TCGA-A2-A3XY 
       91.92        39.65        33.93        29.98        38.40        34.98 
TCGA-A2-A3Y0 TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD 
       38.37        24.39        26.96        21.14        21.90        38.30 
TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A26F TCGA-A7-A26G 
       30.61        35.67        31.73        12.72        24.26        23.74 
TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3J0 TCGA-A7-A426 
       23.80        21.73        20.61        22.32        10.29        11.97 
TCGA-A7-A4SA TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VV 
       14.93        14.50        21.17        12.10        10.72        10.29 
TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06R TCGA-A8-A06T 
       10.42         8.75        13.02        13.02        17.98        53.06 
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        43.00 
TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07U 
       18.97        14.01         9.99        10.98         8.98        24.99 
TCGA-A8-A07W TCGA-A8-A082 TCGA-A8-A086 TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G 
        9.99        18.05        13.02        28.96        33.01        19.96 
TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T 
       12.00        37.05        31.00         0.99        33.01        93.04 
TCGA-A8-A08X TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A09A TCGA-A8-A09B 
       43.00        33.01        30.97        17.95         9.99        12.00 
TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q 
        1.02        49.05        29.98        33.07         1.02        25.02 
TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A2 TCGA-A8-A0A7 
        8.98        19.04         0.99        14.01        19.04         0.99 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2BK 
       13.02        17.03         2.37        10.85         2.66        38.53 
TCGA-AC-A2BM TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A3YI TCGA-AC-A62V 
       38.20        26.04         1.02         2.27        23.24         0.07 
TCGA-AC-A62X TCGA-AC-A6IW TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A03Y 
        1.12         0.69         1.68         1.74         0.33         0.33 
TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AM TCGA-AN-A0AS 
        0.62         1.78         1.71         8.02         0.16         0.33 
TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY 
        7.00         7.59         6.02         0.36         0.33         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XS TCGA-AO-A03O TCGA-AO-A03R 
        0.33         0.33         0.33         0.33        81.63        68.75 
TCGA-AO-A03T TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J7 
       47.87        29.13        21.40        52.18        24.16        20.32 
TCGA-AO-A0JI TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
       50.24       106.78        96.10        77.56        64.04        57.30 
TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS 
       48.36        41.62        82.62        61.87        70.39         0.53 
TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N 
       17.79        24.79       130.09        15.62        32.52         2.56 
TCGA-AQ-A54O TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TW 
       32.91       111.32        49.32        74.79        86.66        98.93 
TCGA-AR-A0U0 TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AP 
       65.36        85.97        61.84        52.77        51.25        39.98 
TCGA-AR-A1AQ TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24Q 
       43.07        76.21        63.62        62.14        20.22       101.52 
TCGA-AR-A24R TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24Z TCGA-AR-A251 
       87.22        53.36        85.35        50.96        79.00        78.48 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LL 
       72.76        58.92        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 
       39.39        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-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N5 TCGA-E9-A1N6 
       34.92        19.89        19.00         9.21        36.82        13.48 
TCGA-E9-A1N9 TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1R2 TCGA-E9-A1R3 
       13.12        35.77        20.05         9.86         0.62         2.10 
TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RG 
        2.76        32.09        20.81        40.24        34.65        21.27 
TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A243 TCGA-E9-A247 
       39.09        22.75        12.89        23.51        17.06        27.22 
TCGA-E9-A248 TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X 
        1.94         0.72        17.75         0.62        15.72        12.33 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UP TCGA-EW-A1IY TCGA-EW-A1J1 TCGA-EW-A1J6 
        0.23        14.70        14.40         8.48        18.90        28.77 
TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P3 TCGA-EW-A1P5 
       22.82        29.85        40.41        41.13        52.96        23.11 
TCGA-EW-A1P6 TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PH 
       18.48         7.86        19.99         6.15        13.94        19.96 
TCGA-EW-A2FV TCGA-GI-A2C9 TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DO 
       25.91       109.87        53.52        43.04        42.71        53.36 
TCGA-GM-A3XL TCGA-GM-A5PV TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A7W5 TCGA-LL-A5YM 
       69.30        13.55        11.84        11.57         4.08        15.32 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 
       14.70        14.47         3.88         4.14         4.50         4.50 
TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA 
        5.59         3.22         7.36        46.55        31.99        58.62 
TCGA-OL-A66I TCGA-OL-A66N TCGA-OL-A6VO TCGA-PL-A8LV TCGA-S3-A6ZF TCGA-S3-A6ZG 
       23.47        26.04        28.21         0.23        16.50         6.81 
TCGA-S3-AA10 TCGA-S3-AA12 TCGA-W8-A86G TCGA-Z7-A8R6 
        7.92         8.52         5.29       105.04 

$`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 
      136.73       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 
       48.46        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        32.75        49.48        31.99         7.30 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 
       21.30        23.21        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        38.01         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        50.04        45.07 
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        22.19         1.12 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62Y TCGA-AC-A6IV 
       16.57        19.79        24.79         1.55         1.81         1.18 
TCGA-AC-A6IX TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A04A 
        0.43         1.12         1.32         0.23         0.33         2.96 
TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF 
        7.36         6.51         0.33         0.33         6.44         4.64 
TCGA-AN-A0FJ TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0XO TCGA-AN-A0XP 
        7.96         7.17         6.28         0.33        12.33         0.30 
TCGA-AN-A0XR 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-A03U TCGA-AO-A0J2 TCGA-AO-A0J6 
       47.84        66.77        84.69        59.05        32.78        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-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM 
       76.77        21.37        26.24        62.04        55.33        71.80 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A12A TCGA-AO-A12H TCGA-AO-A1KO 
      102.58        99.25       108.72        90.58        28.37        14.73 
TCGA-AQ-A04J TCGA-AQ-A0Y5 TCGA-AQ-A7U7 TCGA-AR-A0TR TCGA-AR-A0TV TCGA-AR-A0TX 
       26.93         5.65         9.99         5.26        29.75        64.83 
TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AH 
       55.86        76.14       101.95        83.87       114.02        75.55 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AR TCGA-AR-A1AS 
       48.82        62.56        43.73        43.56        17.23        37.81 
TCGA-AR-A1AV TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       61.28       109.58        50.89        73.02        96.89        78.51 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24T TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A252 
       84.20         0.85        76.01        83.77        56.15        73.18 
TCGA-AR-A2LE TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ TCGA-AR-A5QM 
      128.65        62.86        40.04        38.17        40.54        54.74 
TCGA-B6-A0I9 TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IJ TCGA-B6-A0IK 
       12.13        50.70        65.72       146.50       176.98        18.77 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RI TCGA-B6-A0RN 
      110.14       110.93       140.88        68.45       234.28       172.96 
TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0WS TCGA-B6-A0WT 
      162.05       140.48       100.70        89.46        97.48       188.68 
TCGA-B6-A0WV TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A1KI 
       79.63       129.57       129.70        28.27        68.94        73.51 
TCGA-B6-A1KN TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AZ TCGA-BH-A0B0 
      139.17        49.94       103.63        55.00        28.50        46.95 
TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BF TCGA-BH-A0BJ 
       48.36        56.98        51.68        32.02        25.71        21.70 
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-A0BW TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH 
       11.67        48.13        42.90        31.17        23.44        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DQ TCGA-BH-A0DV TCGA-BH-A0DX 
       22.13        13.91        17.26         3.22        45.17        47.41 
TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE 
        4.41         9.63        46.19        32.65        24.49        31.00 
TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H9 TCGA-BH-A0HA 
       24.43        30.35        37.78        35.51        41.00        52.96 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HW TCGA-BH-A0W3 
       20.38         5.85         2.50        13.61        51.32        23.93 
TCGA-BH-A0W4 TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M 
       24.95         8.81         2.01        20.12        90.84        72.56 
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-A1ET TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F8 TCGA-BH-A1FD TCGA-BH-A1FH 
       82.85        17.69        25.81        24.66        33.17        36.92 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A203 
       63.35        55.00        72.07       144.59         6.90        38.60 
TCGA-BH-A208 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
       57.83        10.65         6.44        20.12         0.99       109.28 
TCGA-C8-A12L TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 
       11.93        11.77         0.07         1.45         0.69         3.85 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HL 
        3.75        12.33        10.92        11.34         0.16        10.42 
TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Y TCGA-C8-A274 TCGA-C8-A278 TCGA-C8-A27B 
        0.30         0.23         0.43         0.03         0.03         0.99 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A145 
        0.03         0.23        11.90        20.88        13.25        13.48 
TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JE 
       21.14        14.17        17.49        16.50        18.71        18.90 
TCGA-D8-A1JI TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1X7 TCGA-D8-A1X8 
       18.97        19.40        20.38        12.20        16.73        25.74 
TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ 
       23.90        27.58         2.66        17.16        14.73        21.83 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A27E 
       17.69         7.96        15.85         6.35        15.16        17.42 
TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27K TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T 
       16.04        13.45         9.44         4.80         0.76        13.08 
TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A109 
       12.26        14.50        18.51         7.33        43.00        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-A14V TCGA-E2-A14W TCGA-E2-A150 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15G 
       34.26        32.02        25.41        21.04        23.87        18.21 
TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15P TCGA-E2-A1B1 
       12.92        17.42         9.04        20.58        19.56        53.03 
TCGA-E2-A1B4 TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       29.95        16.47        38.30        37.41        32.78        33.73 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L8 
       28.44        22.65         3.88        11.08        54.18        39.62 
TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LL TCGA-E2-A2P6 
       19.66        40.47        28.90        18.87        43.04         5.52 
TCGA-E2-A3DX TCGA-E2-A570 TCGA-E9-A1N4 TCGA-E9-A1N8 TCGA-E9-A1NA TCGA-E9-A1NC 
       15.72        30.61        19.20        12.00        36.56        39.55 
TCGA-E9-A1ND TCGA-E9-A1NG TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R4 TCGA-E9-A1R5 
       12.59        21.57        11.90        14.30         6.12         1.38 
TCGA-E9-A1R7 TCGA-E9-A1RD TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 
       21.21         0.66         6.58        34.59        35.64        34.13 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22H TCGA-E9-A244 TCGA-E9-A245 
        0.79        12.53        13.32        24.10         0.69         0.85 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A5FL 
        0.95        24.56         0.76        26.07        18.41         0.26 
TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J2 
       13.81        15.39        12.20        39.72        18.21        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1P1 TCGA-EW-A1P4 
       16.57        15.68        25.94        29.95        39.78        29.82 
TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FR 
       30.08        18.90        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-A2DH TCGA-GM-A2DI 
        7.40        59.57       194.27        53.13        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-A5PX TCGA-LD-A66U TCGA-LD-A74U 
       43.73        66.38        72.03        18.12        21.24         6.67 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y 
        4.60         8.75         9.53        11.44        10.95         7.59 
TCGA-LL-A5YL TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A8F5 TCGA-LQ-A4E4 
       17.06        14.79        11.57         2.63         6.21        27.91 
TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW 
        2.79         2.10        12.66        27.65        34.92        36.36 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J 
       16.87        24.72        22.32        20.38        26.70        65.62 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ TCGA-PL-A8LX 
       33.57        31.07         7.23        14.07        19.73         0.16 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA14 
        0.26         3.95         8.65        10.59         5.56         7.17 
TCGA-S3-AA15 TCGA-S3-AA17 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
        6.87         3.91         9.60         9.14       100.01 

  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 
           21.815            23.440 
[1] "0.0 - 220.9 (21.8)" "0.0 - 234.3 (23.4)"
[1] "hr=" "1"  
D16V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8Q GAIN MUTATED        44       34        4        2       178       102
  8Q GAIN WILD-TYPE      39       46        5        3       164       132
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8Q GAIN MUTATED           2         72         15         31       11
  8Q GAIN WILD-TYPE         0         70         14         32        7
                   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                 44                39
  STAGE IA                34                46
  STAGE IB                 4                 5
  STAGE II                 2                 3
  STAGE IIA              178               164
  STAGE IIB              102               132
  STAGE III                2                 0
  STAGE IIIA              72                70
  STAGE IIIB              15                14
  STAGE IIIC              31                32
  STAGE IV                11                 7
  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   133 298  54  19
  8Q GAIN WILD-TYPE 132 296  70  20
D16V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1             133               132
  T2             298               296
  T3              54                70
  T4              19                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
  8Q GAIN MUTATED   239 157  61  37
  8Q GAIN WILD-TYPE 242 182  52  37
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0             239               242
  N1             157               182
  N2              61                52
  N3              37                37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  8Q GAIN MUTATED          1 433  11  61
  8Q GAIN WILD-TYPE        4 421   8  86
D16V6, multiclass
          clus
vv         8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CM0 (I+)               1                 4
  M0                   433               421
  M1                    11                 8
  MX                    61                86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   499   7
  8Q GAIN WILD-TYPE 515   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    499    7
  8Q GAIN WILD-TYPE  515    4
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE             499               515
  MALE                 7                 4
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  8Q GAIN MUTATED                            1                           407
  8Q GAIN WILD-TYPE                          0                           347
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  8Q GAIN MUTATED                               51                   5
  8Q GAIN WILD-TYPE                            124                   1
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  8Q GAIN MUTATED                                 12                  4
  8Q GAIN WILD-TYPE                               17                 11
                   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                407               347
  INFILTRATING LOBULAR CARCINOMA                51               124
  MEDULLARY CARCINOMA                            5                 1
  MIXED HISTOLOGY (PLEASE SPECIFY)              12                17
  MUCINOUS CARCINOMA                             4                11
  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   156 350
  8Q GAIN WILD-TYPE 126 393
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    156  350
  8Q GAIN WILD-TYPE  126  393
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO              156               126
  YES             350               393
[1] 2 2
[1] FALSE
D16V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q GAIN MUTATED                                  1    27
  8Q GAIN WILD-TYPE                                0    29
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED                          91   331
  8Q GAIN WILD-TYPE                        67   386
D16V11, multiclass
                                  clus
vv                                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         27                29
  BLACK OR AFRICAN AMERICAN                     91                67
  WHITE                                        331               386
[1] 4 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    13 403
  8Q GAIN WILD-TYPE  23 423
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     13  403
  8Q GAIN WILD-TYPE   23  423
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                  13                23
  NOT HISPANIC OR LATINO             403               423
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED   116  19
  9P GAIN WILD-TYPE 770 100
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
              135               870 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               19               100 
$`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        21.14        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        24.99 
TCGA-A8-A07Z TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08X TCGA-A8-A093 TCGA-A8-A09X 
       28.04        38.01        28.96        43.00        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        16.57         1.12 
TCGA-AC-A8OQ TCGA-AN-A0AR TCGA-AN-A0FK TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FX 
        1.12         0.33         7.00         6.02         0.33         0.33 
TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A0JL TCGA-AO-A128 TCGA-AQ-A54N TCGA-AR-A0U0 
       20.32        53.03        55.33       106.78         2.56        65.36 
TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A250 TCGA-AR-A256 TCGA-B6-A0I2 TCGA-B6-A0IH 
       20.22       109.58        56.15        93.83       143.38       112.37 
TCGA-B6-A0IJ TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WZ 
      176.98       140.88       211.56       100.70       131.21       129.57 
TCGA-B6-A0X1 TCGA-B6-A1KC TCGA-B6-A1KI TCGA-BH-A0AY TCGA-BH-A0B9 TCGA-BH-A0BA 
      186.48        43.59        73.51        25.55        51.68        37.22 
TCGA-BH-A0BG TCGA-BH-A0BT TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0RX TCGA-BH-A18F 
       24.85        45.57        32.65        31.00         5.59         8.81 
TCGA-BH-A18Q TCGA-BH-A18V TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1F0 TCGA-BH-A1F6 
       55.63        51.16        42.28        12.00        25.81        97.48 
TCGA-BH-A1FC TCGA-BH-A202 TCGA-C8-A132 TCGA-C8-A138 TCGA-C8-A26Z TCGA-D8-A141 
      114.15         0.72         1.45         3.75         8.28        20.58 
TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1JA TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JT 
       21.14        14.17        16.50        18.15        18.90        13.32 
TCGA-D8-A1XB TCGA-D8-A1XF TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XU TCGA-D8-A1XW 
       18.15        15.22        14.50        19.92        12.99        12.66 
TCGA-D8-A27V TCGA-D8-A3Z6 TCGA-E2-A10B TCGA-E2-A14N TCGA-E2-A154 TCGA-E2-A158 
       12.53        18.51        37.51        47.15        19.43        14.79 
TCGA-E2-A159 TCGA-E2-A1AZ TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1L9 
       25.05        60.53        17.10        33.73        33.70        19.66 
TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A56Z TCGA-E2-A9RU TCGA-E9-A1N6 TCGA-E9-A244 
       43.04        16.93         7.20         9.21        13.48         0.69 
TCGA-E9-A3HO TCGA-EW-A1IY TCGA-EW-A1J1 TCGA-EW-A1P8 TCGA-EW-A1PC TCGA-EW-A1PG 
       26.07         8.48        18.90         7.86         6.15        34.55 
TCGA-EW-A1PH TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A3XL TCGA-GM-A4E0 TCGA-LL-A5YM 
       19.96        42.71        42.28        69.30        72.03        15.32 
TCGA-LL-A6FR TCGA-MS-A51U TCGA-OL-A5RW TCGA-OL-A66I TCGA-OL-A6VO TCGA-PL-A8LV 
        3.88         2.79        36.36        23.47        28.21         0.23 
TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-AA0Z 
        3.95        16.50        10.59 

$`9P GAIN WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        0.39         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
       47.24        20.88        13.68         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-A04V TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO 
       63.12        55.43        36.13       136.73        64.57       112.08 
TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CW 
       92.48        88.60       107.93        75.25         5.19        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-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-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SY 
       24.16        99.19        54.64        27.12        44.88        44.28 
TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 
       17.52        17.13        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-A0YT TCGA-A2-A1FW 
       14.50        18.61        19.33        48.46        23.77        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-A25E TCGA-A2-A25F 
       52.47       107.70        16.31        17.19        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        32.75 
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-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CD 
       24.39        21.30        23.21        26.96        21.90        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-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-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-A426 TCGA-A7-A4SA TCGA-A7-A4SB 
       10.59        11.28        13.41        11.97        14.93        13.74 
TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV 
       21.17        17.92        12.10        10.72        11.05        10.29 
TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R 
        9.37         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 
       53.06        29.03        31.00        26.01         1.02        17.03 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07I 
       53.98         9.01        43.00        19.99        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07W 
       12.00        17.03         9.99        10.98         7.99         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        33.01 
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-A092 
        0.99        33.01        93.04        40.01        33.01        30.97 
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 
       50.04        49.05        45.07        29.98        33.07         1.02 
TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A1 
       25.02         8.98        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-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB 
       38.04         0.95        10.85         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-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN 
        2.27         0.99         0.69        14.83        22.19         1.12 
TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y 
       19.79        23.24        24.79         1.55         0.07         1.81 
TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OR 
        1.18         0.69         0.43         1.68         1.74         1.32 
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-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM 
        1.78         1.71         8.02         7.36         6.51         0.16 
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-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL 
        7.17         6.28         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-A0J8 
       32.78        21.40        52.18        24.16        37.48        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-A0JM TCGA-AO-A124 TCGA-AO-A125 
       26.24        50.24        62.04        71.80       102.58        99.25 
TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
      108.72        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-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP 
        5.65        15.62        32.52        32.91         9.99       111.32 
TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW 
       49.32         5.26        74.79        86.66        29.75        98.93 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 
       64.83        55.86        76.14       101.95        83.87       114.02 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL 
       85.97        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-A24K 
       37.81        76.21        61.28        63.62        62.14        50.89 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q 
       73.02        96.89        78.51        84.20         0.85       101.52 
TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X 
       87.22        76.01        53.36        85.35        50.96        83.77 
TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LE 
       79.00        78.48        73.18        72.76        58.92       128.65 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN 
       20.25        62.86        42.87         7.36        40.04        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP 
       39.39        40.54        20.38        54.74        16.04        20.45 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB 
       10.59        77.62       149.59        12.13       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-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL 
      110.14       110.93        68.45       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-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-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF 
      113.79       129.70        28.27        68.94        58.88       101.52 
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       103.63 
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-A0B6 TCGA-BH-A0B7 
       40.83        39.55        39.16        48.36        56.94        56.98 
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-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-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-A0EB TCGA-BH-A0EI TCGA-BH-A0GY 
        9.63        44.81        46.19        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-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18G 
       23.93        24.95        42.35        44.81        23.05         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-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN 
       30.28        37.55        66.05         7.36        51.39        69.93 
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-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE 
       31.53        89.16        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-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-A12W TCGA-C8-A12X TCGA-C8-A130 
        0.07        12.66        12.66        12.66        12.66         3.12 
TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF 
        1.78         0.69         0.62         3.85        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-A273 
        3.25         0.30         0.23         0.36         0.43         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-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-A1JB TCGA-D8-A1JC TCGA-D8-A1JF 
       13.48        19.20        17.49        18.71        15.78        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-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-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ 
       17.16        14.73        21.83        17.69         7.96        16.41 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1XZ 
       15.85        16.31         6.35        15.16        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-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-A27W TCGA-D8-A3Z5 
        4.80         0.76        10.09        13.08        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-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-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-A155 TCGA-E2-A156 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E 
       21.04        23.87        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-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-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-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        30.61        34.92 
TCGA-E2-A574 TCGA-E2-A576 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 
       19.89        19.00        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-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-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-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT 
        1.94         0.95        24.56         0.72        17.75         0.76 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK 
       18.41         0.62        15.72        12.33         0.23        14.70 
TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
        0.26        13.81        14.40        15.39        12.20        39.72 
TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV 
       18.21        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-A1PA 
       52.96        29.82        23.11        18.48        30.08        18.90 
TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A2FR TCGA-EW-A2FS 
       19.99        13.94        10.52        14.43        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-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       43.04        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-A5PV 
       53.36       110.50        38.20        43.73        66.38        13.55 
TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 
       18.12        11.84        11.57        21.24         6.67         4.08 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y 
        4.60         8.75         9.53        11.44        10.95         7.59 
TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ 
       17.06        14.70        14.47        14.79        11.57         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-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 
        7.36        27.91         2.10        12.66        46.55        31.99 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       58.62        27.65        34.92        16.87        24.72        22.32 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       20.38        26.70        65.62        33.57        31.07        26.04 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ TCGA-PL-A8LX TCGA-PL-A8LY TCGA-S3-A6ZG 
        7.23        14.07        19.73         0.16         0.26         6.81 
TCGA-S3-A6ZH TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 
        8.65         7.92         5.56         8.52         7.17         6.87 
TCGA-S3-AA17 TCGA-W8-A86G TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        3.91         5.29         9.60         9.14       100.01       105.04 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             0.23              0.03 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           211.56            234.28 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           20.580            22.785 
[1] "0.2 - 211.6 (20.6)" "0.0 - 234.3 (22.8)"
[1] "hr=" "1.1"
D17V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9P GAIN MUTATED         9        6        1        1        54        33
  9P GAIN WILD-TYPE      74       74        8        4       288       201
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9P GAIN MUTATED           0          9          4         12        3
  9P GAIN WILD-TYPE         2        133         25         51       15
                   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                74
  STAGE IA                 6                74
  STAGE IB                 1                 8
  STAGE II                 1                 4
  STAGE IIA               54               288
  STAGE IIB               33               201
  STAGE III                0                 2
  STAGE IIIA               9               133
  STAGE IIIB               4                25
  STAGE IIIC              12                51
  STAGE IV                 3                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
  9P GAIN MUTATED    28  85  14   8
  9P GAIN WILD-TYPE 237 509 110  31
D17V4, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1              28               237
  T2              85               509
  T3              14               110
  T4               8                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
  9P GAIN MUTATED    64  46   9  14
  9P GAIN WILD-TYPE 417 293 104  60
D17V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0              64               417
  N1              46               293
  N2               9               104
  N3              14                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
  9P GAIN MUTATED          0 113   3  20
  9P GAIN WILD-TYPE        5 741  16 127
D17V6, multiclass
          clus
vv         9P GAIN MUTATED 9P GAIN WILD-TYPE
  CM0 (I+)               0                 5
  M0                   113               741
  M1                     3                16
  MX                    20               127
[1] 4 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   136   0
  9P GAIN WILD-TYPE 878  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED    136    0
  9P GAIN WILD-TYPE  878   11
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE             136               878
  MALE                 0                11
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  9P GAIN MUTATED                            0                           109
  9P GAIN WILD-TYPE                          1                           645
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  9P GAIN MUTATED                               18                   2
  9P GAIN WILD-TYPE                            157                   4
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  9P GAIN MUTATED                                  1                  1
  9P GAIN WILD-TYPE                               28                 14
                   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                109               645
  INFILTRATING LOBULAR CARCINOMA                18               157
  MEDULLARY CARCINOMA                            2                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               1                28
  MUCINOUS CARCINOMA                             1                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"
D17V9, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    37  99
  9P GAIN WILD-TYPE 245 644
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     37   99
  9P GAIN WILD-TYPE  245  644
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO               37               245
  YES              99               644
[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                          29    91
  9P GAIN WILD-TYPE                       129   626
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                     29               129
  WHITE                                         91               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"
D17V12, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     5 111
  9P GAIN WILD-TYPE  31 715
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      5  111
  9P GAIN WILD-TYPE   31  715
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                31
  NOT HISPANIC OR LATINO             111               715
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    93  18
  9Q GAIN WILD-TYPE 793 101
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              111               894 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               18               101 
$`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        21.14        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 
       38.01        28.96        17.95        14.01         2.37         2.66 
TCGA-AC-A2FM TCGA-AN-A04A TCGA-AN-A0FK TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FX 
       26.04         2.96         7.00         6.02         0.33         0.33 
TCGA-AN-A0XR TCGA-AO-A0J7 TCGA-AO-A128 TCGA-AQ-A04H TCGA-AR-A0TR TCGA-AR-A1AJ 
        0.33        20.32       106.78        24.79         5.26        52.77 
TCGA-AR-A24H TCGA-AR-A250 TCGA-AR-A256 TCGA-AR-A5QM TCGA-B6-A0I2 TCGA-B6-A0IH 
      109.58        56.15        93.83        54.74       143.38       112.37 
TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IQ TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WZ 
      176.98        18.77       140.88       100.70       131.21       129.57 
TCGA-B6-A1KI TCGA-BH-A0AY TCGA-BH-A0BA TCGA-BH-A0BG TCGA-BH-A0E9 TCGA-BH-A0EA 
       73.51        25.55        37.22        24.85        46.19        32.65 
TCGA-BH-A18F TCGA-BH-A18V TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1F2 TCGA-BH-A1FC 
        8.81        51.16        42.28        12.00        31.53       114.15 
TCGA-BH-A202 TCGA-C8-A12M TCGA-C8-A132 TCGA-C8-A138 TCGA-C8-A1HG TCGA-C8-A1HK 
        0.72        11.77         1.45         3.75        11.34        12.03 
TCGA-C8-A26Y TCGA-C8-A275 TCGA-D8-A141 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1JD 
        0.43         0.03        20.58        21.14        14.17        18.15 
TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JT TCGA-D8-A1XB TCGA-D8-A1XF TCGA-D8-A1XL 
       18.90        12.03        13.32        18.15        15.22        19.92 
TCGA-D8-A1XU TCGA-D8-A27V TCGA-D8-A3Z6 TCGA-E2-A10B TCGA-E2-A14N TCGA-E2-A154 
       12.99        12.53        18.51        37.51        47.15        19.43 
TCGA-E2-A1BD TCGA-E2-A1II TCGA-E2-A1L9 TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A56Z 
       17.10        33.70        19.66        43.04        16.93         7.20 
TCGA-E2-A9RU TCGA-E9-A1N6 TCGA-E9-A22E TCGA-E9-A244 TCGA-E9-A3HO TCGA-EW-A1IY 
        9.21        13.48        12.89         0.69        26.07         8.48 
TCGA-EW-A1J1 TCGA-EW-A1P4 TCGA-EW-A1P8 TCGA-EW-A1PC TCGA-EW-A1PG TCGA-EW-A1PH 
       18.90        29.82         7.86         6.15        34.55        19.96 
TCGA-GI-A2C8 TCGA-GM-A2DF TCGA-GM-A3XL TCGA-MS-A51U TCGA-OL-A5RW TCGA-OL-A66I 
        7.40        42.71        69.30         2.79        36.36        23.47 
TCGA-PL-A8LV TCGA-S3-AA0Z TCGA-Z7-A8R6 
        0.23        10.59       105.04 

$`9Q GAIN WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        0.39         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
       47.24        20.88        13.68         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-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL 
       63.12        64.04        55.43        36.13       136.73        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-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 
        5.19        64.04        56.81        21.14        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-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-A0T4 
       44.88        50.43        44.28        17.52        17.13        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-A0YT TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 
       48.46        23.77        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-A25C 
       19.20        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-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       83.01        29.98        32.75        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        24.39        21.30        23.21 
TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH 
       26.96        21.90        38.30        35.31        34.29        35.47 
TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A13G 
       30.61        37.45        35.67        31.73        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-A3J1 TCGA-A7-A3RF 
       20.61        22.32        11.34        10.59        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-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-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        53.06 
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        43.00        19.99        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        24.99 
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-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O 
       33.01        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        33.01        93.04        43.00        40.01 
TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A 
       33.01        30.97        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        50.04        49.05        45.07        29.98 
TCGA-A8-A09M 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-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-A23C TCGA-AC-A23G TCGA-AC-A2B8 
       13.02        17.03        38.04         0.95        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-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        22.19         1.12        16.57        19.79        23.24 
TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV 
       24.79         1.55         0.07         1.12         1.81         1.18 
TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR 
        0.69         0.43         1.68         1.74         1.12         1.32 
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-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-A0FL 
        0.33         0.33         6.44         4.64         7.96         7.59 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL 
        7.17         6.28         0.36         0.33         0.33         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-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-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 
       21.40        52.18        24.16        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-A124 
       26.24        50.24        62.04        55.33        71.80       102.58 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D 
       99.25       108.72        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-A1KS TCGA-AO-A1KT TCGA-AQ-A04J TCGA-AQ-A04L 
       61.87        70.39         0.53        17.79        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        32.52         2.56        32.91         9.99 
TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW 
      111.32        49.32        74.79        86.66        29.75        98.93 
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       101.95        83.87 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AL 
      114.02        85.97        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-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 
       37.81        76.21        61.28        63.62        62.14        20.22 
TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
       50.89        73.02        96.89        78.51        84.20         0.85 
TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W 
      101.52        87.22        76.01        53.36        85.35        50.96 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 
       83.77        79.00        78.48        73.18        72.76        58.92 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM 
      128.65        20.25        62.86        42.87         7.36        40.04 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QN TCGA-AR-A5QP 
       38.17        39.39        40.54        20.38        16.04        20.45 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB 
       10.59        77.62       149.59        12.13       220.90       129.57 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO 
       50.70        65.72       146.50       126.12        84.59       110.14 
TCGA-B6-A0IP TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL 
      110.93       211.56        68.45       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-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-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-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 
       43.59       101.52       139.17       170.17        85.35        54.28 
TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW 
       49.94       103.63        55.00        24.53        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-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       56.94        56.98        51.68        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-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-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-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-A18G TCGA-BH-A18I 
       24.95        42.35        44.81        23.05         2.01         7.23 
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-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-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-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD 
       25.81        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-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-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-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF 
        1.78         0.69         0.62         3.85        12.33        10.92 
TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V 
       11.34         0.16        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-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-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J9 
       13.25        13.97        14.17        13.48        19.20        17.49 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JI 
       16.50        18.71        15.78        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-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 
       12.20        14.70        18.58        17.79        16.73        25.74 
TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ 
       23.90        27.58         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-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-A4Z1 
        0.76        10.09        13.08        12.26        14.50         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-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R 
       28.44        28.87        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-A155 
       28.60        17.03        25.41        27.12        23.24        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-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-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       32.35        28.50        16.47        38.30        37.41        32.78 
TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO 
       33.73        28.44        22.65         3.88        22.19        20.98 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LA TCGA-E2-A1LB 
       11.08        54.18        27.42        39.62        24.59        40.47 
TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P6 
       28.90        18.87       106.75       102.61         8.75         5.52 
TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E9-A1N4 
       15.72        30.61        34.92        19.89        19.00        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-A22G TCGA-E9-A22H TCGA-E9-A243 
       13.32        39.09        22.75        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        24.56         0.72 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X 
       17.75         0.76        18.41         0.62        15.72        12.33 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE 
        0.23        14.70         0.26        13.81        14.40        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        43.73        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U 
       72.03        13.55        18.12        11.84        11.57        21.24 
TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 
        6.67         4.08         4.60         8.75         9.53        11.44 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO 
       10.95         7.59        17.06        15.32        14.70        14.47 
TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z 
       14.79        11.57         2.63         3.88         4.14         4.50 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
        4.50         5.59         3.22         6.21         7.36        27.91 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.10        12.66        46.55        31.99        58.62        27.65 
TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H 
       34.92        16.87        24.72        22.32        20.38        26.70 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P 
       65.62        33.57        31.07        26.04         7.23        14.07 
TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF 
       28.21        19.73         0.16         0.26         3.95        16.50 
TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 
        6.81         8.65         7.92         5.56         8.52         7.17 
TCGA-S3-AA15 TCGA-S3-AA17 TCGA-W8-A86G TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
        6.87         3.91         5.29         9.60         9.14       100.01 

  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             23.16 
[1] "0.0 - 177.0 (19.4)" "0.0 - 234.3 (23.2)"
[1] "hr=" "1.4"
D18V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9Q GAIN MUTATED         8        4        1        1        44        29
  9Q GAIN WILD-TYPE      75       76        8        4       298       205
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9Q GAIN MUTATED           0         10          5          7        2
  9Q GAIN WILD-TYPE         2        132         24         56       16
                   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                  8                75
  STAGE IA                 4                76
  STAGE IB                 1                 8
  STAGE II                 1                 4
  STAGE IIA               44               298
  STAGE IIB               29               205
  STAGE III                0                 2
  STAGE IIIA              10               132
  STAGE IIIB               5                24
  STAGE IIIC               7                56
  STAGE IV                 2                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
  9Q GAIN MUTATED    23  71  12   6
  9Q GAIN WILD-TYPE 242 523 112  33
D18V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1              23               242
  T2              71               523
  T3              12               112
  T4               6                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
  9Q GAIN MUTATED    53  42   7   9
  9Q GAIN WILD-TYPE 428 297 106  65
D18V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0              53               428
  N1              42               297
  N2               7               106
  N3               9                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
  9Q GAIN MUTATED          0  96   2  14
  9Q GAIN WILD-TYPE        5 758  17 133
D18V6, multiclass
          clus
vv         9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CM0 (I+)               0                 5
  M0                    96               758
  M1                     2                17
  MX                    14               133
[1] 4 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   112   0
  9Q GAIN WILD-TYPE 902  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED    112    0
  9Q GAIN WILD-TYPE  902   11
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE             112               902
  MALE                 0                11
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  9Q GAIN MUTATED                            0                            87
  9Q GAIN WILD-TYPE                          1                           667
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  9Q GAIN MUTATED                               16                   3
  9Q GAIN WILD-TYPE                            159                   3
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  9Q GAIN MUTATED                                  1                  1
  9Q GAIN WILD-TYPE                               28                 14
                   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                 87               667
  INFILTRATING LOBULAR CARCINOMA                16               159
  MEDULLARY CARCINOMA                            3                 3
  MIXED HISTOLOGY (PLEASE SPECIFY)               1                28
  MUCINOUS CARCINOMA                             1                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"
D18V9, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    33  79
  9Q GAIN WILD-TYPE 249 664
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     33   79
  9Q GAIN WILD-TYPE  249  664
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO               33               249
  YES              79               664
[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                          16    80
  9Q GAIN WILD-TYPE                       142   637
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                     16               142
  WHITE                                         80               637
[1] 4 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  95
  9Q GAIN WILD-TYPE  32 731
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      4   95
  9Q GAIN WILD-TYPE   32  731
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                32
  NOT HISPANIC OR LATINO              95               731
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED   180  26
  10P GAIN WILD-TYPE 706  93
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               206                799 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                26                 93 
$`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        43.00         8.98        24.99        28.04        38.01 
TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08X TCGA-A8-A092 TCGA-A8-A09A 
       19.96        37.05        31.00        43.00        30.97         9.99 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09Q TCGA-A8-A09X TCGA-AC-A23E TCGA-AC-A2BK 
       50.04        49.05        25.02        14.01         2.37        38.53 
TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A8OQ TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AS 
        0.07         1.12         1.12         1.78         1.71         0.33 
TCGA-AN-A0FZ TCGA-AO-A03O TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J9 
        0.33        81.63        29.13        32.78        21.40        53.03 
TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A1KR TCGA-AO-A1KS 
       55.33       102.58       106.78        90.58        70.39         0.53 
TCGA-AQ-A04L TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TS TCGA-AR-A0TT 
      130.09         2.56        32.91         9.99        74.79        86.66 
TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AQ TCGA-AR-A1AW 
       85.97        61.84        52.77        51.25        43.07        63.62 
TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A251 
       20.22       109.58        50.89        53.36        85.35        78.48 
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-A0EE TCGA-BH-A0GY TCGA-BH-A0H7 TCGA-BH-A0HU TCGA-BH-A0HY 
       32.65        31.00        30.35        23.08        12.89        50.79 
TCGA-BH-A0RX TCGA-BH-A18L TCGA-BH-A18T TCGA-BH-A1EN TCGA-BH-A1EV TCGA-BH-A1EW 
        5.59        26.66         7.36        69.93        12.00        55.69 
TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1FC TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12W 
       31.53        97.48       114.15        12.66        11.77        12.66 
TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A1HM TCGA-C8-A26X TCGA-C8-A274 TCGA-C8-A27B 
        3.12         1.78         2.30         0.36         0.03         0.99 
TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A147 TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JF 
       20.88        13.97        19.20        18.71        18.15        12.03 
TCGA-D8-A1JL TCGA-D8-A1X5 TCGA-D8-A1X9 TCGA-D8-A1XF TCGA-D8-A1XU TCGA-D8-A1XW 
       20.09        18.58        23.90        15.22        12.99        12.66 
TCGA-D8-A1XZ TCGA-D8-A3Z6 TCGA-E2-A107 TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14R 
       15.32        18.51        34.42        47.15        44.68        38.60 
TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A159 TCGA-E2-A15G TCGA-E2-A1AZ 
       25.41        27.12        19.43        25.05        18.21        60.53 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A573 TCGA-E2-A574 
      106.75       102.61         8.75        16.93        34.92        19.89 
TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1RB TCGA-E9-A1RH TCGA-E9-A244 TCGA-E9-A247 
       13.48        13.12        20.81        34.59         0.69        27.22 
TCGA-E9-A295 TCGA-E9-A3QA TCGA-E9-A5UP TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW 
        0.72         0.62        14.40        28.77        25.94        22.82 
TCGA-EW-A1OZ TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PH TCGA-EW-A2FS TCGA-EW-A2FV 
       40.41        19.99         6.15        19.96        52.73        25.91 
TCGA-EW-A423 TCGA-GI-A2C9 TCGA-GM-A2DB TCGA-GM-A2DF TCGA-GM-A2DH TCGA-JL-A3YW 
       10.16       109.87        53.13        42.71        42.28        11.84 
TCGA-LD-A7W5 TCGA-LD-A9QF TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A6FQ TCGA-LL-A73Z 
        4.08         8.75        15.32        14.47         2.63         4.50 
TCGA-LL-A8F5 TCGA-MS-A51U TCGA-OL-A5S0 TCGA-OL-A6VO TCGA-PL-A8LV TCGA-S3-AA0Z 
        6.21         2.79        20.38        28.21         0.23        10.59 
TCGA-S3-AA10 TCGA-S3-AA17 
        7.92         3.91 

$`10P GAIN WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI 
        0.39         8.52        14.37        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       136.73        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-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-A0ER TCGA-A2-A0ES TCGA-A2-A0ET 
       89.36        80.28       107.61        74.40        37.05        35.05 
TCGA-A2-A0EU TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU 
       34.29        29.75        24.72        24.16        99.19        54.64 
TCGA-A2-A0SV TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       27.12        44.28        17.52        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-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX 
       19.33        48.46        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-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-A3XZ 
       29.98        32.75        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        24.39        21.30        23.21        26.96 
TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH 
       21.14        21.90        38.30        35.31        34.29        35.47 
TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H 
       30.61        37.45        33.11        12.72        23.61        29.56 
TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY 
       31.36        24.26        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-A4SB TCGA-A7-A4SE TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VW 
       13.74        21.17        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        53.06        29.03 
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-A07L TCGA-A8-A07O TCGA-A8-A07P 
       18.97        14.01        12.00        17.03         9.99        10.98 
TCGA-A8-A07S TCGA-A8-A07W TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 
        7.99         9.99        18.05        15.06        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O 
        0.99        28.96        33.01        12.00         9.99        31.00 
TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A093 
        0.99        33.01        93.04        40.01        33.01        17.95 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09I 
       41.98        12.00         9.99        12.00         1.02        45.07 
TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       29.98        33.07         1.02         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-A23C TCGA-AC-A23G TCGA-AC-A23H 
       13.02        17.03        38.04         0.95        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        22.19         1.12        16.57        19.79 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW 
       23.24        24.79         1.55         1.81         1.18         0.69 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y 
        0.43         1.68         1.74         1.32         0.33         0.33 
TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A0AJ TCGA-AN-A0AK 
        0.23         0.33         0.62         2.96         8.02         7.36 
TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR 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-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-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-A03P 
        5.33         5.59        80.28        47.84        66.77        84.69 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       68.75        47.87        59.05        52.18        24.16        37.48 
TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD 
       20.32        22.36        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        50.24        62.04        71.80 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
       99.25       108.72        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-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       17.79        24.79        26.93         5.65        15.62        32.52 
TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX 
      111.32        49.32         5.26        29.75        98.93        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       101.95        83.87       114.02 
TCGA-AR-A1AH TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP 
       75.55        48.82        62.56        43.73        43.56        39.98 
TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A24L 
       17.23        37.81        76.21        61.28        62.14        73.02 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R 
       96.89        78.51        84.20         0.85       101.52        87.22 
TCGA-AR-A24T TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 
       76.01        50.96        83.77        79.00        56.15        73.18 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       72.76        58.92        93.83       128.65        20.25        62.86 
TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
       42.87        40.04        38.17        39.39        40.54        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-A0IC TCGA-B6-A0IG TCGA-B6-A0IK 
      149.59        12.13       220.90        50.70       146.50        18.77 
TCGA-B6-A0IM TCGA-B6-A0IP TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL 
      126.12       110.93        68.45       189.01       234.28        81.17 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT 
       78.02       172.96       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-A0X4 TCGA-B6-A0X5 
       21.47       113.79       129.57       129.70        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A408 
       58.88        73.51       139.17       170.17        85.35        49.94 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AZ TCGA-BH-A0B0 
      103.63        55.00        24.53        38.79        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-A0BJ TCGA-BH-A0BM 
       37.22        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-A0BT 
       35.67        48.69        27.19        53.69        53.95        45.57 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 
       49.94        11.67        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-A0DV TCGA-BH-A0DX 
       48.23        17.26        15.65         3.22        45.17        47.41 
TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E9 TCGA-BH-A0EB 
       16.27         4.41        15.68        14.30        46.19        24.49 
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-A0HW TCGA-BH-A0HX TCGA-BH-A0W3 TCGA-BH-A0W4 
       13.61        36.85        51.32        27.25        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-A18N TCGA-BH-A18P TCGA-BH-A18Q 
       20.12        90.84        72.56        37.74        30.28        55.63 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ES 
       37.55        66.05        51.39        51.16        91.99       113.82 
TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F5 
       82.85        42.28        49.58        17.69        25.81        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-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-A12Q TCGA-C8-A12U TCGA-C8-A12V 
       11.93        11.77        11.77         0.07        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 
       12.66         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-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-A275 TCGA-C8-A278 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-A143 TCGA-D8-A145 TCGA-D8-A146 
       11.90        13.25        20.58        14.17        13.48        21.14 
TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JG 
       14.17        17.49        16.50        15.78        18.90        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-A1JT TCGA-D8-A1JU TCGA-D8-A1X6 TCGA-D8-A1X7 
       21.01        12.20        13.32        14.70        17.79        16.73 
TCGA-D8-A1X8 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG 
       25.74        27.58        18.15         2.66        17.16        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-A1XY TCGA-D8-A1Y0 
       15.85        16.31         6.35        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-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-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B 
        7.33        43.00        27.52        46.59        40.41        37.51 
TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14S 
       40.11        28.44        28.87        40.96        38.24        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-A15A 
       17.03        23.24        21.04        23.87        14.79        23.34 
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-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-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-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-A1LL 
       19.66        24.59        40.47        28.90        18.87        43.04 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A576 TCGA-E2-A9RU 
        5.52        15.72         7.20        30.61        19.00         9.21 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND 
       19.20        36.82        12.00        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-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-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-A245 
       22.75        12.89        23.51        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        24.56        17.75         0.76        26.07 
TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL 
       18.41        15.72        12.33         0.23        14.70         0.26 
TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
       13.81        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        43.73        69.30        66.38        72.03        13.55 
TCGA-GM-A5PX TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 
       18.12        11.57        21.24         6.67         4.60         9.53 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YP 
       11.44        10.95         7.59        17.06        14.70        14.79 
TCGA-LL-A6FP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 
       11.57         3.88         4.14         4.50         5.59         3.22 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 
        7.36        27.91         2.10        12.66        46.55        31.99 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY 
       58.62        27.65        34.92        36.36        16.87        24.72 
TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L 
       22.32        26.70        23.47        65.62        33.57        31.07 
TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ TCGA-PL-A8LX TCGA-PL-A8LY 
       26.04         7.23        14.07        19.73         0.16         0.26 
TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA11 TCGA-S3-AA12 
        3.95        16.50         6.81         8.65         5.56         8.52 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-W8-A86G TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
        7.17         6.87         5.29         9.60         9.14       100.01 
TCGA-Z7-A8R6 
      105.04 

  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 
             24.92              22.09 
[1] "0.0 - 211.6 (24.9)" "0.0 - 234.3 (22.1)"
[1] "hr=" "1"  
D19V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10P GAIN MUTATED        17       12        1        1        78        39
  10P GAIN WILD-TYPE      66       68        8        4       264       195
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10P GAIN MUTATED           0         27          7         13        7
  10P GAIN WILD-TYPE         2        115         22         50       11
                    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                 66
  STAGE IA                 12                 68
  STAGE IB                  1                  8
  STAGE II                  1                  4
  STAGE IIA                78                264
  STAGE IIB                39                195
  STAGE III                 0                  2
  STAGE IIIA               27                115
  STAGE IIIB                7                 22
  STAGE IIIC               13                 50
  STAGE IV                  7                 11
  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    45 128  23  11
  10P GAIN WILD-TYPE 220 466 101  28
D19V4, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1               45                220
  T2              128                466
  T3               23                101
  T4               11                 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 GAIN MUTATED   105  57  26  16
  10P GAIN WILD-TYPE 376 282  87  58
D19V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0              105                376
  N1               57                282
  N2               26                 87
  N3               16                 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 GAIN MUTATED          1 178   7  23
  10P GAIN WILD-TYPE        4 676  12 124
D19V6, multiclass
          clus
vv         10P GAIN MUTATED 10P GAIN WILD-TYPE
  CM0 (I+)                1                  4
  M0                    178                676
  M1                      7                 12
  MX                     23                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"
D19V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED   207   2
  10P GAIN WILD-TYPE 807   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED    207    2
  10P GAIN WILD-TYPE  807    9
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE              207                807
  MALE                  2                  9
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  10P GAIN MUTATED                            0                           179
  10P GAIN WILD-TYPE                          1                           575
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  10P GAIN MUTATED                               16                   4
  10P GAIN WILD-TYPE                            159                   2
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  10P GAIN MUTATED                                  4                  0
  10P GAIN WILD-TYPE                               25                 15
                    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                 179                575
  INFILTRATING LOBULAR CARCINOMA                 16                159
  MEDULLARY CARCINOMA                             4                  2
  MIXED HISTOLOGY (PLEASE SPECIFY)                4                 25
  MUCINOUS CARCINOMA                              0                 15
  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    68 141
  10P GAIN WILD-TYPE 214 602
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     68  141
  10P GAIN WILD-TYPE  214  602
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                68                214
  YES              141                602
[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                          49   129
  10P GAIN WILD-TYPE                       109   588
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                      49                109
  WHITE                                         129                588
[1] 4 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     7 163
  10P GAIN WILD-TYPE  29 663
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      7  163
  10P GAIN WILD-TYPE   29  663
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    7                 29
  NOT HISPANIC OR LATINO              163                663
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED   102  17
  10Q GAIN WILD-TYPE 784 102
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               119                886 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                17                102 
$`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 
       38.01        31.00        30.97         9.99        50.04        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       106.78        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        74.79        86.66        61.84 
TCGA-AR-A1AJ TCGA-AR-A1AQ TCGA-AR-A1AW TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24U 
       52.77        43.07        63.62       109.58        50.89        53.36 
TCGA-AR-A24V TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IO 
       85.35       129.57        65.72       112.37       176.98       110.14 
TCGA-B6-A0IQ TCGA-B6-A0RO TCGA-B6-A0WV TCGA-B6-A1KC TCGA-BH-A0AY TCGA-BH-A0B6 
      140.88       162.05        79.63        43.59        25.55        56.94 
TCGA-BH-A0BL TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0EA 
       44.05         2.56        38.47         9.63        44.81        32.65 
TCGA-BH-A0EE TCGA-BH-A18L TCGA-BH-A1EN TCGA-BH-A1EV TCGA-C8-A12O TCGA-C8-A12P 
       31.00        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        34.92        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-E9-A5UP TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1PC TCGA-EW-A423 TCGA-GM-A2DB 
       14.40        28.77        25.94         6.15        10.16        53.13 
TCGA-GM-A2DH TCGA-LD-A9QF TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A6FQ TCGA-LL-A73Z 
       42.28         8.75        15.32        14.47         2.63         4.50 
TCGA-MS-A51U TCGA-OL-A5S0 TCGA-PL-A8LV TCGA-S3-AA0Z TCGA-S3-AA10 
        2.79        20.38         0.23        10.59         7.92 

$`10Q GAIN WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SH 
        0.39         8.52        14.37        43.43        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-A04R TCGA-A2-A04T TCGA-A2-A04V TCGA-A2-A04W 
       18.21       104.81        82.16        73.84        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       136.73        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-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-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-A0SV TCGA-A2-A0SW TCGA-A2-A0SY 
       24.16        99.19        54.64        27.12        44.88        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-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-A0YM TCGA-A2-A0YT 
       14.50        18.61        19.33        48.46        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-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        32.75        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        24.39        21.30        23.21        26.96 
TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH 
       21.14        21.90        38.30        35.31        34.29        35.47 
TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13F 
       30.61        37.45        35.67        33.11        31.73        12.72 
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-A4SD TCGA-A7-A4SE 
       14.70        11.97        14.93        13.74        14.50        21.17 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV 
       17.92        14.73        12.10        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-A06T TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 
       53.06        29.03        26.01         1.02        53.98         9.01 
TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J 
       43.00        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        24.99 
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-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L 
       28.96        33.01        19.96        12.00        37.05         9.99 
TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z 
       31.00         0.99        33.01        93.04        43.00        40.01 
TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09B 
       33.01        17.95        41.98        12.00         9.99        12.00 
TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N 
        1.02        49.05        45.07        29.98        33.07         1.02 
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-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-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 
       22.19         1.12        16.57        19.79        23.24        24.79 
TCGA-AC-A5XS TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO 
        1.55         1.81         1.18         0.69         0.43         1.68 
TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 
        1.74         1.12         1.32         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-A0FY 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-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J4 
       84.69        68.75        47.87        59.05        29.13        52.18 
TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0JA TCGA-AO-A0JB 
       24.16        37.48        20.32        22.36        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        50.24 
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       108.72 
TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G 
       96.10        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-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54O 
       24.79        26.93         5.65        15.62        32.52        32.91 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TV TCGA-AR-A0TW 
        9.99       111.32        49.32         5.26        29.75        98.93 
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       101.95        83.87 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM 
      114.02        85.97        75.55        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        37.81        76.21 
TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       61.28        62.14        20.22        73.02        96.89        78.51 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24W 
       84.20         0.85       101.52        87.22        76.01        50.96 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 
       83.77        79.00        56.15        78.48        73.18        72.76 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK 
       58.92        93.83       128.65        20.25        62.86        42.87 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
        7.36        40.04        38.17        39.39        40.54        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-A0IC TCGA-B6-A0IG TCGA-B6-A0IK 
      149.59        12.13       220.90        50.70       146.50        18.77 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH 
      126.12        84.59       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-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-A1KF TCGA-B6-A1KI TCGA-B6-A1KN 
       28.27        68.94        58.88       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       103.63        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-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-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-A0DV 
       13.91        48.23        17.26        15.65         3.22        45.17 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E9 
       47.41        16.27         4.41        15.68        14.30        46.19 
TCGA-BH-A0EB TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       24.49        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-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-A18N TCGA-BH-A18P TCGA-BH-A18Q 
       20.12        90.84        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-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-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-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-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12X 
       11.77        11.77         0.07        12.66        12.66        12.66 
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-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-A140 TCGA-D8-A141 TCGA-D8-A142 
        0.03         0.23        11.90        13.25        20.58        13.97 
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-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-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-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR 
       21.83        14.50        17.69         7.96        16.41        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-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-A108 TCGA-E2-A109 
       14.50        18.51         7.33        43.00        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-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-A153 
       34.26        32.02        31.96        28.60        17.03        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-A15E TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J 
       17.29        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-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-A1LK TCGA-E2-A1LL 
       40.47        28.90        18.87       106.75         8.75        43.04 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A574 TCGA-E2-A576 
        5.52        15.72         7.20        30.61        19.89        19.00 
TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1NA TCGA-E9-A1NC 
        9.21        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        24.56        17.75 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y 
        0.76        26.07        18.41        15.72        12.33         0.23 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
       14.70         0.26        13.81        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-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-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-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        43.73 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW 
       69.30        66.38        72.03        13.55        18.12        11.84 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LL-A440 
       11.57        21.24         6.67         4.08         4.60         9.53 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YP 
       11.44        10.95         7.59        17.06        14.70        14.79 
TCGA-LL-A6FP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 
       11.57         3.88         4.14         4.50         5.59         3.22 
TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 
        6.21         7.36        27.91         2.10        12.66        46.55 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX 
       31.99        58.62        27.65        34.92        36.36        16.87 
TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K 
       24.72        22.32        26.70        23.47        65.62        33.57 
TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ 
       31.07        26.04         7.23        14.07        28.21        19.73 
TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH 
        0.16         0.26         3.95        16.50         6.81         8.65 
TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-W8-A86G 
        5.56         8.52         7.17         6.87         3.91         5.29 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        9.60         9.14       100.01       105.04 

  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 
             25.02              22.19 
[1] "0.0 - 177.0 (25.0)" "0.0 - 234.3 (22.2)"
[1] "hr=" "1.1"
D20V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10Q GAIN MUTATED         9        8        0        0        44        28
  10Q GAIN WILD-TYPE      74       72        9        5       298       206
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10Q GAIN MUTATED           0         16          5          5        3
  10Q GAIN WILD-TYPE         2        126         24         58       15
                    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                 74
  STAGE IA                  8                 72
  STAGE IB                  0                  9
  STAGE II                  0                  5
  STAGE IIA                44                298
  STAGE IIB                28                206
  STAGE III                 0                  2
  STAGE IIIA               16                126
  STAGE IIIB                5                 24
  STAGE IIIC                5                 58
  STAGE IV                  3                 15
  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    24  79  13   5
  10Q GAIN WILD-TYPE 241 515 111  34
D20V4, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1               24                241
  T2               79                515
  T3               13                111
  T4                5                 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
  10Q GAIN MUTATED    62  37  13   6
  10Q GAIN WILD-TYPE 419 302 100  68
D20V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0               62                419
  N1               37                302
  N2               13                100
  N3                6                 68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  10Q GAIN MUTATED          0 107   3  12
  10Q GAIN WILD-TYPE        5 747  16 135
D20V6, multiclass
          clus
vv         10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CM0 (I+)                0                  5
  M0                    107                747
  M1                      3                 16
  MX                     12                135
[1] 4 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   121   1
  10Q GAIN WILD-TYPE 893  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED    121    1
  10Q GAIN WILD-TYPE  893   10
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE              121                893
  MALE                  1                 10
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  10Q GAIN MUTATED                            0                           103
  10Q GAIN WILD-TYPE                          1                           651
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  10Q GAIN MUTATED                               10                   3
  10Q GAIN WILD-TYPE                            165                   3
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  10Q GAIN MUTATED                                  3                  0
  10Q GAIN WILD-TYPE                               26                 15
                    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                 103                651
  INFILTRATING LOBULAR CARCINOMA                 10                165
  MEDULLARY CARCINOMA                             3                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)                3                 26
  MUCINOUS CARCINOMA                              0                 15
  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  80
  10Q GAIN WILD-TYPE 240 663
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     42   80
  10Q GAIN WILD-TYPE  240  663
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                42                240
  YES               80                663
[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                          24    79
  10Q GAIN WILD-TYPE                       134   638
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                      24                134
  WHITE                                          79                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"
D20V12, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     5  94
  10Q GAIN WILD-TYPE  31 732
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      5   94
  10Q GAIN WILD-TYPE   31  732
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                 31
  NOT HISPANIC OR LATINO               94                732
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED   115  16
  11P GAIN WILD-TYPE 771 103
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
               131                874 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                16                103 
$`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        38.01        12.00        33.01         9.99 
TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-AC-A23C 
       29.98        33.07        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 
      108.72        90.58        77.56       130.09        15.62        98.93 
TCGA-AR-A24K TCGA-AR-A24V TCGA-AR-A250 TCGA-AR-A2LR TCGA-B6-A0I2 TCGA-B6-A0IB 
       50.89        85.35        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-A152 TCGA-E2-A15A TCGA-E2-A15M TCGA-E2-A15R TCGA-E2-A1AZ 
       34.26        27.12        23.34         7.73        17.06        60.53 
TCGA-E2-A1BC TCGA-E2-A1II TCGA-E2-A1IU TCGA-E2-A574 TCGA-E9-A1N8 TCGA-E9-A1R4 
       16.47        33.70        11.08        19.89        12.00         6.12 
TCGA-E9-A1R6 TCGA-E9-A1RB TCGA-E9-A1RE TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 
        2.76        20.81        34.65        17.06         0.69        27.22 
TCGA-E9-A249 TCGA-E9-A5FL TCGA-EW-A1J1 TCGA-EW-A1J6 TCGA-EW-A1OY TCGA-EW-A1P5 
        0.95         0.26        18.90        28.77        29.85        23.11 
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        11.44 
TCGA-LL-A73Y TCGA-OL-A66I TCGA-OL-A6VO TCGA-PL-A8LZ TCGA-S3-AA17 
        4.14        23.47        28.21         3.95         3.91 

$`11P GAIN WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        0.39         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SJ TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ 
       47.24        13.68        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-A04V 
      104.81        18.02        41.95        82.16        73.84        63.12 
TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
       36.13       136.73        64.57       112.08        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX 
      107.93        75.55         5.19        63.45        64.04        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-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EV 
      107.61        79.76        74.40        37.05        35.05        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-A0T4 
       44.88        50.43        44.28        17.52        17.13        20.52 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG 
       17.46        18.90        32.55        25.28        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        48.46        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-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-A3XS TCGA-A2-A3XU TCGA-A2-A3XV 
       91.92        10.59        20.88        33.93        29.98        32.75 
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-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 
       24.39        21.30        23.21        26.96        21.14        21.90 
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-A26H TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3J1 TCGA-A7-A3RF 
       23.80        21.73        22.32        11.34        11.28        13.41 
TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D 
       11.97        14.93        13.74        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        53.06        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        43.00 
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-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 
       10.98         7.99        24.99         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        28.96        33.01 
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-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A093 
       33.01        93.04        43.00        40.01        30.97        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        50.04 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       49.05        45.07         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-A0A9 
        0.99        14.01        12.00        19.04        13.02        13.02 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BK 
       17.03        38.04         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-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        22.19         1.12        16.57        19.79        23.24 
TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX 
       24.79         1.55         1.12         1.18         0.69         0.43 
TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y 
        1.68         1.74         1.12         1.32         0.33         0.33 
TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AK 
        0.23         0.33         0.62         2.96         1.71         7.36 
TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR 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-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV 
        7.96         7.59         7.17         6.28         6.02         0.33 
TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FZ 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-A0XV TCGA-AN-A0XW TCGA-AO-A03M 
        0.33         0.33         0.33         5.33         5.59        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-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 
       29.13        32.78        52.18        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        50.24        62.04        55.33 
TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12D 
       71.80       102.58        99.25       106.78        96.10        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-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J 
       61.87        70.39         0.53        17.79        24.79        26.93 
TCGA-AQ-A0Y5 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP 
        5.65        32.52         2.56        32.91         9.99       111.32 
TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TX 
       49.32         5.26        74.79        86.66        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       101.95        83.87       114.02 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL 
       85.97        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 
       37.81        76.21        61.28        63.62        62.14        20.22 
TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
      109.58        73.02        96.89        78.51        84.20         0.85 
TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24W TCGA-AR-A24X 
      101.52        87.22        76.01        53.36        50.96        83.77 
TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
       79.00        78.48        73.18        72.76        58.92        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM 
      128.65        20.25        62.86        42.87         7.36        40.04 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP 
       38.17        39.39        40.54        54.74        16.04        20.45 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC 
       10.59        77.62       149.59        12.13       220.90        50.70 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
       65.72       146.50       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-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-A0X1 
       79.63        17.98        21.47       113.79       129.57       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-A40B TCGA-B6-A40C TCGA-BH-A0AV 
      170.17        85.35        54.28       103.63        55.00        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-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       24.49        31.00        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-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-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R 
       90.84        26.66        37.74        30.28        55.63        37.55 
TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1ET 
       66.05         7.36        51.39        69.93       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-A203 
       45.63        72.07       144.59        72.07         6.90        38.60 
TCGA-BH-A204 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
       83.31        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-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-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-A27B 
        8.28         9.67         0.03         0.03         0.03         0.99 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A141 TCGA-D8-A142 
        0.03         0.23        11.90        20.88        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-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-A1JK TCGA-D8-A1JL TCGA-D8-A1JM 
       14.01        18.97        20.09        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-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-A1XL TCGA-D8-A1XM 
        2.66        17.16        14.73        21.83        19.92        17.69 
TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU 
        7.96        16.41        15.85        16.31         6.35        12.99 
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-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-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-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-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z 
       33.30        43.33        32.02        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-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-A15O 
       12.92        17.42        19.40         9.04        20.58        13.02 
TCGA-E2-A15P TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 
       19.56        14.07        14.99        53.62        53.03        29.95 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       32.35        28.50        17.10        38.30        37.41        32.78 
TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO 
       33.73        28.44        22.65         3.88        22.19        20.98 
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-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 
       16.93         5.52        15.72         7.20        30.61        34.92 
TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 
       19.00         9.21        19.20        36.82        13.48        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-A1R5 
        9.86        11.90        14.30         0.62         2.10         1.38 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RF TCGA-E9-A1RG 
       21.21        32.09        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-A22G TCGA-E9-A22H TCGA-E9-A245 
       39.09        22.75        12.89        23.51        24.10         0.85 
TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO 
        1.94        24.56         0.72        17.75         0.76        26.07 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK 
       18.41         0.62        15.72        12.33         0.23        14.70 
TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
       13.81        14.40        15.39        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OW 
       18.21        13.25        16.57        15.68        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-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-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 
       25.91        22.09        21.27        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        43.73        69.30        66.38        72.03        13.55 
TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 
       18.12        11.84        11.57        21.24         6.67         4.08 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL 
        4.60         8.75         9.53        10.95         7.59        17.06 
TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ 
       15.32        14.70        14.47        14.79        11.57         2.63 
TCGA-LL-A6FR TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 
        3.88         4.50         4.50         5.59         3.22         6.21 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 
        7.36        27.91         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 
       31.99        58.62        27.65        34.92        36.36        16.87 
TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K 
       24.72        22.32        20.38        26.70        65.62        33.57 
TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ TCGA-PL-A8LV 
       31.07        26.04         7.23        14.07        19.73         0.23 
TCGA-PL-A8LX TCGA-PL-A8LY TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z 
        0.16         0.26        16.50         6.81         8.65        10.59 
TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-W8-A86G 
        7.92         5.56         8.52         7.17         6.87         5.29 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        9.60         9.14       100.01       105.04 

  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 
            20.880             22.935 
[1] "0.1 - 143.4 (20.9)" "0.0 - 234.3 (22.9)"
[1] "hr=" "1.1"
D21V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11P GAIN MUTATED        10       12        2        1        51        27
  11P GAIN WILD-TYPE      73       68        7        4       291       207
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11P GAIN MUTATED           0         15          3          6        3
  11P GAIN WILD-TYPE         2        127         26         57       15
                    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                  10                 73
  STAGE IA                 12                 68
  STAGE IB                  2                  7
  STAGE II                  1                  4
  STAGE IIA                51                291
  STAGE IIB                27                207
  STAGE III                 0                  2
  STAGE IIIA               15                127
  STAGE IIIB                3                 26
  STAGE IIIC                6                 57
  STAGE IV                  3                 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
  11P GAIN MUTATED    32  81  15   3
  11P GAIN WILD-TYPE 233 513 109  36
D21V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1               32                233
  T2               81                513
  T3               15                109
  T4                3                 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
  11P GAIN MUTATED    71  40  10   8
  11P GAIN WILD-TYPE 410 299 103  66
D21V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0               71                410
  N1               40                299
  N2               10                103
  N3                8                 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
  11P GAIN MUTATED          1 111   3  16
  11P GAIN WILD-TYPE        4 743  16 131
D21V6, multiclass
          clus
vv         11P GAIN MUTATED 11P GAIN WILD-TYPE
  CM0 (I+)                1                  4
  M0                    111                743
  M1                      3                 16
  MX                     16                131
[1] 4 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   129   2
  11P GAIN WILD-TYPE 885   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED    129    2
  11P GAIN WILD-TYPE  885    9
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE              129                885
  MALE                  2                  9
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  11P GAIN MUTATED                            0                           109
  11P GAIN WILD-TYPE                          1                           645
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  11P GAIN MUTATED                                9                   1
  11P GAIN WILD-TYPE                            166                   5
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  11P GAIN MUTATED                                  1                  2
  11P GAIN WILD-TYPE                               28                 13
                    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                 109                645
  INFILTRATING LOBULAR CARCINOMA                  9                166
  MEDULLARY CARCINOMA                             1                  5
  MIXED HISTOLOGY (PLEASE SPECIFY)                1                 28
  MUCINOUS CARCINOMA                              2                 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"
D21V9, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    37  94
  11P GAIN WILD-TYPE 245 649
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     37   94
  11P GAIN WILD-TYPE  245  649
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                37                245
  YES               94                649
[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                          19    94
  11P GAIN WILD-TYPE                       139   623
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                      19                139
  WHITE                                          94                623
[1] 4 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     6 106
  11P GAIN WILD-TYPE  30 720
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      6  106
  11P GAIN WILD-TYPE   30  720
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                 30
  NOT HISPANIC OR LATINO              106                720
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    75  16
  11Q GAIN WILD-TYPE 811 103
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                91                914 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                16                103 
$`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        38.01        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        98.93 
TCGA-AR-A24K TCGA-AR-A24V TCGA-B6-A0IE TCGA-B6-A0IO TCGA-B6-A0RS TCGA-B6-A0X0 
       50.89        85.35        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-A152 TCGA-E2-A15A TCGA-E2-A15R TCGA-E2-A1AZ 
       16.54        14.14        27.12        23.34        17.06        60.53 
TCGA-E2-A1B0 TCGA-E2-A1II TCGA-E2-A574 TCGA-E9-A1N8 TCGA-E9-A1R6 TCGA-E9-A1RB 
       53.62        33.70        19.89        12.00         2.76        20.81 
TCGA-E9-A244 TCGA-E9-A249 TCGA-E9-A5FL TCGA-EW-A1J6 TCGA-EW-A1P5 TCGA-EW-A1P8 
        0.69         0.95         0.26        28.77        23.11         7.86 
TCGA-EW-A2FW TCGA-EW-A3U0 TCGA-GM-A2DB TCGA-GM-A2DH TCGA-LL-A441 TCGA-OL-A66I 
       22.09        17.49        53.13        42.28        11.44        23.47 
TCGA-PL-A8LZ 
        3.95 

$`11Q GAIN WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        0.39         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP 
       47.24        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       136.73 
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-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-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EV 
      107.61        79.76        74.40        37.05        35.05        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-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-A0YK TCGA-A2-A0YL 
       15.42        21.90        21.67        14.50        19.33        48.46 
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-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-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       33.93        29.98        32.75        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        24.39        21.30        23.21 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH 
       26.96        21.14        21.90        35.31        34.29        35.47 
TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E 
       30.61        37.45        35.67        33.11        31.73        10.72 
TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26H TCGA-A7-A26I 
       12.72        23.61        29.56        31.36        23.80        21.73 
TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 
       20.61        22.32        11.34        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-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        53.06 
TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 
       29.03        31.00        26.01         1.02        53.98         9.01 
TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O 
       43.00        19.99        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        24.99         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        28.96        33.01 
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-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 
       33.01        93.04        43.00        40.01        33.01        30.97 
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-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N 
       50.04        49.05        45.07        29.98        33.07         1.02 
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-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD 
       19.04        13.02        21.04        13.02        17.03        38.04 
TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK 
        0.95         2.37        10.85         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-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        22.19         1.12        16.57        19.79        23.24 
TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX 
       24.79         1.55         1.12         1.18         0.69         0.43 
TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y 
        1.68         1.74         1.12         1.32         0.33         0.33 
TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AK 
        0.23         0.33         0.62         2.96         1.71         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-A0FT 
        4.64         7.96         7.59         7.17         6.28         6.02 
TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FZ 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-A0XV 
       12.33         0.30         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 
       52.18        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-A124 
       26.24        50.24        62.04        55.33        71.80       102.58 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A12E 
       99.25       108.72       106.78        96.10        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-A0Y5 
       70.39         0.53        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-A0TP 
       15.62        32.52         2.56        32.91         9.99       111.32 
TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TX 
       49.32         5.26        74.79        86.66        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       101.95        83.87       114.02 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL 
       85.97        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 
       37.81        76.21        61.28        63.62        62.14        20.22 
TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
      109.58        73.02        96.89        78.51        84.20         0.85 
TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24W TCGA-AR-A24X 
      101.52        87.22        76.01        53.36        50.96        83.77 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 
       79.00        56.15        78.48        73.18        72.76        58.92 
TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL 
       93.83       128.65        20.25        62.86        42.87         7.36 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM 
       40.04        38.17        39.39        40.54        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-A0IG TCGA-B6-A0IH 
       12.13       220.90       129.57        50.70       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-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RU 
      172.96       162.05       102.77       140.48        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-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-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY 
      103.63        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-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ 
       25.71        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-A0DH 
       44.02        48.13        42.90        45.83        31.17        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT 
       22.13        13.91        48.23         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-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-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-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S 
       26.66        37.74        30.28        55.63        37.55        66.05 
TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW 
       69.93       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-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-A204 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T 
        6.90        83.31        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-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-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-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 
       20.88        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-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-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-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR 
       14.73        19.92        17.69         7.96        16.41        15.85 
TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XZ TCGA-D8-A1Y0 
       16.31         6.35        12.99        15.16        15.32        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H 
        3.81        14.24        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-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-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-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-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-A15G TCGA-E2-A15H 
       22.82        17.29        20.71        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-A15S TCGA-E2-A15T TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       19.56        14.07        14.99        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-A1IN TCGA-E2-A1IO 
       33.73        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        30.61 
TCGA-E2-A573 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 
       34.92        19.00         9.21        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-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RC TCGA-E9-A1RD 
        6.12         1.38        21.21        32.09        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-A245 TCGA-E9-A247 TCGA-E9-A248 
       23.51        24.10        17.06         0.85        27.22         1.94 
TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 
       24.56         0.72        17.75         0.76        26.07        18.41 
TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UO 
        0.62        15.72        12.33         0.23        14.70        13.81 
TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
       14.40        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-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC 
       29.82        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-A423 TCGA-EW-A424 TCGA-GI-A2C8 
       52.73        25.91        21.27        10.16        10.59         7.40 
TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF 
      109.87        59.57       194.27        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-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 
      110.50        38.20        43.73        69.30        66.38        72.03 
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        21.24         6.67 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y 
        4.08         4.60         8.75         9.53        10.95         7.59 
TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP 
       17.06        15.32        14.70        14.47        14.79        11.57 
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-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 
        3.22         6.21         7.36        27.91         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        31.99        58.62        27.65        34.92 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H 
       36.36        16.87        24.72        22.32        20.38        26.70 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P 
       65.62        33.57        31.07        26.04         7.23        14.07 
TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PL-A8LV TCGA-PL-A8LX TCGA-PL-A8LY TCGA-S3-A6ZF 
       28.21        19.73         0.23         0.16         0.26        16.50 
TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 
        6.81         8.65        10.59         7.92         5.56         8.52 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-W8-A86G TCGA-XX-A899 TCGA-XX-A89A 
        7.17         6.87         3.91         5.29         9.60         9.14 
TCGA-Z7-A8R5 TCGA-Z7-A8R6 
      100.01       105.04 

  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              22.55 
[1] "0.1 - 130.2 (21.8)" "0.0 - 234.3 (22.5)"
[1] "hr=" "1.5"
D22V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11Q GAIN MUTATED         9        5        1        1        34        22
  11Q GAIN WILD-TYPE      74       75        8        4       308       212
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11Q GAIN MUTATED           0          9          3          4        1
  11Q GAIN WILD-TYPE         2        133         26         59       17
                    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                   9                 74
  STAGE IA                  5                 75
  STAGE IB                  1                  8
  STAGE II                  1                  4
  STAGE IIA                34                308
  STAGE IIB                22                212
  STAGE III                 0                  2
  STAGE IIIA                9                133
  STAGE IIIB                3                 26
  STAGE IIIC                4                 59
  STAGE IV                  1                 17
  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    22  57   8   3
  11Q GAIN WILD-TYPE 243 537 116  36
D22V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1               22                243
  T2               57                537
  T3                8                116
  T4                3                 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
  11Q GAIN MUTATED    47  32   7   4
  11Q GAIN WILD-TYPE 434 307 106  70
D22V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0               47                434
  N1               32                307
  N2                7                106
  N3                4                 70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  11Q GAIN MUTATED          0  81   1   9
  11Q GAIN WILD-TYPE        5 773  18 138
D22V6, multiclass
          clus
vv         11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CM0 (I+)                0                  5
  M0                     81                773
  M1                      1                 18
  MX                      9                138
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    90   1
  11Q GAIN WILD-TYPE 924  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     90    1
  11Q GAIN WILD-TYPE  924   10
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               90                924
  MALE                  1                 10
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  11Q GAIN MUTATED                            0                            74
  11Q GAIN WILD-TYPE                          1                           680
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  11Q GAIN MUTATED                                4                   2
  11Q GAIN WILD-TYPE                            171                   4
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  11Q GAIN MUTATED                                  2                  1
  11Q GAIN WILD-TYPE                               27                 14
                    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                  74                680
  INFILTRATING LOBULAR CARCINOMA                  4                171
  MEDULLARY CARCINOMA                             2                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                2                 27
  MUCINOUS CARCINOMA                              1                 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"
D22V9, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    23  68
  11Q GAIN WILD-TYPE 259 675
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     23   68
  11Q GAIN WILD-TYPE  259  675
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                23                259
  YES               68                675
[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                          15    66
  11Q GAIN WILD-TYPE                       143   651
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                      15                143
  WHITE                                          66                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"
D22V12, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     4  74
  11Q GAIN WILD-TYPE  32 752
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      4   74
  11Q GAIN WILD-TYPE   32  752
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 32
  NOT HISPANIC OR LATINO               74                752
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED   185  28
  12P GAIN WILD-TYPE 701  91
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               213                792 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                28                 91 
$`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        24.99         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        33.01        30.97         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        16.57         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 
       32.91        49.32        83.87        85.97        51.25        43.07 
TCGA-AR-A1AV TCGA-AR-A24H TCGA-AR-A24Q TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24Z 
       61.28       109.58       101.52        85.35        50.96        79.00 
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-A1HK 
       38.60        11.93        12.66        12.66         3.12        12.03 
TCGA-C8-A1HM TCGA-C8-A26Z TCGA-C8-A278 TCGA-D8-A13Z TCGA-D8-A143 TCGA-D8-A147 
        2.30         8.28         0.03        20.88        14.17        19.20 
TCGA-D8-A1J8 TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1XD 
       14.17        15.78        18.15        20.09        19.40        17.16 
TCGA-D8-A1XJ TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A27M 
       21.83        12.99        16.54        15.32        15.52        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-A1AZ TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1LL 
       13.02        14.07        60.53        33.73        33.70        43.04 
TCGA-E2-A2P5 TCGA-E2-A56Z TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NF 
       16.93         7.20        13.48        12.00        13.12        20.05 
TCGA-E9-A1NI TCGA-E9-A1R6 TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RG TCGA-E9-A243 
        9.86         2.76        20.81        40.24        21.27        17.06 
TCGA-E9-A247 TCGA-E9-A295 TCGA-E9-A2JS TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1P4 
       27.22         0.72        17.75        28.77        22.82        29.82 
TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A2FV TCGA-GI-A2C9 TCGA-GM-A2DD TCGA-GM-A2DI 
       23.11         7.86        25.91       109.87        43.04        61.91 
TCGA-GM-A3XL TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A6FP 
       69.30        21.24         4.08         9.53        11.44        11.57 
TCGA-LL-A6FQ TCGA-LL-A7SZ TCGA-OL-A5RV TCGA-OL-A5RZ TCGA-OL-A66O TCGA-S3-A6ZF 
        2.63         5.59        34.92        22.32         7.23        16.50 
TCGA-S3-A6ZG TCGA-S3-AA10 TCGA-Z7-A8R5 
        6.81         7.92       100.01 

$`12P GAIN WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SH 
        0.39         8.52        14.37        43.43        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-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
       41.95        82.16        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 
      136.73        64.57        24.79       112.08        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D1 TCGA-A2-A0D2 
      107.93        75.25        63.45        64.04        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-A0EW TCGA-A2-A0EX TCGA-A2-A0ST 
       79.76        74.40        37.05        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-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-A0YI 
       20.75        32.55        25.28        15.42        21.90        14.50 
TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV 
       18.61        19.33        48.46        31.73        23.77        23.47 
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-A3XU TCGA-A2-A3XV TCGA-A2-A3XX 
       20.88        39.65        83.01        29.98        32.75        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        24.39        21.30 
TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CG TCGA-A7-A0CH 
       23.21        26.96        21.14        21.90        34.29        35.47 
TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13G 
       30.61        37.45        35.67        33.11        31.73        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-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-A4SF TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VY 
       14.93        17.92        10.72        11.05        10.29         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        53.06        29.03 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A07B TCGA-A8-A07E 
       31.00        26.01         1.02        17.03        43.00        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-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 
       10.98         7.99        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        38.01        28.96        33.01        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        43.00        40.01        33.01 
TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09D 
       17.95        41.98        12.00         9.99        12.00        50.04 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R 
       49.05        45.07        29.98        33.07        25.02         8.98 
TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 
       19.04        15.02         0.99        19.04        13.02        21.04 
TCGA-A8-A0A7 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A23H 
        0.99        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-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN 
       38.79        50.70         0.92         2.27         0.99         0.69 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ 
       14.83        22.19         1.12        19.79        23.24        24.79 
TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX 
        1.55         0.07         1.81         1.18         0.69         0.43 
TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A041 
        1.68         1.74         1.12         1.32         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-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FV 
        4.64         7.00         7.59         7.17         6.28         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-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-A0J3 TCGA-AO-A0J4 
       68.75        47.87        59.05        29.13        21.40        52.18 
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-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL 
       76.77        21.37        26.24        50.24        62.04        55.33 
TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A 
       71.80        99.25       108.72       106.78        96.10        90.58 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       77.56        64.04        41.62        28.37        14.73        82.62 
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-A7U7 TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TS 
       32.52         2.56         9.99       111.32         5.26        74.79 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
       86.66        29.75        98.93        64.83        55.86        76.14 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ 
       65.36       101.95       114.02        75.55        61.84        52.77 
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-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K 
       37.81        76.21        63.62        62.14        20.22        50.89 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R 
       73.02        96.89        78.51        84.20         0.85        87.22 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 
       76.01        53.36        83.77        78.48        73.18        72.76 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK 
       58.92        93.83       128.65        20.25        62.86        42.87 
TCGA-AR-A2LL TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP 
        7.36        38.17        39.39        40.54        16.04        20.45 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB 
       10.59        77.62       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-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-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-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 
      188.68        17.98        21.47       129.57       129.70        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 
       68.94        58.88       101.52       139.17       170.17        85.35 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 
      103.63        55.00        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-A0BC 
       40.83        39.55        39.16        56.94        56.98        32.02 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP 
       18.21        25.71        21.70        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-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-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-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0EI 
       14.30         9.63        46.19        32.65        31.00        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-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-A1EN TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EX 
        7.36        51.39        69.93       113.82        82.85        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-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A204 
       55.00        72.07       144.59        72.07         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-A12M TCGA-C8-A12N TCGA-C8-A12P TCGA-C8-A12Q 
      109.28         8.94        11.77        11.77        11.77         0.07 
TCGA-C8-A12U TCGA-C8-A12V 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-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-A1HN TCGA-C8-A26V TCGA-C8-A26W 
       11.34         0.16        10.42         3.25         0.30         0.23 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A27A 
        0.36         0.43         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-A145 TCGA-D8-A146 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
       13.97        13.48        21.14        17.49        16.50        18.71 
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-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU 
       20.12        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-A1XF TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XL 
       18.15         2.66        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-A1XW TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E 
       15.16        12.66         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-A27T TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A4Z1 
        4.80         0.76        13.08        12.53        14.50         7.33 
TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N 
       43.00        27.52        40.41        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-A14V TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 
       34.26        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-A15C 
       19.43        21.04        23.87        14.79        25.05        22.82 
TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J 
       17.29        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-A15T 
        9.04        20.58         7.73        19.56        17.06        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-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-A570 
      106.75       102.61         8.75         5.52        15.72        30.61 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1N5 
       34.92        19.89        19.00         9.21        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-A1RH TCGA-E9-A1RI 
       32.09         0.66        34.65         6.58        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-A244 TCGA-E9-A245 TCGA-E9-A248 
       12.89        23.51        24.10         0.69         0.85         1.94 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA 
        0.95        24.56         0.76        26.07        18.41         0.62 
TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO 
       15.72        12.33         0.23        14.70         0.26        13.81 
TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
       14.40        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-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-A1P6 
       29.85        40.41        41.13        39.78        52.96        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-GI-A2C8 TCGA-GM-A2D9 
       21.27        17.49        10.16        10.59         7.40        59.57 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DK 
      194.27        53.13        53.52        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-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW 
       43.73        66.38        72.03        13.55        18.12        11.84 
TCGA-JL-A3YX TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A442 TCGA-LL-A50Y 
       11.57         6.67         4.60         8.75        10.95         7.59 
TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FR 
       17.06        15.32        14.70        14.47        14.79         3.88 
TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 
        4.14         4.50         4.50         3.22         6.21         7.36 
TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 
       27.91         2.79         2.10        12.66        46.55        31.99 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5S0 
       58.62        27.65        36.36        16.87        24.72        20.38 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       26.70        23.47        65.62        33.57        31.07        26.04 
TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PL-A8LV TCGA-PL-A8LX TCGA-PL-A8LY 
       14.07        28.21        19.73         0.23         0.16         0.26 
TCGA-PL-A8LZ TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 
        3.95         8.65        10.59         5.56         8.52         7.17 
TCGA-S3-AA15 TCGA-S3-AA17 TCGA-W8-A86G TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
        6.87         3.91         5.29         9.60         9.14       105.04 

  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 
             23.05              22.19 
[1] "0.0 - 186.5 (23.1)" "0.0 - 234.3 (22.2)"
[1] "hr=" "1.3"
D23V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12P GAIN MUTATED        18       12        1        2        74        41
  12P GAIN WILD-TYPE      65       68        8        3       268       193
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12P GAIN MUTATED           0         36          6         18        5
  12P GAIN WILD-TYPE         2        106         23         45       13
                    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                 65
  STAGE IA                 12                 68
  STAGE IB                  1                  8
  STAGE II                  2                  3
  STAGE IIA                74                268
  STAGE IIB                41                193
  STAGE III                 0                  2
  STAGE IIIA               36                106
  STAGE IIIB                6                 23
  STAGE IIIC               18                 45
  STAGE IV                  5                 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
  12P GAIN MUTATED    42 141  25   9
  12P GAIN WILD-TYPE 223 453  99  30
D23V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1               42                223
  T2              141                453
  T3               25                 99
  T4                9                 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
  12P GAIN MUTATED   101  62  29  21
  12P GAIN WILD-TYPE 380 277  84  53
D23V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0              101                380
  N1               62                277
  N2               29                 84
  N3               21                 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
  12P GAIN MUTATED          0 184   5  28
  12P GAIN WILD-TYPE        5 670  14 119
D23V6, multiclass
          clus
vv         12P GAIN MUTATED 12P GAIN WILD-TYPE
  CM0 (I+)                0                  5
  M0                    184                670
  M1                      5                 14
  MX                     28                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"
D23V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED   212   5
  12P GAIN WILD-TYPE 802   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED    212    5
  12P GAIN WILD-TYPE  802    6
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE              212                802
  MALE                  5                  6
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  12P GAIN MUTATED                            1                           173
  12P GAIN WILD-TYPE                          0                           581
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  12P GAIN MUTATED                               25                   2
  12P GAIN WILD-TYPE                            150                   4
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  12P GAIN MUTATED                                  7                  1
  12P GAIN WILD-TYPE                               22                 14
                    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                 173                581
  INFILTRATING LOBULAR CARCINOMA                 25                150
  MEDULLARY CARCINOMA                             2                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                7                 22
  MUCINOUS CARCINOMA                              1                 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"
D23V9, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    68 149
  12P GAIN WILD-TYPE 214 594
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     68  149
  12P GAIN WILD-TYPE  214  594
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                68                214
  YES              149                594
[1] 2 2
[1] FALSE
D23V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P GAIN MUTATED                                  0     9
  12P GAIN WILD-TYPE                                1    47
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED                          36   151
  12P GAIN WILD-TYPE                       122   566
D23V11, multiclass
                                  clus
vv                                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           9                 47
  BLACK OR AFRICAN AMERICAN                      36                122
  WHITE                                         151                566
[1] 4 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     5 175
  12P GAIN WILD-TYPE  31 651
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      5  175
  12P GAIN WILD-TYPE   31  651
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                 31
  NOT HISPANIC OR LATINO              175                651
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED   157  24
  12Q GAIN WILD-TYPE 729  95
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               181                824 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                24                 95 
$`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        53.06        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        33.01        30.97         9.99         1.02 
TCGA-A8-A09I TCGA-A8-A09N TCGA-A8-A09X TCGA-A8-A0A1 TCGA-AC-A23E TCGA-AC-A23H 
       45.07         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        16.57         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        32.91        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 
       61.28        96.89       101.52        85.35        50.96        79.00 
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-A0E7 TCGA-BH-A0EB TCGA-BH-A0GY TCGA-BH-A0H7 TCGA-BH-A0HX 
       45.83        44.81        24.49        30.35        23.08        27.25 
TCGA-BH-A0WA TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18R TCGA-BH-A1EU 
       23.05        90.84        26.66        37.74        37.55        42.28 
TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1FC TCGA-BH-A1FM TCGA-C8-A12L TCGA-C8-A12O 
       12.00        55.69       114.15        45.63        11.93        12.66 
TCGA-C8-A130 TCGA-C8-A138 TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A26Z TCGA-C8-A278 
        3.12         3.75        11.34        12.03         8.28         0.03 
TCGA-D8-A13Z TCGA-D8-A1J8 TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1XD 
       20.88        14.17        15.78        18.15        18.90        17.16 
TCGA-D8-A1XJ TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A27M TCGA-D8-A27R 
       21.83        12.99        16.54        15.32        13.48        10.09 
TCGA-D8-A27W TCGA-D8-A3Z6 TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10B TCGA-E2-A10C 
       12.26        18.51        34.42        46.59        37.51        40.11 
TCGA-E2-A14O TCGA-E2-A14W TCGA-E2-A152 TCGA-E2-A15A TCGA-E2-A15G TCGA-E2-A15O 
       44.68        32.02        27.12        23.34        18.21        13.02 
TCGA-E2-A15S TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1L8 TCGA-E2-A1LL TCGA-E2-A56Z 
       14.07        33.73        33.70        39.62        43.04         7.20 
TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1R6 
       13.48        12.00        13.12        20.05         9.86         2.76 
TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A247 TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A54Y 
       20.81        40.24        27.22         0.72        17.75         0.23 
TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1P5 TCGA-EW-A2FV TCGA-GM-A2DI 
       28.77        22.82        29.85        23.11        25.91        61.91 
TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LL-A5YM TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A740 
       21.24         4.08        15.32        11.57         2.63         4.50 
TCGA-LL-A7SZ TCGA-OL-A5RV TCGA-OL-A66O TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-AA10 
        5.59        34.92         7.23        16.50         6.81         7.92 
TCGA-Z7-A8R5 
      100.01 

$`12Q GAIN WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        0.39         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SQ 
       47.24        20.88        13.68        31.79         7.96        18.21 
TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04V TCGA-A2-A04W 
      104.81        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       136.73        64.57        24.79       112.08 
TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV 
       92.48        88.60       107.93        75.25         5.19        63.45 
TCGA-A2-A0CW TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM 
       64.04        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-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-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-A0YE 
       20.52        17.46        18.90        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        48.46 
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-A25C TCGA-A2-A25D 
       19.56        16.47        52.47       107.70        17.19        18.15 
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-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW 
       32.75        38.40        34.98        31.99        38.37         7.30 
TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 
       24.39        21.30        23.21        26.96        21.14        21.90 
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-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-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-A4SA TCGA-A7-A4SD 
       10.29        11.28        13.41        11.97        14.93        14.50 
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-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06U 
       10.42         8.75        13.02        13.02         1.02        29.03 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A07B TCGA-A8-A07E 
       31.00        26.01         1.02        17.03        43.00        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-A07U TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 
        7.99        24.99        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        38.01        28.96        33.01        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        43.00        40.01        33.01 
TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09D 
       17.95        41.98        12.00         9.99        12.00        50.04 
TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T 
       49.05        29.98        33.07        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-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A2B8 
       13.02        17.03        38.04         0.95        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-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-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ 
       14.83        22.19         1.12        19.79        23.24        24.79 
TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX 
        1.55         0.07         1.81         1.18         0.69         0.43 
TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A041 
        1.68         1.74         1.12         1.32         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-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        6.44         7.96         7.00         7.59         7.17         6.28 
TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0FY 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-A03M TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U 
        5.59        47.84        81.63        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        52.18        24.16        37.48        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-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 
       50.24        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 
      108.72       106.78        96.10        90.58        77.56        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-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        32.52 
TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV 
        2.56         9.99       111.32        74.79        86.66        29.75 
TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 
       98.93        64.83        55.86        76.14        65.36       101.95 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AL 
      114.02        85.97        75.55        61.84        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 
       37.81        76.21        63.62        62.14        20.22       109.58 
TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R 
       50.89        73.02        78.51        84.20         0.85        87.22 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 
       76.01        53.36        83.77        78.48        73.18        72.76 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK 
       58.92        93.83       128.65        20.25        62.86        42.87 
TCGA-AR-A2LL TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QN 
        7.36        38.17        39.39        40.54        20.38        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-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-A402 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV 
      170.17        85.35        54.28       103.63        55.00        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-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD 
       39.16        56.94        56.98        51.68        32.02        18.21 
TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP 
       25.71        24.85        21.70        61.68        35.67        48.69 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BZ TCGA-BH-A0C0 
       27.19        53.69        53.95        49.94        49.05        41.75 
TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI 
       48.13        42.90        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-A0E9 TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0EI 
       14.30         9.63        46.19        32.65        31.00        24.43 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 
       10.78        15.16        37.78        35.51        24.56        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-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 
       36.85        12.89        51.32        50.79         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-A18M TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18S TCGA-BH-A18T 
       20.12        72.56        30.28        55.63        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-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-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-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-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-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-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A1HM 
       12.33        10.92        11.34         0.16        10.42         2.30 
TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A273 
        3.25         0.30         0.23         0.36         0.43         9.67 
TCGA-C8-A274 TCGA-C8-A275 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-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-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JF 
       21.14        19.20        17.49        16.50        18.71        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-A1XA 
       18.58        17.79        16.73        25.74        23.90        27.58 
TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XL 
       18.15         2.66        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-A1XW TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 
       15.16        12.66        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-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-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-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-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A2P6 
       18.87       106.75       102.61         8.75        16.93         5.52 
TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU 
       15.72        30.61        34.92        19.89        19.00         9.21 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE 
       19.20        36.82        36.56        39.55        12.59        35.77 
TCGA-E9-A1NG TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 
       21.57        11.90        14.30         0.62         2.10         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF 
        1.38        21.21        32.09         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-A244 TCGA-E9-A245 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A 
       17.06         0.69         0.85         1.94         0.95        24.56 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X 
        0.76        26.07        18.41         0.62        15.72        12.33 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW 
       14.70         0.26        13.81        14.40        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-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-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-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 
       19.96        55.00        52.73        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-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 
       43.73        69.30        66.38        72.03        13.55        18.12 
TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 
       11.84        11.57         6.67         4.60         8.75         9.53 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO 
       11.44        10.95         7.59        17.06        14.70        14.47 
TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A7T0 TCGA-LL-A8F5 
       14.79         3.88         4.14         4.50         3.22         6.21 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 
        7.36        27.91         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 
       31.99        58.62        27.65        36.36        16.87        24.72 
TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K 
       22.32        20.38        26.70        23.47        65.62        33.57 
TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PL-A8LV 
       31.07        26.04        14.07        28.21        19.73         0.23 
TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA11 
        0.16         0.26         3.95         8.65        10.59         5.56 
TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-W8-A86G TCGA-XX-A899 
        8.52         7.17         6.87         3.91         5.29         9.60 
TCGA-XX-A89A TCGA-Z7-A8R6 
        9.14       105.04 

  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 
            23.050             22.255 
[1] "0.0 - 186.5 (23.1)" "0.0 - 234.3 (22.3)"
[1] "hr=" "1.3"
D24V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12Q GAIN MUTATED        14        9        0        1        57        35
  12Q GAIN WILD-TYPE      69       71        9        4       285       199
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12Q GAIN MUTATED           0         39          6         15        5
  12Q GAIN WILD-TYPE         2        103         23         48       13
                    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                 69
  STAGE IA                  9                 71
  STAGE IB                  0                  9
  STAGE II                  1                  4
  STAGE IIA                57                285
  STAGE IIB                35                199
  STAGE III                 0                  2
  STAGE IIIA               39                103
  STAGE IIIB                6                 23
  STAGE IIIC               15                 48
  STAGE IV                  5                 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
  12Q GAIN MUTATED    32 120  23   9
  12Q GAIN WILD-TYPE 233 474 101  30
D24V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1               32                233
  T2              120                474
  T3               23                101
  T4                9                 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
  12Q GAIN MUTATED    70  59  31  18
  12Q GAIN WILD-TYPE 411 280  82  56
D24V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               70                411
  N1               59                280
  N2               31                 82
  N3               18                 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
  12Q GAIN MUTATED          0 156   5  23
  12Q GAIN WILD-TYPE        5 698  14 124
D24V6, multiclass
          clus
vv         12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CM0 (I+)                0                  5
  M0                    156                698
  M1                      5                 14
  MX                     23                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"
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED   179   5
  12Q GAIN WILD-TYPE 835   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED    179    5
  12Q GAIN WILD-TYPE  835    6
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE              179                835
  MALE                  5                  6
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  12Q GAIN MUTATED                            0                           146
  12Q GAIN WILD-TYPE                          1                           608
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  12Q GAIN MUTATED                               24                   1
  12Q GAIN WILD-TYPE                            151                   5
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  12Q GAIN MUTATED                                  8                  1
  12Q GAIN WILD-TYPE                               21                 14
                    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                 146                608
  INFILTRATING LOBULAR CARCINOMA                 24                151
  MEDULLARY CARCINOMA                             1                  5
  MIXED HISTOLOGY (PLEASE SPECIFY)                8                 21
  MUCINOUS CARCINOMA                              1                 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"
D24V9, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    58 126
  12Q GAIN WILD-TYPE 224 617
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     58  126
  12Q GAIN WILD-TYPE  224  617
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                58                224
  YES              126                617
[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                          30   123
  12Q GAIN WILD-TYPE                       128   594
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                      30                128
  WHITE                                         123                594
[1] 4 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     4 146
  12Q GAIN WILD-TYPE  32 680
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      4  146
  12Q GAIN WILD-TYPE   32  680
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 32
  NOT HISPANIC OR LATINO              146                680
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    75  12
  13Q GAIN WILD-TYPE 811 107
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                87                918 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                12                107 
$`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        33.01        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        86.66       114.02        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-LD-A7W5 TCGA-LL-A6FQ 
       30.08        25.91        10.16        11.57         4.08         2.63 
TCGA-LL-A73Y TCGA-MS-A51U TCGA-S3-A6ZG 
        4.14         2.79         6.81 

$`13Q GAIN WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        0.39         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
       47.24        20.88        13.68         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-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       136.73 
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-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU 
       34.29        31.82        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-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-A0YM TCGA-A2-A0YT TCGA-A2-A1FV 
       14.50        19.33        48.46        31.73        23.77        23.47 
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-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV 
       20.88        39.65        33.93        83.01        29.98        32.75 
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-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 
       24.39        21.30        23.21        26.96        21.14        21.90 
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-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-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-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        53.06 
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        43.00        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        24.99 
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        38.01        28.96        33.01        12.00         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        33.01        93.04        43.00 
TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B 
       40.01        30.97        17.95         9.99         9.99        12.00 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N 
       50.04        49.05        45.07        29.98        33.07         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-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB 
       38.79        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        22.19         1.12        16.57        19.79 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y 
       23.24        24.79         1.55         0.07         1.12         1.81 
TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OQ 
        1.18         0.69         0.43         1.68         1.74         1.12 
TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C 
        1.32         0.33         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-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-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-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-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 
       84.69        68.75        47.87        29.13        32.78        21.40 
TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA 
       52.18        24.16        37.48        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        50.24 
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       108.72 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
      106.78        96.10        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        32.52 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
        2.56        32.91         9.99       111.32        49.32         5.26 
TCGA-AR-A0TS TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
       74.79        29.75        98.93        64.83        55.86        76.14 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
       65.36       101.95        83.87        85.97        75.55        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-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
       39.98        43.07        17.23        37.81        76.21        61.28 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L 
       63.62        62.14        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 
       96.89        78.51        84.20         0.85       101.52        87.22 
TCGA-AR-A24T TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 
       76.01        85.35        50.96        83.77        79.00        78.48 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH 
       73.18        72.76        58.92        93.83       128.65        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       62.86        42.87         7.36        40.04        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       40.54        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-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
       84.59       110.93       140.88        68.45       189.01       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT 
       81.17        78.02       172.96       102.77       140.48        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-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
       21.47       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       103.63        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-A0BA 
       39.55        39.16        48.36        56.94        56.98        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-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-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0EI 
        9.63        44.81        46.19        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-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-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY 
        2.50        13.61        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-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-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-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 
       12.00        55.69        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-A209 
       72.07         6.90         0.72        38.60        83.31       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-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-A132 TCGA-C8-A135 
       12.66        12.66        12.66         3.12         1.45         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-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 
        0.23         0.36         0.43         8.28         9.67         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-A146 
       20.88        13.25        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-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-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-A1XG 
       23.90        27.58        18.15         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-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-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-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-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-A14U 
       44.68        40.96        38.24        38.60        33.17        43.33 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 
       34.26        32.02        17.03        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-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-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-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-A1LG TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL 
       40.47        28.90        18.87       102.61         8.75        43.04 
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        30.61        34.92 
TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 
       19.00         9.21        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        24.56         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-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE 
       12.33         0.23        14.70        13.81        14.40        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-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY 
       16.57        15.68        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-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD 
       18.48         7.86        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-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 
       22.09        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-A2DF 
       59.57       194.27        53.13        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        43.73        69.30        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-LD-A66U TCGA-LD-A74U 
       72.03        13.55        18.12        11.84        21.24         6.67 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y 
        4.60         8.75         9.53        11.44        10.95         7.59 
TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP 
       17.06        15.32        14.70        14.47        14.79        11.57 
TCGA-LL-A6FR TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 
        3.88         4.50         4.50         5.59         3.22         6.21 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 
        7.36        27.91         2.10        12.66        46.55        31.99 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY 
       58.62        27.65        34.92        36.36        16.87        24.72 
TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K 
       22.32        20.38        26.70        23.47        65.62        33.57 
TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ 
       31.07        26.04         7.23        14.07        28.21        19.73 
TCGA-PL-A8LV TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZH 
        0.23         0.16         0.26         3.95        16.50         8.65 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 
       10.59         7.92         5.56         8.52         7.17         6.87 
TCGA-S3-AA17 TCGA-W8-A86G TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        3.91         5.29         9.60         9.14       100.01       105.04 

  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 
            20.380             22.785 
[1] "0.0 - 211.6 (20.4)" "0.0 - 234.3 (22.8)"
[1] "hr=" "1.2"
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      78       75        9        5       308       219
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  13Q GAIN MUTATED           0         17          2          5        1
  13Q GAIN WILD-TYPE         2        125         27         58       17
                    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                 78
  STAGE IA                  5                 75
  STAGE IB                  0                  9
  STAGE II                  0                  5
  STAGE IIA                34                308
  STAGE IIB                15                219
  STAGE III                 0                  2
  STAGE IIIA               17                125
  STAGE IIIB                2                 27
  STAGE IIIC                5                 58
  STAGE IV                  1                 17
  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  58   7   3
  13Q GAIN WILD-TYPE 247 536 117  36
D25V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1               18                247
  T2               58                536
  T3                7                117
  T4                3                 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
  13Q GAIN MUTATED    41  26  14   6
  13Q GAIN WILD-TYPE 440 313  99  68
D25V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0               41                440
  N1               26                313
  N2               14                 99
  N3                6                 68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  13Q GAIN MUTATED          0  80   1   6
  13Q GAIN WILD-TYPE        5 774  18 141
D25V6, multiclass
          clus
vv         13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CM0 (I+)                0                  5
  M0                     80                774
  M1                      1                 18
  MX                      6                141
[1] 4 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    87   0
  13Q GAIN WILD-TYPE 927  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     87    0
  13Q GAIN WILD-TYPE  927   11
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               87                927
  MALE                  0                 11
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  13Q GAIN MUTATED                            0                            72
  13Q GAIN WILD-TYPE                          1                           682
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  13Q GAIN MUTATED                                4                   0
  13Q GAIN WILD-TYPE                            171                   6
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  13Q GAIN MUTATED                                  1                  2
  13Q GAIN WILD-TYPE                               28                 13
                    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                  72                682
  INFILTRATING LOBULAR CARCINOMA                  4                171
  MEDULLARY CARCINOMA                             0                  6
  MIXED HISTOLOGY (PLEASE SPECIFY)                1                 28
  MUCINOUS CARCINOMA                              2                 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"
D25V9, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    28  59
  13Q GAIN WILD-TYPE 254 684
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     28   59
  13Q GAIN WILD-TYPE  254  684
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                28                254
  YES               59                684
[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                           9    65
  13Q GAIN WILD-TYPE                       149   652
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                       9                149
  WHITE                                          65                652
[1] 4 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  68
  13Q GAIN WILD-TYPE  30 758
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      6   68
  13Q GAIN WILD-TYPE   30  758
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                 30
  NOT HISPANIC OR LATINO               68                758
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED   121  15
  14Q GAIN WILD-TYPE 765 104
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               136                869 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                15                104 
$`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 
       24.39        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 
       38.01        12.00        33.01        33.01        30.97        41.98 
TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09M TCGA-A8-A09R TCGA-A8-A09X TCGA-A8-A0A2 
        9.99         1.02        33.07         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        96.89        87.22 
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-E2-A9RU TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1RC TCGA-E9-A1RE 
       16.93         9.21        20.05         9.86        40.24        34.65 
TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A22E TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A295 
        6.58        34.59        12.89         0.69        27.22         0.72 
TCGA-E9-A5FL TCGA-E9-A5UP TCGA-EW-A1IY TCGA-EW-A1OZ TCGA-EW-A1P3 TCGA-EW-A1PG 
        0.26        14.40         8.48        40.41        52.96        34.55 
TCGA-EW-A2FS TCGA-GM-A2DB TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A6FQ TCGA-LL-A8F5 
       52.73        53.13        15.32        14.47         2.63         6.21 
TCGA-MS-A51U TCGA-OL-A5RW TCGA-S3-A6ZG TCGA-Z7-A8R6 
        2.79        36.36         6.81       105.04 

$`14Q GAIN WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        0.39         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN 
       47.24        20.88        13.68        31.79         7.96        39.32 
TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q 
       28.01        19.20        18.21       104.81        18.02        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-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
       36.13       136.73        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-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-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-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX 
       24.16        99.19        54.64        27.12        44.88        50.43 
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-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       21.90        14.50        18.61        19.33        48.46        31.73 
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-A25D 
       19.56        16.47        52.47       107.70        16.31        18.15 
TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU 
       91.92        10.59        20.88        33.93        83.01        29.98 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 
       32.75        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        21.30        23.21        26.96        21.14        21.90 
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-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-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF 
       11.97        14.93        13.74        14.50        21.17        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-A06R TCGA-A8-A06T 
        8.75        13.02        13.02         1.02        17.98        53.06 
TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07B 
       29.03        31.00        26.01         1.02         9.01        43.00 
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        24.99         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-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O 
       28.96        33.01        19.96        37.05         9.99        31.00 
TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A093 
       31.00         0.99        93.04        43.00        40.01        17.95 
TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I 
       12.00         9.99        12.00        50.04        49.05        45.07 
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-A0A1 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0AB TCGA-A8-A0AD 
       12.00        13.02        21.04         0.99        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-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        22.19 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS 
        1.12        16.57        19.79        23.24        24.79         1.55 
TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO 
        0.07         1.12         1.18         0.69         0.43         1.68 
TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 
        1.74         1.12         1.32         0.33         0.33         0.23 
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-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-A0FX TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN 
        6.02         0.33         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-A03R TCGA-AO-A03T TCGA-AO-A03U 
        5.33         5.59        47.84        68.75        47.87        59.05 
TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       29.13        32.78        21.40        52.18        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-A124 TCGA-AO-A125 
       26.24        50.24        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 
      108.72       106.78        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-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        32.52         2.56        32.91 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT 
        9.99       111.32        49.32         5.26        74.79        86.66 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 
       29.75        98.93        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-A1AI 
      101.95        83.87       114.02        85.97        75.55        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-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
       39.98        43.07        17.23        37.81        76.21        61.28 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24N 
       63.62        62.14        20.22       109.58        73.02        78.51 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V 
       84.20         0.85       101.52        76.01        53.36        85.35 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 
       50.96        83.77        79.00        78.48        73.18        72.76 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LL 
       58.92        93.83       128.65        20.25        62.86         7.36 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QN 
       40.04        38.17        39.39        40.54        20.38        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-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-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-A0WW TCGA-B6-A0WX TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
       17.98        21.47       129.70       186.48        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A402 
       58.88        43.59       101.52        73.51       170.17        54.28 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY 
      103.63        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-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-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-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-A0DH TCGA-BH-A0DI 
       48.13        42.90        45.83        31.17        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-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-A0H7 TCGA-BH-A0H9 
       15.16        37.78        35.51        24.56        23.08        41.00 
TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ 
       52.96        26.50         5.85         2.50        13.61        36.85 
TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 
       12.89        51.32        50.79         5.59        23.93        24.95 
TCGA-BH-A0W5 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J 
       42.35        23.05         8.81         2.01         7.23        20.12 
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-A18V TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET 
        7.36        51.39        51.16        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-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-A1FN 
       74.73       122.89        36.92        63.35        55.00        72.07 
TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 
      144.59         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-A12W 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-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HK 
        3.85        12.33        10.92        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-A140 TCGA-D8-A142 
        0.99         0.03         0.23        11.90        13.25        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-A1JE TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JL 
       18.90        12.03        14.01        18.97        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-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-A1XM 
        2.66        17.16        14.73        21.83        14.50        17.69 
TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU 
        7.96        16.41        15.85        16.31         6.35        12.99 
TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 
       15.16        12.66        16.54        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-A3Z5 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A107 
       13.08        12.53        14.50         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-A14O TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U 
       44.68        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-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-A15J TCGA-E2-A15L TCGA-E2-A15M 
       17.29        21.63        12.92        19.40        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-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       54.18        27.42        39.62        24.59        40.47        28.90 
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-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E9-A1N4 TCGA-E9-A1N5 
       30.61        34.92        19.89        19.00        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-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-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-A1RG TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 
        0.66        21.27        35.64        34.13         0.79        12.53 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 
       13.32        39.09        22.75        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        24.56        17.75         0.76 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y 
       26.07        18.41         0.62        15.72        12.33         0.23 
TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ 
       14.70        13.81        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        43.73        69.30 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX 
       66.38        72.03        13.55        18.12        11.84        11.57 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 
       21.24         6.67         4.08         4.60         8.75         9.53 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YP 
       11.44        10.95         7.59        17.06        14.70        14.79 
TCGA-LL-A6FP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ 
       11.57         3.88         4.14         4.50         4.50         5.59 
TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 
        3.22         7.36        27.91         2.10        12.66        46.55 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY 
       31.99        58.62        27.65        34.92        16.87        24.72 
TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K 
       22.32        20.38        26.70        23.47        65.62        33.57 
TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ 
       31.07        26.04         7.23        14.07        28.21        19.73 
TCGA-PL-A8LV TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZH 
        0.23         0.16         0.26         3.95        16.50         8.65 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 
       10.59         7.92         5.56         8.52         7.17         6.87 
TCGA-S3-AA17 TCGA-W8-A86G TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
        3.91         5.29         9.60         9.14       100.01 

  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 
             23.34              22.32 
[1] "0.3 - 162.1 (23.3)" "0.0 - 234.3 (22.3)"
[1] "hr=" "1.2"
D26V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  14Q GAIN MUTATED         9        5        1        0        47        28
  14Q GAIN WILD-TYPE      74       75        8        5       295       206
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  14Q GAIN MUTATED           1         27          4         10        1
  14Q GAIN WILD-TYPE         1        115         25         53       17
                    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                   9                 74
  STAGE IA                  5                 75
  STAGE IB                  1                  8
  STAGE II                  0                  5
  STAGE IIA                47                295
  STAGE IIB                28                206
  STAGE III                 1                  1
  STAGE IIIA               27                115
  STAGE IIIB                4                 25
  STAGE IIIC               10                 53
  STAGE IV                  1                 17
  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    26  91  15   5
  14Q GAIN WILD-TYPE 239 503 109  34
D26V4, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1               26                239
  T2               91                503
  T3               15                109
  T4                5                 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
  14Q GAIN MUTATED    56  43  24  11
  14Q GAIN WILD-TYPE 425 296  89  63
D26V5, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0               56                425
  N1               43                296
  N2               24                 89
  N3               11                 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
  14Q GAIN MUTATED          0 119   1  17
  14Q GAIN WILD-TYPE        5 735  18 130
D26V6, multiclass
          clus
vv         14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CM0 (I+)                0                  5
  M0                    119                735
  M1                      1                 18
  MX                     17                130
[1] 4 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   137   0
  14Q GAIN WILD-TYPE 877  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED    137    0
  14Q GAIN WILD-TYPE  877   11
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE              137                877
  MALE                  0                 11
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  14Q GAIN MUTATED                            0                           108
  14Q GAIN WILD-TYPE                          1                           646
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  14Q GAIN MUTATED                               14                   0
  14Q GAIN WILD-TYPE                            161                   6
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  14Q GAIN MUTATED                                  7                  2
  14Q GAIN WILD-TYPE                               22                 13
                    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                 108                646
  INFILTRATING LOBULAR CARCINOMA                 14                161
  MEDULLARY CARCINOMA                             0                  6
  MIXED HISTOLOGY (PLEASE SPECIFY)                7                 22
  MUCINOUS CARCINOMA                              2                 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"
D26V9, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    41  96
  14Q GAIN WILD-TYPE 241 647
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     41   96
  14Q GAIN WILD-TYPE  241  647
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                41                241
  YES               96                647
[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                          21    91
  14Q GAIN WILD-TYPE                       137   626
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                      21                137
  WHITE                                          91                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"
D26V12, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     2 111
  14Q GAIN WILD-TYPE  34 715
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      2  111
  14Q GAIN WILD-TYPE   34  715
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 34
  NOT HISPANIC OR LATINO              111                715
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    75   8
  15Q GAIN WILD-TYPE 811 111
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                83                922 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 8                111 
$`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        24.99        38.01        31.00        12.00 
TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09M TCGA-AC-A2QH TCGA-AN-A0XU TCGA-AO-A0J2 
       49.05        29.98        33.07         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       111.32        83.87 
TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A24K TCGA-AR-A254 TCGA-AR-A2LH TCGA-B6-A0I5 
       61.28        62.14        50.89        72.76        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-E9-A54X TCGA-EW-A1IY TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1P5 TCGA-EW-A1PB 
       12.33         8.48        28.77        22.82        23.11        19.99 
TCGA-GM-A2DF TCGA-GM-A2DK TCGA-LL-A5YM TCGA-OL-A5RV TCGA-PL-A8LX 
       42.71        62.33        15.32        34.92         0.16 

$`15Q GAIN WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SH 
        0.39         8.52        14.37        43.43        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-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       136.73 
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-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 
       75.55        75.25         5.19        64.04        56.81        21.14 
TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO 
       34.55        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-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-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-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ 
       18.21        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-A1FX 
       19.33        48.46        31.73        23.77        23.47        36.79 
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-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD 
       16.31        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-A3XZ 
       33.93        29.98        32.75        49.48        38.40        31.99 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 
       38.37         7.30        24.39        21.30        23.21        26.96 
TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ 
       21.14        21.90        38.30        34.29        35.47        30.61 
TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H 
       35.67        33.11        31.73        10.72        23.61        29.56 
TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD 
       31.36        24.26        23.80        21.73        20.61        22.32 
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-A4SF TCGA-A7-A56D TCGA-A7-A5ZV 
       14.93        13.74        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-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y 
       13.02        17.98        53.06        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        43.00        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-A07R TCGA-A8-A07S TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 
        8.98         7.99         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        28.96        33.01        19.96 
TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08S 
       12.00        37.05         9.99        31.00         0.99        33.01 
TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 
       93.04        43.00        40.01        33.01        30.97        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        50.04 
TCGA-A8-A09I TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       45.07         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-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-A2QI 
       55.43        36.99        38.79        26.04        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        22.19         1.12 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V 
       16.57        19.79        23.24        24.79         1.55         0.07 
TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO 
        1.12         1.81         1.18         0.69         0.43         1.68 
TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 
        1.74         1.12         1.32         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-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-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-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-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-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-A0J7 
       29.13        21.40        52.18        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        50.24        62.04        55.33 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B 
       99.25       108.72       106.78        96.10        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-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 
        5.65        15.62        32.52         2.56        32.91         9.99 
TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW 
       49.32         5.26        74.79        86.66        29.75        98.93 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 
       64.83        55.86        76.14        65.36       101.95       114.02 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL 
       85.97        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-A1AY TCGA-AR-A24H TCGA-AR-A24L 
       37.81        76.21        63.62        20.22       109.58        73.02 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R 
       96.89        78.51        84.20         0.85       101.52        87.22 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
       76.01        53.36        85.35        50.96        83.77        79.00 
TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE 
       56.15        78.48        73.18        58.92        93.83       128.65 
TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       62.86        42.87         7.36        40.04        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       40.54        20.38        54.74        16.04        20.45        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC 
       77.62       143.38        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-A0IN 
       65.72       146.50       112.37       176.98        18.77        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-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 
      101.52        73.51       139.17       170.17        85.35        54.28 
TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW 
       49.94       103.63        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-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-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-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-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ 
       15.65         3.22        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-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 
       32.65        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-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-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-A18L TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18Q 
       20.12        90.84        26.66        72.56        30.28        55.63 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO 
       37.55        66.05         7.36        51.39        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-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-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-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-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-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-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-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-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Y 
       12.03        10.42         3.25         0.30         0.23         0.43 
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-A1JK 
       12.03        12.03        14.01        18.97        20.09        20.12 
TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU 
       20.09        19.40        20.38        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-A1XJ 
       18.15         2.66        17.16        15.22        14.73        21.83 
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-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-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-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-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N 
       46.59        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-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-A15F TCGA-E2-A15G 
       14.79        25.05        23.34        22.82        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-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       28.44        22.65        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-A1LI TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 
      102.61         8.75        16.93         5.52        15.72        30.61 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1N5 
       34.92        19.89        19.00         9.21        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        24.56         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        14.70 
TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
        0.26        13.81        14.40        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-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-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-A2DL TCGA-GM-A2DM 
       53.52        43.04        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        43.73        69.30 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX 
       66.38        72.03        13.55        18.12        11.84        11.57 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 
       21.24         6.67         4.08         4.60         8.75         9.53 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO 
       11.44        10.95         7.59        17.06        14.70        14.47 
TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z 
       14.79        11.57         2.63         3.88         4.14         4.50 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
        4.50         5.59         3.22         6.21         7.36        27.91 
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        31.99        58.62 
TCGA-OL-A5RU TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 
       27.65        36.36        16.87        24.72        22.32        20.38 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       26.70        23.47        65.62        33.57        31.07        26.04 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PL-A8LV TCGA-PL-A8LY 
        7.23        14.07        28.21        19.73         0.23         0.26 
TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 
        3.95        16.50         6.81         8.65        10.59         7.92 
TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-W8-A86G 
        5.56         8.52         7.17         6.87         3.91         5.29 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        9.60         9.14       100.01       105.04 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.16               0.03 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            149.59             234.28 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            28.770             22.075 
[1] "0.2 - 149.6 (28.8)" "0.0 - 234.3 (22.1)"
[1] "hr=" "1.3"
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      73       75        9        5       313       217
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  15Q GAIN MUTATED           1         12          2          5        3
  15Q GAIN WILD-TYPE         1        130         27         58       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                 73
  STAGE IA                  5                 75
  STAGE IB                  0                  9
  STAGE II                  0                  5
  STAGE IIA                29                313
  STAGE IIB                17                217
  STAGE III                 1                  1
  STAGE IIIA               12                130
  STAGE IIIB                2                 27
  STAGE IIIC                5                 58
  STAGE IV                  3                 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   3
  15Q GAIN WILD-TYPE 243 547 112  36
D27V4, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1               22                243
  T2               47                547
  T3               12                112
  T4                3                 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
  15Q GAIN MUTATED    40  27   9   7
  15Q GAIN WILD-TYPE 441 312 104  67
D27V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0               40                441
  N1               27                312
  N2                9                104
  N3                7                 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
  15Q GAIN MUTATED          0  73   3   8
  15Q GAIN WILD-TYPE        5 781  16 139
D27V6, multiclass
          clus
vv         15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CM0 (I+)                0                  5
  M0                     73                781
  M1                      3                 16
  MX                      8                139
[1] 4 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    83   1
  15Q GAIN WILD-TYPE 931  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     83    1
  15Q GAIN WILD-TYPE  931   10
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE               83                931
  MALE                  1                 10
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  15Q GAIN MUTATED                            0                            73
  15Q GAIN WILD-TYPE                          1                           681
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  15Q GAIN MUTATED                                2                   0
  15Q GAIN WILD-TYPE                            173                   6
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  15Q GAIN MUTATED                                  1                  2
  15Q GAIN WILD-TYPE                               28                 13
                    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                  73                681
  INFILTRATING LOBULAR CARCINOMA                  2                173
  MEDULLARY CARCINOMA                             0                  6
  MIXED HISTOLOGY (PLEASE SPECIFY)                1                 28
  MUCINOUS CARCINOMA                              2                 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"
D27V9, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    29  55
  15Q GAIN WILD-TYPE 253 688
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     29   55
  15Q GAIN WILD-TYPE  253  688
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                29                253
  YES               55                688
[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                          13    51
  15Q GAIN WILD-TYPE                       145   666
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                      13                145
  WHITE                                          51                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"
D27V12, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     3  66
  15Q GAIN WILD-TYPE  33 760
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      3   66
  15Q GAIN WILD-TYPE   33  760
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 33
  NOT HISPANIC OR LATINO               66                760
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED   386  56
  16P GAIN WILD-TYPE 500  63
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               442                563 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                56                 63 
$`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-A04V TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
       18.02        63.12        24.79       112.08        92.48        88.60 
TCGA-A2-A0CS TCGA-A2-A0CX TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EO 
       75.55        56.81        33.76        28.77       101.72        80.28 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW 
       35.05        34.29        31.82        54.64        27.12        44.88 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T5 TCGA-A2-A0YD TCGA-A2-A0YE 
       17.13         8.38        18.71        17.46        25.28        18.21 
TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YJ TCGA-A2-A0YT TCGA-A2-A1FW 
       15.42        21.90        21.67        18.61        23.77        17.36 
TCGA-A2-A1G0 TCGA-A2-A259 TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A4S1 TCGA-A2-A4S2 
       20.25        52.47        38.40        34.98        26.96        21.14 
TCGA-A7-A0CE TCGA-A7-A0DB TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26H TCGA-A7-A425 
       35.31        33.11        29.56        31.36        23.80        14.70 
TCGA-A7-A426 TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A6VX 
       11.97        13.74        21.17        17.92        12.10        10.42 
TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y 
       13.02         1.02        17.98        29.03        31.00        26.01 
TCGA-A8-A06Z TCGA-A8-A07F TCGA-A8-A07J TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S 
        1.02        18.97        12.00        10.98         8.98         7.99 
TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A 
        9.99        28.04        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-A08P 
       38.01        28.96        33.01        19.96        12.00        31.00 
TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 
       33.01        93.04        40.01        33.01        30.97        17.95 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09E TCGA-A8-A09K 
       41.98        12.00         9.99        12.00        49.05        29.98 
TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A7 TCGA-A8-A0A9 
       19.04        15.02        14.01        12.00         0.99        13.02 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2FG 
       17.03        38.04         2.37        10.85         1.48        36.99 
TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3QP TCGA-AC-A3W5 TCGA-AC-A5XS 
       50.70         0.92         0.99        22.19        16.57         1.55 
TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6NO TCGA-AN-A03X 
        0.07         1.12         1.81         1.18         1.68         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-A0AM TCGA-AN-A0FK TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ 
        0.16         7.00         0.33         0.36         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XO TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AO-A03L 
        0.33        12.33         0.33         0.33         0.33        80.28 
TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03V TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 
       66.77        81.63        29.13        20.32        22.36        53.03 
TCGA-AO-A0JE TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A12A 
       76.77        55.33        71.80       102.58        99.25        90.58 
TCGA-AO-A12E TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A0Y5 
       57.30        82.62        61.87         0.53        24.79         5.65 
TCGA-AQ-A1H2 TCGA-AQ-A54O TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TV TCGA-AR-A0TW 
       15.62        32.91         5.26        74.79        29.75        98.93 
TCGA-AR-A0U2 TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AP TCGA-AR-A1AS 
       83.87        61.84        51.25        48.82        39.98        37.81 
TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A24L TCGA-AR-A24N TCGA-AR-A24P TCGA-AR-A24Q 
       61.28        62.14        73.02        78.51         0.85       101.52 
TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LK TCGA-AR-A2LL 
       83.77        56.15        72.76        58.92        42.87         7.36 
TCGA-AR-A2LM TCGA-AR-A2LO TCGA-AR-A5QM TCGA-AR-A5QP TCGA-B6-A0I2 TCGA-B6-A0IB 
       40.04        39.39        54.74        20.45       143.38       129.57 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IO TCGA-B6-A0IP 
       50.70        65.72       146.50       112.37       110.14       110.93 
TCGA-B6-A0IQ TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP 
      140.88       234.28        78.02       172.96       162.05       102.77 
TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WY TCGA-B6-A0WZ 
      140.48       100.70        97.48       188.68       113.79       129.57 
TCGA-B6-A0X1 TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40B 
      186.48       101.52        73.51        85.35        49.94       103.63 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0B3 
       55.00        24.53        38.79        20.45        25.55        39.55 
TCGA-BH-A0B5 TCGA-BH-A0BA TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0BQ 
       48.36        37.22        24.85        44.05        48.69        27.19 
TCGA-BH-A0BT TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DH TCGA-BH-A0DL 
       45.57        44.02        48.13        42.90        38.01        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-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB 
       16.27         9.63        44.81        46.19        32.65        24.49 
TCGA-BH-A0EE TCGA-BH-A0GY TCGA-BH-A0H3 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HI 
       31.00        30.35        37.78        24.56        41.00        20.38 
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-A18L TCGA-BH-A18M TCGA-BH-A18N 
       23.05         8.81         7.23        26.66        72.56        37.74 
TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1EV TCGA-BH-A1EX 
       55.63         7.36        51.16        91.99        12.00        49.58 
TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1FB TCGA-BH-A1FG TCGA-BH-A1FM TCGA-BH-A1FN 
       31.53        89.16       120.62       122.89        45.63        72.07 
TCGA-BH-A202 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A42V TCGA-C8-A12L TCGA-C8-A12N 
        0.72        83.31        57.83         8.94        11.93        11.77 
TCGA-C8-A12O TCGA-C8-A12U TCGA-C8-A12W TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A138 
       12.66        12.66        12.66         1.78         1.45         3.75 
TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26W TCGA-C8-A26Y 
       11.34        12.03         2.30         3.25         0.23         0.43 
TCGA-C8-A26Z TCGA-C8-A274 TCGA-D8-A13Z TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 
        8.28         0.03        20.88        20.58        13.97        14.17 
TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JD TCGA-D8-A1JE 
       13.48        21.14        14.17        17.49        18.15        18.90 
TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1X5 TCGA-D8-A1X6 
       12.03        12.03        20.09        20.12        18.58        17.79 
TCGA-D8-A1X7 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XF TCGA-D8-A1XJ 
       16.73        27.58        18.15         2.66        15.22        21.83 
TCGA-D8-A1XL TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XY 
       19.92        15.85        16.31        12.99        12.66        16.54 
TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       15.32         3.81        14.24        14.43         9.44        16.41 
TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-E2-A107 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C 
       12.26        14.50        34.42        40.41        37.51        40.11 
TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14X 
       28.87        44.68        38.24        43.33        34.26        31.96 
TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A156 TCGA-E2-A15C 
       17.03        27.12        23.24        19.43        23.87        22.82 
TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15K TCGA-E2-A15M 
       17.29        20.71        18.21        17.42         9.04         7.73 
TCGA-E2-A15O TCGA-E2-A1B0 TCGA-E2-A1B5 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IF 
       13.02        53.62        32.35        16.47        17.10        37.41 
TCGA-E2-A1IJ TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LG 
       28.44        20.98        11.08        39.62        19.66        18.87 
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        30.61        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        24.56         0.72        17.75        18.41        15.72 
TCGA-E9-A54Y TCGA-E9-A5FL TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IY TCGA-EW-A1J3 
        0.23         0.26        14.40        15.39         8.48        16.57 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OZ TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 
       25.94        22.82        40.41        52.96        29.82        23.11 
TCGA-EW-A1P6 TCGA-EW-A1PG TCGA-EW-A2FS TCGA-EW-A3E8 TCGA-GI-A2C8 TCGA-GI-A2C9 
       18.48        34.55        52.73        21.27         7.40       109.87 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DI TCGA-GM-A2DN TCGA-GM-A3XN 
      194.27        53.13        43.04        61.91        77.33        66.38 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YX TCGA-LD-A66U TCGA-LL-A5YL TCGA-LL-A5YM 
       13.55        18.12        11.57        21.24        17.06        15.32 
TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A7SZ TCGA-LL-A9Q3 
       14.79        11.57         2.63         4.14         5.59         7.36 
TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D8 TCGA-OL-A5RV TCGA-OL-A5RX 
       27.91         2.79         2.10        31.99        34.92        16.87 
TCGA-OL-A5RZ TCGA-OL-A66K TCGA-OL-A66N TCGA-OL-A6VQ TCGA-PL-A8LZ TCGA-S3-A6ZG 
       22.32        33.57        26.04        19.73         3.95         6.81 
TCGA-S3-A6ZH TCGA-W8-A86G TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        8.65         5.29       100.01       105.04 

$`16P GAIN WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SH TCGA-A1-A0SK 
        0.39         8.52        14.37        43.43        47.24        31.79 
TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04Q TCGA-A2-A04R 
        7.96        39.32        19.20        18.21        41.95        82.16 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK 
       73.84        22.06        64.04        55.43        36.13       136.73 
TCGA-A2-A0CL TCGA-A2-A0CR TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW 
       64.57       107.93        75.25         5.19        63.45        64.04 
TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D4 TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0EQ 
       21.14        34.55        25.22        89.36       107.61        79.76 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST 
       74.40        37.05        29.75        24.72        24.16        99.19 
TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T4 TCGA-A2-A0T6 TCGA-A2-A0T7 
       50.43        44.28        17.52        20.52        18.90        20.75 
TCGA-A2-A0YC TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV 
       32.55        14.50        19.33        48.46        31.73        23.47 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A25A 
       36.79        22.45        19.20        19.56        16.47       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        32.75        49.48 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       31.99        38.37         7.30        24.39        21.30        23.21 
TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 
       21.90        38.30        34.29        35.47        30.61        37.45 
TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A26F 
       35.67        31.73        10.72        12.72        23.61        24.26 
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-A4SA TCGA-A7-A4SD TCGA-A7-A56D 
       10.29        11.28        13.41        14.93        14.50        14.73 
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-A06T TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E 
       53.06        17.03        53.98         9.01        43.00        19.99 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07U TCGA-A8-A082 
       18.97        14.01        17.03         9.99        24.99        18.05 
TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A099 
       37.05         9.99        31.00         0.99        43.00         9.99 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q 
        1.02        50.04        45.07        33.07         1.02        25.02 
TCGA-A8-A09R TCGA-A8-A09W TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-AC-A23C 
        8.98         0.99        19.04        13.02        21.04         0.95 
TCGA-AC-A23H TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FK 
        2.66        38.53        38.20        40.57        55.43        38.79 
TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3TN 
       26.04         1.02         2.27         0.69        14.83         1.12 
TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A8OP 
       19.79        23.24        24.79         0.69         0.43         1.74 
TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AN-A046 TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL 
        1.12         1.32         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        52.18 
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        50.24        62.04       108.72       106.78 
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        32.52 
TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TT TCGA-AR-A0TX 
        2.56         9.99       111.32        49.32        86.66        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       101.95       114.02        85.97 
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        76.21        63.62        20.22       109.58        50.89 
TCGA-AR-A24M TCGA-AR-A24O TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V 
       96.89        84.20        87.22        76.01        53.36        85.35 
TCGA-AR-A24W TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A256 TCGA-AR-A2LE 
       50.96        79.00        78.48        73.18        93.83       128.65 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LN TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QN 
       20.25        62.86        38.17        40.54        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-A2IU TCGA-B6-A402 TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 
      139.17       170.17        54.28        28.50        46.95        40.83 
TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD 
       39.16        56.94        56.98        51.68        32.02        18.21 
TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BR TCGA-BH-A0BS 
       25.71        21.70        61.68        35.67        53.69        53.95 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0DD TCGA-BH-A0DE 
       49.94        11.67        49.05        41.75        45.83        31.17 
TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DQ TCGA-BH-A0E0 TCGA-BH-A0E1 
       23.44        22.13        13.91         3.22         4.41        15.68 
TCGA-BH-A0E2 TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H5 TCGA-BH-A0H7 
       14.30        24.43        10.78        15.16        35.51        23.08 
TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HW 
       52.96        26.50         5.85         2.50        13.61        51.32 
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-A1HG TCGA-C8-A1HJ 
        0.62         3.85        12.33        10.92        11.34         0.16 
TCGA-C8-A1HL TCGA-C8-A26V TCGA-C8-A26X TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A278 
       10.42         0.30         0.36         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-A147 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JH TCGA-D8-A1JI 
       19.20        16.50        18.71        15.78        14.01        18.97 
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-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XK 
       14.70        25.74        23.90        17.16        14.73        14.50 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1Y0 
       17.69         7.96        16.41         6.35        15.16        15.52 
TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27M 
       14.14        17.42        16.04        13.45        13.05        13.48 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z6 
        4.80         0.76        10.09        13.08        12.53        18.51 
TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10E TCGA-E2-A14N 
        7.33        43.00        27.52        46.59        28.44        47.15 
TCGA-E2-A14P TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14W TCGA-E2-A14Y 
       40.96        38.60        33.17        33.30        32.02        28.60 
TCGA-E2-A150 TCGA-E2-A155 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15F 
       25.41        21.04        14.79        25.05        23.34        21.63 
TCGA-E2-A15H TCGA-E2-A15J TCGA-E2-A15L TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
       12.92        19.40        20.58        19.56        17.06        14.07 
TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B6 TCGA-E2-A1IE 
       14.99        60.53        53.03        29.95        28.50        38.30 
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-A1L6 TCGA-E2-A1L7 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH 
       54.18        27.42        24.59        40.47        28.90       106.75 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A3DX TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 
      102.61         8.75        15.72        34.92        19.89        19.00 
TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC 
        9.21        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-A54X TCGA-E9-A5FK 
        1.94         0.76        26.07         0.62        12.33        14.70 
TCGA-E9-A5UO TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 
       13.81        12.20        39.72        18.21        18.90        13.25 
TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P1 
       15.68        28.77        29.95        29.85        41.13        39.78 
TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD 
       30.08         7.86        18.90        19.99         6.15        13.94 
TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A2FW 
       10.52        14.43        19.96        55.00        25.91        22.09 
TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-GM-A2D9 TCGA-GM-A2DC TCGA-GM-A2DF 
       17.49        10.16        10.59        59.57        53.52        42.71 
TCGA-GM-A2DH TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DO TCGA-GM-A3NW 
       42.28        62.33        90.84        76.64        53.36       110.50 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A4E0 TCGA-JL-A3YW TCGA-LD-A74U 
       38.20        43.73        69.30        72.03        11.84         6.67 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
        4.08         4.60         8.75         9.53        11.44        10.95 
TCGA-LL-A50Y TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FR TCGA-LL-A73Z TCGA-LL-A740 
        7.59        14.70        14.47         3.88         4.50         4.50 
TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5DA TCGA-OL-A5RU 
        3.22         6.21        12.66        46.55        58.62        27.65 
TCGA-OL-A5RW TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J 
       36.36        24.72        20.38        26.70        23.47        65.62 
TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-PL-A8LV TCGA-PL-A8LX 
       31.07         7.23        14.07        28.21         0.23         0.16 
TCGA-PL-A8LY TCGA-S3-A6ZF TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 
        0.26        16.50        10.59         7.92         5.56         8.52 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-XX-A899 TCGA-XX-A89A 
        7.17         6.87         3.91         9.60         9.14 

  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 
             22.34              22.45 
[1] "0.0 - 234.3 (22.3)" "0.0 - 220.9 (22.4)"
[1] "hr=" "1.1"
D28V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16P GAIN MUTATED        39       32        4        4       140       107
  16P GAIN WILD-TYPE      44       48        5        1       202       127
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16P GAIN MUTATED           1         66         17         23        9
  16P GAIN WILD-TYPE         1         76         12         40        9
                    vv
clus                 STAGE TIS STAGE X
  16P GAIN MUTATED           1       7
  16P GAIN WILD-TYPE         0       9
D28V3, multiclass
            clus
vv           16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                  39                 44
  STAGE IA                 32                 48
  STAGE IB                  4                  5
  STAGE II                  4                  1
  STAGE IIA               140                202
  STAGE IIB               107                127
  STAGE III                 1                  1
  STAGE IIIA               66                 76
  STAGE IIIB               17                 12
  STAGE IIIC               23                 40
  STAGE IV                  9                  9
  STAGE TIS                 1                  0
  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
  16P GAIN MUTATED   110 261  59  18
  16P GAIN WILD-TYPE 155 333  65  21
D28V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1              110                155
  T2              261                333
  T3               59                 65
  T4               18                 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
  16P GAIN MUTATED   207 150  56  27
  16P GAIN WILD-TYPE 274 189  57  47
D28V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0              207                274
  N1              150                189
  N2               56                 57
  N3               27                 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
  16P GAIN MUTATED          1 376   9  64
  16P GAIN WILD-TYPE        4 478  10  83
D28V6, multiclass
          clus
vv         16P GAIN MUTATED 16P GAIN WILD-TYPE
  CM0 (I+)                1                  4
  M0                    376                478
  M1                      9                 10
  MX                     64                 83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED   444   6
  16P GAIN WILD-TYPE 570   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED    444    6
  16P GAIN WILD-TYPE  570    5
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE              444                570
  MALE                  6                  5
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  16P GAIN MUTATED                            1                           332
  16P GAIN WILD-TYPE                          0                           422
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  16P GAIN MUTATED                               84                   2
  16P GAIN WILD-TYPE                             91                   4
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  16P GAIN MUTATED                                 15                  2
  16P GAIN WILD-TYPE                               14                 13
                    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                 332                422
  INFILTRATING LOBULAR CARCINOMA                 84                 91
  MEDULLARY CARCINOMA                             2                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)               15                 14
  MUCINOUS CARCINOMA                              2                 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"
D28V9, binary
                    cls
clus                   0   1
  16P GAIN MUTATED   118 332
  16P GAIN WILD-TYPE 164 411
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED    118  332
  16P GAIN WILD-TYPE  164  411
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO               118                164
  YES              332                411
[1] 2 2
[1] FALSE
D28V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P GAIN MUTATED                                  1    22
  16P GAIN WILD-TYPE                                0    34
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED                          53   320
  16P GAIN WILD-TYPE                       105   397
D28V11, multiclass
                                  clus
vv                                 16P GAIN MUTATED 16P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                          22                 34
  BLACK OR AFRICAN AMERICAN                      53                105
  WHITE                                         320                397
[1] 4 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    10 354
  16P GAIN WILD-TYPE  26 472
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     10  354
  16P GAIN WILD-TYPE   26  472
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                   10                 26
  NOT HISPANIC OR LATINO              354                472
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED   109  24
  16Q GAIN WILD-TYPE 777  95
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               133                872 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                24                 95 
$`16Q GAIN MUTATED`
TCGA-A1-A0SG TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A2-A04P TCGA-A2-A0CM TCGA-A2-A0CX 
       14.27        20.88        13.68        18.02        24.79        56.81 
TCGA-A2-A0D2 TCGA-A2-A0ET TCGA-A2-A0EV TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0YG 
       33.76        35.05        31.82        27.12        44.88        21.90 
TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A4S1 TCGA-A7-A425 
       23.77        17.36        38.40        34.98        26.96        14.70 
TCGA-A7-A426 TCGA-A7-A5ZV TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A07W TCGA-A8-A08F 
       11.97        12.10        26.01         1.02         9.99        33.01 
TCGA-A8-A08I TCGA-A8-A0A7 TCGA-AC-A3BB TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV 
       12.00         0.99         0.99         0.07         1.81         1.18 
TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A0AJ TCGA-AN-A0FY TCGA-AN-A0XO 
        0.23         0.62         2.96         8.02         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        32.91         5.26 
TCGA-AR-A0TS TCGA-AR-A0TW TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A250 TCGA-AR-A255 
       74.79        98.93        61.28        62.14        56.15        58.92 
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-A1FB TCGA-BH-A1FN TCGA-BH-A204 TCGA-BH-A208 TCGA-C8-A12L 
       49.58       120.62        72.07        83.31        57.83        11.93 
TCGA-C8-A12W TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A1HK TCGA-C8-A26Y TCGA-C8-A26Z 
       12.66         1.78         1.45        12.03         0.43         8.28 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1JF TCGA-D8-A1JK 
       13.97        14.17        13.48        21.14        12.03        20.12 
TCGA-D8-A1X7 TCGA-D8-A1XB TCGA-D8-A1XF TCGA-D8-A1XJ TCGA-D8-A1XU TCGA-D8-A1XW 
       16.73        18.15        15.22        21.83        12.99        12.66 
TCGA-D8-A1XZ TCGA-D8-A1Y2 TCGA-D8-A27I TCGA-D8-A27W TCGA-E2-A10F TCGA-E2-A14X 
       15.32        14.24        14.43        12.26        28.87        31.96 
TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A15M TCGA-E2-A1B0 TCGA-E2-A1B5 TCGA-E2-A1IJ 
       27.12        19.43         7.73        53.62        32.35        28.44 
TCGA-E2-A1LL TCGA-E9-A1NI TCGA-E9-A1RC TCGA-E9-A22B TCGA-E9-A247 TCGA-E9-A2JS 
       43.04         9.86        40.24        22.75        27.22        17.75 
TCGA-E9-A5FL TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-GI-A2C9 TCGA-GM-A2DA 
        0.26        22.82        29.82        23.11       109.87       194.27 
TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A3XN TCGA-LL-A5YM TCGA-LL-A5YP TCGA-LL-A6FQ 
       53.13        43.04        66.38        15.32        14.79         2.63 
TCGA-LL-A73Y TCGA-LL-A7SZ TCGA-OK-A5Q2 TCGA-OL-A5RZ TCGA-PL-A8LZ TCGA-S3-A6ZH 
        4.14         5.59         2.10        22.32         3.95         8.65 
TCGA-Z7-A8R5 
      100.01 

$`16Q GAIN WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SH 
        0.39         8.52        14.37        43.43        48.10        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-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-A0CO 
       64.04        55.43        36.13       136.73        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-A0EQ TCGA-A2-A0ER 
      101.72        89.36        80.28       107.61        79.76        74.40 
TCGA-A2-A0ES TCGA-A2-A0EU TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST 
       37.05        34.29        29.75        24.72        24.16        99.19 
TCGA-A2-A0SU TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 
       54.64        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-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ 
       25.28        18.21        15.42        21.67        14.50        18.61 
TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ 
       19.33        48.46        31.73        23.47        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-A3XU TCGA-A2-A3XV TCGA-A2-A3XW 
       39.65        33.93        83.01        29.98        32.75        49.48 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       31.99        38.37         7.30        24.39        21.30        23.21 
TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH 
       21.14        21.90        38.30        35.31        34.29        35.47 
TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E 
       30.61        37.45        35.67        33.11        31.73        10.72 
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-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD 
       10.29        11.28        13.41        14.93        13.74        14.50 
TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV 
       21.17        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-A06Q 
        9.37        10.42         8.75        13.02        13.02         1.02 
TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A076 
       17.98        53.06        29.03        31.00        17.03        53.98 
TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I 
        9.01        43.00        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-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 
       24.99        28.04        18.05        15.06        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08L 
        0.99        38.01        28.96        19.96        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        33.01        93.04        43.00 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 
       40.01        33.01        30.97        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        50.04        49.05 
TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R 
       45.07        29.98        33.07         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-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-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
        1.02         0.92         2.27         0.69        14.83        22.19 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS 
        1.12        16.57        19.79        23.24        24.79         1.55 
TCGA-AC-A62X TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OQ 
        1.12         0.69         0.43         1.68         1.74         1.12 
TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A046 TCGA-AN-A04C TCGA-AN-A04D 
        1.32         0.33         0.33         0.33         1.78         1.71 
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-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-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A0J2 
       81.63        84.69        68.75        47.87        59.05        32.78 
TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 
       21.40        52.18        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-A0JF 
       53.03        21.53        50.70        50.86        72.00        21.37 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 
       26.24        50.24        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 
      108.72       106.78        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-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        32.52         2.56         9.99       111.32 
TCGA-AR-A0TQ TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
       49.32        86.66        29.75        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       101.95        83.87       114.02        85.97        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        37.81        76.21 
TCGA-AR-A1AW TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M 
       63.62        20.22       109.58        50.89        73.02        96.89 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24T 
       78.51        84.20         0.85       101.52        87.22        76.01 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 
       53.36        85.35        50.96        83.77        79.00        78.48 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       73.18        72.76        93.83       128.65        20.25        62.86 
TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       42.87         7.36        40.04        38.17        39.39        40.54 
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-A0RN TCGA-B6-A0RP TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV 
       81.17       172.96       102.77        89.46       131.21       157.41 
TCGA-B6-A0WS TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 
       97.48        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-A1KN 
      186.48        28.27        68.94        58.88        43.59       139.17 
TCGA-B6-A2IU TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
      170.17        54.28        49.94       103.63        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-A0BM 
       37.22        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-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-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-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-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-A0H5 TCGA-BH-A0HA 
       30.35        10.78        15.16        37.78        35.51        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-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18J 
       24.95        44.81        23.05         8.81         2.01        20.12 
TCGA-BH-A18K TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T 
       90.84        37.74        30.28        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-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 
       12.00        55.69        17.69        25.81        31.53        89.16 
TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG 
       97.48        24.66       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-A1FU 
       36.92        63.35        55.00        45.63       144.59        72.07 
TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q 
        6.90         0.72        38.60       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-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V 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-A1HL TCGA-C8-A1HM 
       10.92        11.34        11.34         0.16        10.42         2.30 
TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A273 TCGA-C8-A274 
        3.25         0.30         0.23         0.36         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-A147 TCGA-D8-A1J8 
       11.90        20.88        13.25        20.58        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-A1JG 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-A1X5 
       20.38        21.01        12.20        13.32        14.70        18.58 
TCGA-D8-A1X6 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD 
       17.79        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-A1XQ 
       14.73        14.50        19.92        17.69         7.96        16.41 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1Y0 
       15.85        16.31         6.35        15.16        16.54        15.52 
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-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-A10B TCGA-E2-A10C 
       34.42        27.52        46.59        40.41        37.51        40.11 
TCGA-E2-A10E TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R 
       28.44        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-A14Y 
       33.17        33.30        43.33        34.26        32.02        28.60 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 
       17.03        25.41        23.24        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-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-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE 
       53.03        29.95        28.50        16.47        17.10        38.30 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IK TCGA-E2-A1IL 
       37.41        32.78        33.73        33.70        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-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-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N4 
       30.61        34.92        19.89        19.00         9.21        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-A1QZ TCGA-E9-A1R0 
       12.59        35.77        20.05        21.57        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-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG 
       32.09        20.81         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-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 
       39.09        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-A2JT 
        0.85         1.94         0.95        24.56         0.72         0.76 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y 
       26.07        18.41         0.62        15.72        12.33         0.23 
TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
       14.70        13.81        14.40        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-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-A2DC 
       17.49        10.16        10.59         7.40        59.57        53.52 
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        43.73        69.30 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U 
       72.03        13.55        18.12        11.84        11.57        21.24 
TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 
        6.67         4.08         4.60         8.75         9.53        11.44 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP 
       10.95         7.59        17.06        14.70        14.47        11.57 
TCGA-LL-A6FR TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 
        3.88         4.50         4.50         3.22         6.21         7.36 
TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA 
       27.91         2.79        12.66        46.55        31.99        58.62 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5S0 
       27.65        34.92        36.36        16.87        24.72        20.38 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       26.70        23.47        65.62        33.57        31.07        26.04 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PL-A8LV TCGA-PL-A8LX 
        7.23        14.07        28.21        19.73         0.23         0.16 
TCGA-PL-A8LY TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 
        0.26        16.50         6.81        10.59         7.92         5.56 
TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-W8-A86G TCGA-XX-A899 
        8.52         7.17         6.87         3.91         5.29         9.60 
TCGA-XX-A89A TCGA-Z7-A8R6 
        9.14       105.04 

  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              22.11 
[1] "0.1 - 194.3 (23.8)" "0.0 - 234.3 (22.1)"
[1] "hr=" "1.5"
D29V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16Q GAIN MUTATED        11        6        1        1        39        33
  16Q GAIN WILD-TYPE      72       74        8        4       303       201
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16Q GAIN MUTATED           0         24          7          7        4
  16Q GAIN WILD-TYPE         2        118         22         56       14
                    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                  11                 72
  STAGE IA                  6                 74
  STAGE IB                  1                  8
  STAGE II                  1                  4
  STAGE IIA                39                303
  STAGE IIB                33                201
  STAGE III                 0                  2
  STAGE IIIA               24                118
  STAGE IIIB                7                 22
  STAGE IIIC                7                 56
  STAGE IV                  4                 14
  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    28  77  20   8
  16Q GAIN WILD-TYPE 237 517 104  31
D29V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1               28                237
  T2               77                517
  T3               20                104
  T4                8                 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
  16Q GAIN MUTATED    59  44  21   7
  16Q GAIN WILD-TYPE 422 295  92  67
D29V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               59                422
  N1               44                295
  N2               21                 92
  N3                7                 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
  16Q GAIN MUTATED          1 109   4  21
  16Q GAIN WILD-TYPE        4 745  15 126
D29V6, multiclass
          clus
vv         16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CM0 (I+)                1                  4
  M0                    109                745
  M1                      4                 15
  MX                     21                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"
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED   131   4
  16Q GAIN WILD-TYPE 883   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED    131    4
  16Q GAIN WILD-TYPE  883    7
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE              131                883
  MALE                  4                  7
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  16Q GAIN MUTATED                            1                           106
  16Q GAIN WILD-TYPE                          0                           648
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  16Q GAIN MUTATED                               16                   1
  16Q GAIN WILD-TYPE                            159                   5
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  16Q GAIN MUTATED                                  4                  1
  16Q GAIN WILD-TYPE                               25                 14
                    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                 106                648
  INFILTRATING LOBULAR CARCINOMA                 16                159
  MEDULLARY CARCINOMA                             1                  5
  MIXED HISTOLOGY (PLEASE SPECIFY)                4                 25
  MUCINOUS CARCINOMA                              1                 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"
D29V9, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    34 101
  16Q GAIN WILD-TYPE 248 642
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     34  101
  16Q GAIN WILD-TYPE  248  642
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                34                248
  YES              101                642
[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                          25    94
  16Q GAIN WILD-TYPE                       133   623
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                      25                133
  WHITE                                          94                623
[1] 4 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     2 119
  16Q GAIN WILD-TYPE  34 707
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      2  119
  16Q GAIN WILD-TYPE   34  707
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 34
  NOT HISPANIC OR LATINO              119                707
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    87  15
  17P GAIN WILD-TYPE 799 104
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               102                903 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                15                104 
$`17P GAIN MUTATED`
TCGA-5T-A9QA TCGA-A1-A0SJ TCGA-A2-A0CX TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV 
        0.39        13.68        56.81        35.05        34.29        31.82 
TCGA-A2-A0YJ TCGA-A2-A0YT TCGA-A2-A1FX TCGA-A2-A259 TCGA-A2-A3XU TCGA-A2-A3XX 
       18.61        23.77        36.79        52.47        29.98        38.40 
TCGA-A2-A3XZ TCGA-A7-A0CD TCGA-A7-A26J TCGA-A7-A3J0 TCGA-A8-A07P TCGA-A8-A08G 
       31.99        38.30        20.61        10.29        10.98        19.96 
TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A097 TCGA-A8-A09B TCGA-A8-A09E 
       37.05        31.00        33.01        12.00        12.00        49.05 
TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A8OP TCGA-AN-A04A 
       10.85         2.66        26.04         1.02         1.74         2.96 
TCGA-AO-A03L TCGA-AO-A0J5 TCGA-AO-A0J7 TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A12B 
       80.28        24.16        20.32        55.33       102.58        77.56 
TCGA-AO-A12E TCGA-AO-A1KQ TCGA-AR-A0TQ TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A24K 
       57.30        61.87        49.32        61.28        63.62        50.89 
TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A252 TCGA-AR-A2LK TCGA-AR-A2LL TCGA-B6-A0WX 
      101.52        87.22        73.18        42.87         7.36        21.47 
TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A401 TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0B4 
       43.59        73.51        85.35        24.53        20.45        39.16 
TCGA-BH-A0BG TCGA-BH-A0BT TCGA-BH-A0C0 TCGA-BH-A0C7 TCGA-BH-A0HQ TCGA-BH-A0HW 
       24.85        45.57        41.75        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-OL-A6VO TCGA-S3-A6ZG 
       14.79         5.59         2.79        33.57        28.21         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       136.73 
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 
       48.46        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        32.75        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 
       24.39        21.30        23.21        26.96        21.14        21.90 
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        53.06 
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        43.00        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        24.99 
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        38.01        28.96        33.01        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        43.00        40.01        33.01 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09C 
       30.97        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 
       50.04        45.07        29.98        33.07         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        22.19         1.12 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V 
       16.57        19.79        23.24        24.79         1.55         0.07 
TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO 
        1.12         1.81         1.18         0.69         0.43         1.68 
TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 
        1.12         1.32         0.33         0.33         0.23         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-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-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-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-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA 
       21.40        52.18        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-A0JI TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 
       50.24        62.04        71.80        99.25       108.72       106.78 
TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
       96.10        90.58        64.04        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        32.52         2.56 
TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT 
       32.91         9.99       111.32         5.26        74.79        86.66 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 
       29.75        98.93        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-A1AI 
      101.95        83.87       114.02        85.97        75.55        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-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AX 
       39.98        43.07        17.23        37.81        76.21        62.14 
TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       20.22       109.58        73.02        96.89        78.51        84.20 
TCGA-AR-A24P TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X 
        0.85        76.01        53.36        85.35        50.96        83.77 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
       79.00        56.15        78.48        72.76        58.92        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
      128.65        20.25        62.86        40.04        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       40.54        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-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-A0WY 
      157.41        97.48       188.68        79.63        17.98       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-A1KN TCGA-B6-A2IU TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B 
      101.52       139.17       170.17        54.28        49.94       103.63 
TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 
       55.00        38.79        25.55        28.50        46.95        40.83 
TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA 
       39.55        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-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE 
       11.67        49.05        44.02        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-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-A0HU TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 
       13.61        12.89        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-A18P 
        7.23        20.12        90.84        26.66        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-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-A1EY TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 
       55.69        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-A202 TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q 
        0.72        38.60        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-A12X 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-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-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z 
        2.30         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-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 
       13.97        13.48        21.14        19.20        14.17        17.49 
TCGA-D8-A1JA TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH 
       16.50        15.78        18.15        18.90        12.03        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-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-A1XC TCGA-D8-A1XD TCGA-D8-A1XF 
       25.74        23.90        27.58         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-A1XU TCGA-D8-A1XV TCGA-D8-A1XW 
       16.41        15.85         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-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-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-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-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-A15H 
       22.82        17.29        20.71        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-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-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-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z 
      102.61        43.04        16.93         5.52        15.72         7.20 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1N5 
       30.61        34.92        19.00         9.21        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        24.56         0.72        17.75         0.76 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FK 
       26.07        18.41         0.62        15.72        12.33        14.70 
TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
        0.26        13.81        14.40        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-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 
       28.77        25.94        22.82        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-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 
       19.96        55.00        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-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-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 
       43.73        69.30        66.38        72.03        13.55        18.12 
TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 
       11.84        11.57        21.24         6.67         4.08         4.60 
TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL 
        8.75         9.53        11.44        10.95         7.59        17.06 
TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR 
       15.32        14.70        14.47        11.57         2.63         3.88 
TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 
        4.14         4.50         4.50         3.22         6.21         7.36 
TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA 
       27.91         2.10        12.66        46.55        31.99        58.62 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       27.65        34.92        36.36        16.87        24.72        22.32 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66N 
       20.38        26.70        23.47        65.62        31.07        26.04 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ TCGA-PL-A8LV TCGA-PL-A8LX TCGA-PL-A8LY 
        7.23        14.07        19.73         0.23         0.16         0.26 
TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 
        3.95        16.50         8.65        10.59         7.92         5.56 
TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-W8-A86G TCGA-XX-A899 
        8.52         7.17         6.87         3.91         5.29         9.60 
TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        9.14       100.01       105.04 

  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 
             30.49              21.83 
[1] "0.2 - 114.2 (30.5)" "0.0 - 234.3 (21.8)"
[1] "hr=" "1.5"
D30V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17P GAIN MUTATED         5        7        1        1        36        22
  17P GAIN WILD-TYPE      78       73        8        4       306       212
                    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        123         23         61       16
                    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                   5                 78
  STAGE IA                  7                 73
  STAGE IB                  1                  8
  STAGE II                  1                  4
  STAGE IIA                36                306
  STAGE IIB                22                212
  STAGE III                 1                  1
  STAGE IIIA               19                123
  STAGE IIIB                6                 23
  STAGE IIIC                2                 61
  STAGE IV                  2                 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
  17P GAIN MUTATED    22  56  15   9
  17P GAIN WILD-TYPE 243 538 109  30
D30V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1               22                243
  T2               56                538
  T3               15                109
  T4                9                 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
  17P GAIN MUTATED    43  37  17   3
  17P GAIN WILD-TYPE 438 302  96  71
D30V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0               43                438
  N1               37                302
  N2               17                 96
  N3                3                 71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  17P GAIN MUTATED          0  89   2  11
  17P GAIN WILD-TYPE        5 765  17 136
D30V6, multiclass
          clus
vv         17P GAIN MUTATED 17P GAIN WILD-TYPE
  CM0 (I+)                0                  5
  M0                     89                765
  M1                      2                 17
  MX                     11                136
[1] 4 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    97   5
  17P GAIN WILD-TYPE 917   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     97    5
  17P GAIN WILD-TYPE  917    6
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               97                917
  MALE                  5                  6
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  17P GAIN MUTATED                            0                            82
  17P GAIN WILD-TYPE                          1                           672
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  17P GAIN MUTATED                               10                   1
  17P GAIN WILD-TYPE                            165                   5
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  17P GAIN MUTATED                                  0                  3
  17P GAIN WILD-TYPE                               29                 12
                    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                  82                672
  INFILTRATING LOBULAR CARCINOMA                 10                165
  MEDULLARY CARCINOMA                             1                  5
  MIXED HISTOLOGY (PLEASE SPECIFY)                0                 29
  MUCINOUS CARCINOMA                              3                 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"
D30V9, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    37  65
  17P GAIN WILD-TYPE 245 678
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     37   65
  17P GAIN WILD-TYPE  245  678
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                37                245
  YES               65                678
[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                          18    69
  17P GAIN WILD-TYPE                       140   648
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                      18                140
  WHITE                                          69                648
[1] 4 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  82
  17P GAIN WILD-TYPE  32 744
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      4   82
  17P GAIN WILD-TYPE   32  744
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 32
  NOT HISPANIC OR LATINO               82                744
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED   174  31
  17Q GAIN WILD-TYPE 712  88
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               205                800 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                31                 88 
$`17Q GAIN MUTATED`
TCGA-5T-A9QA TCGA-A1-A0SH TCGA-A1-A0SJ TCGA-A2-A04R TCGA-A2-A0CU TCGA-A2-A0CX 
        0.39        47.24        13.68        82.16         5.19        56.81 
TCGA-A2-A0D2 TCGA-A2-A0D4 TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0T3 
       33.76        25.22        35.05        34.29        31.82        18.71 
TCGA-A2-A0T7 TCGA-A2-A0YT TCGA-A2-A1FX TCGA-A2-A1G0 TCGA-A2-A259 TCGA-A2-A25D 
       20.75        23.77        36.79        20.25        52.47        18.15 
TCGA-A2-A25E TCGA-A2-A3XU TCGA-A2-A3XX TCGA-A2-A3XZ TCGA-A7-A0CD TCGA-A7-A0DA 
       91.92        29.98        38.40        31.99        38.30        35.67 
TCGA-A7-A13F TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3J0 TCGA-A7-A4SA 
       12.72        23.80        20.61        22.32        10.29        14.93 
TCGA-A7-A4SF TCGA-A8-A06O TCGA-A8-A06U TCGA-A8-A06Z TCGA-A8-A07G TCGA-A8-A07P 
       17.92        13.02        29.03         1.02        18.97        10.98 
TCGA-A8-A07W TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08S 
        9.99        33.01        19.96        37.05        31.00        33.01 
TCGA-A8-A092 TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09E TCGA-A8-A09M 
       30.97        12.00         9.99        12.00        49.05        33.07 
TCGA-A8-A09R TCGA-A8-A09X TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2FM TCGA-AC-A2QH 
        8.98        14.01        10.85         2.66        26.04         1.02 
TCGA-AC-A8OP TCGA-AN-A041 TCGA-AN-A04A TCGA-AN-A0FD TCGA-AN-A0FZ TCGA-AN-A0XL 
        1.74         0.23         2.96         6.44         0.33         0.33 
TCGA-AO-A03L TCGA-AO-A03P TCGA-AO-A0J5 TCGA-AO-A0J7 TCGA-AO-A124 TCGA-AO-A12B 
       80.28        84.69        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        32.52        32.91        49.32        83.87 
TCGA-AR-A1AK TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L 
       51.25        61.28        63.62       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        87.22        85.35        79.00        73.18        58.92 
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-B6-A402 TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B4 
       85.35        54.28        24.53        20.45        28.50        39.16 
TCGA-BH-A0BT TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DP 
       45.57        49.05        41.75        42.90        31.17        15.65 
TCGA-BH-A0HQ TCGA-BH-A0HW TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18S TCGA-BH-A18U 
       36.85        51.32        26.66        37.74        66.05        51.39 
TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1FC TCGA-BH-A1FG TCGA-BH-A1FJ 
       55.69        49.58        25.81       114.15       122.89        63.35 
TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A209 TCGA-C8-A12W TCGA-C8-A130 
        0.72        38.60        83.31       130.16        12.66         3.12 
TCGA-C8-A132 TCGA-C8-A138 TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HM TCGA-C8-A1HN 
        1.45         3.75        11.34        11.34         2.30         3.25 
TCGA-C8-A27A TCGA-C8-A3M8 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A1JB TCGA-D8-A1JF 
       12.20         0.23        13.97        14.17        18.71        12.03 
TCGA-D8-A1JG TCGA-D8-A1JJ TCGA-D8-A1JT TCGA-D8-A1X7 TCGA-D8-A1XB TCGA-D8-A1XF 
       12.03        20.09        13.32        16.73        18.15        15.22 
TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XS TCGA-D8-A1XY TCGA-D8-A1Y2 TCGA-D8-A27R 
       19.92        17.69        16.31        16.54        14.24        10.09 
TCGA-D8-A27W TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10C TCGA-E2-A14O TCGA-E2-A14T 
       12.26        34.42        46.59        40.11        44.68        33.30 
TCGA-E2-A14W TCGA-E2-A15A TCGA-E2-A15T TCGA-E2-A1B1 TCGA-E2-A1B5 TCGA-E2-A1IE 
       32.02        23.34        14.99        53.03        32.35        38.30 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1LA TCGA-E2-A1LK TCGA-E2-A56Z 
       32.78        33.73        28.44        24.59         8.75         7.20 
TCGA-E2-A574 TCGA-E9-A1N8 TCGA-E9-A1NF TCGA-E9-A1QZ TCGA-E9-A1R2 TCGA-E9-A1R4 
       19.89        12.00        20.05        11.90         0.62         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RE TCGA-E9-A1RH TCGA-E9-A1RI 
        1.38         2.76        21.21        34.65        34.59        35.64 
TCGA-E9-A226 TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A247 TCGA-E9-A2JS TCGA-E9-A54Y 
       34.13        22.75        12.89        27.22        17.75         0.23 
TCGA-E9-A5UO TCGA-E9-A5UP TCGA-EW-A1J2 TCGA-EW-A1J5 TCGA-EW-A1OX TCGA-EW-A1OY 
       13.81        14.40        13.25        15.68        29.95        29.85 
TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A2FS TCGA-EW-A423 
       52.96        23.11         6.15        13.94        52.73        10.16 
TCGA-GM-A2DC TCGA-GM-A2DK TCGA-GM-A3XL TCGA-LL-A5YM TCGA-LL-A7SZ TCGA-LL-A7T0 
       53.52        62.33        69.30        15.32         5.59         3.22 
TCGA-MS-A51U TCGA-OL-A5RZ TCGA-OL-A66K TCGA-OL-A6VO TCGA-S3-A6ZG TCGA-S3-A6ZH 
        2.79        22.32        33.57        28.21         6.81         8.65 
TCGA-S3-AA10 
        7.92 

$`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       136.73        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 
       48.46        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        32.75        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        24.39        21.30        23.21 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH 
       26.96        21.14        21.90        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        53.06        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        43.00        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        24.99        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        38.01 
TCGA-A8-A08C TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08T 
       28.96        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-A099 
       43.00        40.01        33.01        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        50.04        45.07        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        22.19         1.12        16.57        19.79 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y 
       23.24        24.79         1.55         0.07         1.12         1.81 
TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OQ TCGA-AC-A8OR 
        1.18         0.69         0.43         1.68         1.12         1.32 
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-A0AS 
        8.02         7.36         6.51         0.16         0.33         0.33 
TCGA-AN-A0AT TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN 
        0.33         4.64         7.96         7.00         7.59         7.17 
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-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-A03N TCGA-AO-A03O 
        0.33         5.33         5.59        47.84        66.77        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-A0JA TCGA-AO-A0JB 
       52.18        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        50.24 
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       108.72       106.78 
TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
       96.10        90.58        64.04        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-A54N TCGA-AQ-A7U7 
       26.93       130.09         5.65        15.62         2.56         9.99 
TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW 
      111.32         5.26        74.79        86.66        29.75        98.93 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 
       64.83        55.86        76.14        65.36       101.95       114.02 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AL TCGA-AR-A1AM 
       85.97        75.55        61.84        52.77        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        37.81 
TCGA-AR-A1AU TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       76.21        62.14        20.22        96.89        78.51        84.20 
TCGA-AR-A24Q TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A250 
      101.52        76.01        53.36        50.96        83.77        56.15 
TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       78.48        72.76        93.83       128.65        20.25        62.86 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM 
       40.04        38.17        39.39        40.54        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-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-A1KN TCGA-B6-A2IU TCGA-B6-A408 
       68.94        58.88       101.52       139.17       170.17        49.94 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0B2 
      103.63        55.00        38.79        25.55        46.95        40.83 
TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA 
       39.55        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-A0C1 TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DG 
       49.94        11.67        44.02        48.13        45.83        23.44 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DQ 
       38.01        22.13        13.91        48.23        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-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-A0HU 
       26.50        20.38         5.85         2.50        13.61        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-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-A18T 
       90.84        72.56        30.28        55.63        37.55         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-A1EV TCGA-BH-A1EY TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 
       12.00        17.69        31.53        89.16        97.48        24.66 
TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FH TCGA-BH-A1FL TCGA-BH-A1FM 
      120.62        33.17        74.73        36.92        55.00        45.63 
TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A208 TCGA-BH-A28O 
       72.07       144.59        72.07         6.90        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-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-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-A105 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B 
       18.51         7.33        43.00        27.52        40.41        37.51 
TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R 
       28.44        28.87        47.15        40.96        38.24        38.60 
TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z 
       33.17        43.33        34.26        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-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-A1AZ 
        7.73        13.02        19.56        17.06        14.07        60.53 
TCGA-E2-A1B0 TCGA-E2-A1B4 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IF 
       53.62        29.95        28.50        16.47        17.10        37.41 
TCGA-E2-A1II TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       33.70        22.65         3.88        22.19        20.98        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A1LE 
       54.18        27.42        39.62        19.66        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-A570 TCGA-E2-A573 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N4 
       15.72        30.61        34.92        19.00         9.21        19.20 
TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND 
       36.82        13.48        13.12        36.56        39.55        12.59 
TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1R0 TCGA-E9-A1R3 TCGA-E9-A1RA 
       35.77        21.57         9.86        14.30         2.10        32.09 
TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A227 
       20.81        40.24         0.66         6.58        21.27         0.79 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 
       12.53        13.32        39.09        23.51        24.10        17.06 
TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
        0.69         0.85         1.94         0.95        24.56         0.72 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X 
        0.76        26.07        18.41         0.62        15.72        12.33 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
       14.70         0.26        15.39        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW 
       18.21        18.90        16.57        28.77        25.94        22.82 
TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 
       40.41        41.13        39.78        29.82        18.48        30.08 
TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
        7.86        18.90        19.99        10.52        14.43        34.55 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 
       19.96        55.00        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-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-A3XN 
       77.33        53.36       110.50        38.20        43.73        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U 
       72.03        13.55        18.12        11.84        11.57        21.24 
TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 
        6.67         4.08         4.60         8.75         9.53        11.44 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP 
       10.95         7.59        17.06        14.70        14.47        14.79 
TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 
       11.57         2.63         3.88         4.14         4.50         4.50 
TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 
        6.21         7.36        27.91         2.10        12.66        46.55 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX 
       31.99        58.62        27.65        34.92        36.36        16.87 
TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66L 
       24.72        20.38        26.70        23.47        65.62        31.07 
TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ TCGA-PL-A8LV TCGA-PL-A8LX 
       26.04         7.23        14.07        19.73         0.23         0.16 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA12 
        0.26         3.95        16.50        10.59         5.56         8.52 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-W8-A86G TCGA-XX-A899 TCGA-XX-A89A 
        7.17         6.87         3.91         5.29         9.60         9.14 
TCGA-Z7-A8R5 TCGA-Z7-A8R6 
      100.01       105.04 

  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 
             24.53              21.90 
[1] "0.2 - 186.5 (24.5)" "0.0 - 234.3 (21.9)"
[1] "hr=" "1.7"
D31V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17Q GAIN MUTATED        14       15        2        2        75        44
  17Q GAIN WILD-TYPE      69       65        7        3       267       190
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17Q GAIN MUTATED           1         31          8         11        4
  17Q GAIN WILD-TYPE         1        111         21         52       14
                    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                 69
  STAGE IA                 15                 65
  STAGE IB                  2                  7
  STAGE II                  2                  3
  STAGE IIA                75                267
  STAGE IIB                44                190
  STAGE III                 1                  1
  STAGE IIIA               31                111
  STAGE IIIB                8                 21
  STAGE IIIC               11                 52
  STAGE IV                  4                 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
  17Q GAIN MUTATED    47 128  22  11
  17Q GAIN WILD-TYPE 218 466 102  28
D31V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1               47                218
  T2              128                466
  T3               22                102
  T4               11                 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
  17Q GAIN MUTATED    96  68  26  12
  17Q GAIN WILD-TYPE 385 271  87  62
D31V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               96                385
  N1               68                271
  N2               26                 87
  N3               12                 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
  17Q GAIN MUTATED          1 180   4  23
  17Q GAIN WILD-TYPE        4 674  15 124
D31V6, multiclass
          clus
vv         17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CM0 (I+)                1                  4
  M0                    180                674
  M1                      4                 15
  MX                     23                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"
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED   201   7
  17Q GAIN WILD-TYPE 813   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED    201    7
  17Q GAIN WILD-TYPE  813    4
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE              201                813
  MALE                  7                  4
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  17Q GAIN MUTATED                            0                           167
  17Q GAIN WILD-TYPE                          1                           587
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  17Q GAIN MUTATED                               23                   2
  17Q GAIN WILD-TYPE                            152                   4
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  17Q GAIN MUTATED                                  3                  5
  17Q GAIN WILD-TYPE                               26                 10
                    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                 167                587
  INFILTRATING LOBULAR CARCINOMA                 23                152
  MEDULLARY CARCINOMA                             2                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                3                 26
  MUCINOUS CARCINOMA                              5                 10
  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    68 140
  17Q GAIN WILD-TYPE 214 603
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     68  140
  17Q GAIN WILD-TYPE  214  603
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                68                214
  YES              140                603
[1] 2 2
[1] FALSE
D31V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q GAIN MUTATED                                  0    12
  17Q GAIN WILD-TYPE                                1    44
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED                          33   140
  17Q GAIN WILD-TYPE                       125   577
D31V11, multiclass
                                  clus
vv                                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          12                 44
  BLACK OR AFRICAN AMERICAN                      33                125
  WHITE                                         140                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"
D31V12, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     6 170
  17Q GAIN WILD-TYPE  30 656
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      6  170
  17Q GAIN WILD-TYPE   30  656
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                 30
  NOT HISPANIC OR LATINO              170                656
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED   148  18
  18P GAIN WILD-TYPE 738 101
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               166                839 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                18                101 
$`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        28.96        12.00 
TCGA-A8-A08P TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A091 TCGA-A8-A097 TCGA-A8-A09K 
       31.00        93.04        43.00        33.01        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-AC-A6NO TCGA-AN-A03Y TCGA-AN-A04C TCGA-AN-A0AT 
        1.81         0.69         1.68         0.33         1.78         0.33 
TCGA-AN-A0FJ TCGA-AN-A0FY TCGA-AO-A03P TCGA-AO-A0J2 TCGA-AO-A0JL TCGA-AO-A124 
        7.96         0.33        84.69        32.78        55.33       102.58 
TCGA-AO-A12A TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A54N 
       90.58        48.36        61.87         0.53        17.79         2.56 
TCGA-AR-A0TS TCGA-AR-A0U0 TCGA-AR-A1AJ TCGA-AR-A1AQ TCGA-AR-A24K TCGA-AR-A24Q 
       74.79        65.36        52.77        43.07        50.89       101.52 
TCGA-AR-A24U TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A2LH TCGA-B6-A0I1 TCGA-B6-A0I2 
       53.36        79.00        56.15        20.25        77.62       143.38 
TCGA-B6-A0IB TCGA-B6-A0IH TCGA-B6-A0IM TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RO 
      129.57       112.37       126.12       140.88       211.56       162.05 
TCGA-B6-A0RU TCGA-B6-A0WS TCGA-B6-A1KC TCGA-B6-A401 TCGA-B6-A408 TCGA-BH-A0BG 
      131.21        97.48        43.59        85.35        49.94        24.85 
TCGA-BH-A0BL TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT 
       44.05        44.02        45.83        15.65         2.56        38.47 
TCGA-BH-A0E0 TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0WA TCGA-BH-A18N 
        4.41        46.19        24.49        31.00        23.05        37.74 
TCGA-BH-A18T TCGA-BH-A1FC TCGA-BH-A1FU TCGA-BH-A208 TCGA-C8-A12L TCGA-C8-A12M 
        7.36       114.15        72.07        57.83        11.93        11.77 
TCGA-C8-A12U TCGA-C8-A1HG TCGA-C8-A27A TCGA-D8-A13Z TCGA-D8-A1JC TCGA-D8-A1JF 
       12.66        11.34        12.20        20.88        15.78        12.03 
TCGA-D8-A1JL TCGA-D8-A1JP TCGA-D8-A1JT TCGA-D8-A1XW TCGA-D8-A1Y2 TCGA-D8-A27H 
       20.09        21.01        13.32        12.66        14.24        13.05 
TCGA-D8-A27N TCGA-E2-A10B TCGA-E2-A14P TCGA-E2-A14T TCGA-E2-A14X TCGA-E2-A150 
        4.80        37.51        40.96        33.30        31.96        25.41 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15G TCGA-E2-A15O TCGA-E2-A1IN TCGA-E2-A1IU 
       22.82        17.29        18.21        13.02        22.19        11.08 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LH TCGA-E2-A2P5 TCGA-E2-A56Z TCGA-E9-A1N6 
       27.42        39.62       106.75        16.93         7.20        13.48 
TCGA-E9-A1N8 TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1RA 
       12.00        20.05         9.86         2.10         6.12        32.09 
TCGA-E9-A1RD TCGA-E9-A1RH TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A249 TCGA-E9-A5UP 
        0.66        34.59        23.51         0.69         0.95        14.40 
TCGA-E9-A6HE TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1PB 
       15.39        28.77        22.82        29.82        23.11        19.99 
TCGA-EW-A3U0 TCGA-GI-A2C9 TCGA-GM-A2DC TCGA-GM-A3XL TCGA-LL-A5YO TCGA-LL-A5YP 
       17.49       109.87        53.52        69.30        14.47        14.79 
TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-OL-A5D7 TCGA-OL-A66I 
        3.88         4.14         5.59         6.21        46.55        23.47 
TCGA-OL-A6VO TCGA-PL-A8LZ TCGA-S3-A6ZG TCGA-S3-AA12 
       28.21         3.95         6.81         8.52 

$`18P GAIN WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        0.39         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
       47.24        20.88        13.68         7.96        39.32        28.01 
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-A0CO 
       64.04        55.43        36.13       136.73        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-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D3 
       63.45        64.04        56.81        21.14        34.55        28.77 
TCGA-A2-A0D4 TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES 
       25.22        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-A0SX TCGA-A2-A0SY 
       99.19        54.64        27.12        44.88        50.43        44.28 
TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.52        17.13        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-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FW 
       21.67        14.50        19.33        48.46        23.77        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-A3XT TCGA-A2-A3XU TCGA-A2-A3XV 
       10.59        20.88        39.65        83.01        29.98        32.75 
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        24.39 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE 
       21.30        23.21        26.96        21.14        21.90        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13F TCGA-A7-A13G 
       34.29        35.47        37.45        33.11        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-A4SF 
       13.41        14.70        11.97        14.93        13.74        17.92 
TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VX TCGA-A7-A6VY 
       14.73        12.10        10.72        11.05        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        53.06        29.03 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F 
       31.00        26.01        53.98        43.00        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-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 
        7.99        24.99         9.99        28.04        18.05        15.06 
TCGA-A8-A085 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08J 
       36.95         0.99        38.01        33.01        19.96        37.05 
TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08Z TCGA-A8-A092 
        9.99        31.00         0.99        33.01        40.01        30.97 
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-A09I TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q 
       50.04        49.05        45.07        33.07         1.02        25.02 
TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 
       19.04        15.02        14.01        12.00        19.04        13.02 
TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G 
       21.04         0.99        38.04         0.95         2.37        10.85 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG 
        2.66         1.48        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-A3W5 TCGA-AC-A3W6 
        0.69        14.83        22.19         1.12        16.57        19.79 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IV 
       23.24        24.79         1.55         0.07         1.12         1.18 
TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A041 
        0.43         1.74         1.12         1.32         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-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-A0FT TCGA-AN-A0FV 
        7.00         7.59         7.17         6.28         6.02         0.33 
TCGA-AN-A0FW TCGA-AN-A0FX 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-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03R 
        5.59        80.28        47.84        66.77        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        52.18        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        50.24 
TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 
       62.04        71.80        99.25       108.72       106.78        96.10 
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-A1KR TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 
       82.62        70.39        24.79        26.93       130.09         5.65 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ 
       15.62        32.52        32.91         9.99       111.32        49.32 
TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
        5.26        86.66        29.75        98.93        64.83        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH 
       76.14       101.95        83.87       114.02        85.97        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-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       39.98        17.23        37.81        76.21        61.28        63.62 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       62.14        20.22       109.58        73.02        96.89        78.51 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24V TCGA-AR-A24W 
       84.20         0.85        87.22        76.01        85.35        50.96 
TCGA-AR-A24X TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
       83.77        78.48        73.18        72.76        58.92        93.83 
TCGA-AR-A2LE TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN 
      128.65        62.86        42.87         7.36        40.04        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP 
       39.39        40.54        20.38        54.74        16.04        20.45 
TCGA-AR-A5QQ TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IE 
       10.59       149.59        12.13       220.90        50.70        65.72 
TCGA-B6-A0IG TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP 
      146.50       176.98        18.77        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-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WT 
      102.77       140.48       100.70        89.46       157.41       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-A1KF TCGA-B6-A1KI 
      186.48        28.27        68.94        58.88       101.52        73.51 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A402 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
      139.17       170.17        54.28       103.63        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-A0BM 
       37.22        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-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-A0C3 TCGA-BH-A0C7 
       49.94        11.67        49.05        41.75        48.13        42.90 
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-A0DQ TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 
       17.26         3.22        45.17        47.41        16.27        15.68 
TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EI TCGA-BH-A0GY 
       14.30         9.63        44.81        32.65        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-A18U TCGA-BH-A18V 
       30.28        55.63        37.55        66.05        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-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-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-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-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-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK 
        3.75        12.33        10.92        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-A140 TCGA-D8-A141 
        0.99         0.03         0.23        11.90        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-A1JD TCGA-D8-A1JE TCGA-D8-A1JG 
       17.49        16.50        18.71        18.15        18.90        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-A1JS TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 
       12.20        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-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-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-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O 
       40.41        40.11        28.44        28.87        47.15        44.68 
TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W 
       38.24        38.60        33.17        43.33        34.26        32.02 
TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 
       28.60        17.03        27.12        23.24        19.43        21.04 
TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15E TCGA-E2-A15F 
       23.87        14.79        25.05        23.34        20.71        21.63 
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-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-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-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LA 
       22.65         3.88        20.98        54.18        19.66        24.59 
TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL 
       40.47        28.90        18.87       102.61         8.75        43.04 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 
        5.52        15.72        30.61        34.92        19.89        19.00 
TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC 
        9.21        19.20        36.82        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-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RE 
        1.38         2.76        21.21        20.81        40.24        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-A24A TCGA-E9-A295 TCGA-E9-A2JS 
        0.85        27.22         1.94        24.56         0.72        17.75 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X 
        0.76        26.07        18.41         0.62        15.72        12.33 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-EW-A1IW TCGA-EW-A1IX 
        0.23        14.70         0.26        13.81        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-A1P8 TCGA-EW-A1PA TCGA-EW-A1PC 
       52.96        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-A423 TCGA-EW-A424 
       52.73        25.91        22.09        21.27        10.16        10.59 
TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DF 
        7.40        59.57       194.27        53.13        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-A3XN TCGA-GM-A4E0 
       53.36       110.50        38.20        43.73        66.38        72.03 
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        21.24         6.67 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
        4.08         4.60         8.75         9.53        11.44        10.95 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A6FP TCGA-LL-A6FQ 
        7.59        17.06        15.32        14.70        11.57         2.63 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
        4.50         4.50         3.22         7.36        27.91         2.79 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
        2.10        12.66        31.99        58.62        27.65        34.92 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H 
       36.36        16.87        24.72        22.32        20.38        26.70 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P 
       65.62        33.57        31.07        26.04         7.23        14.07 
TCGA-OL-A6VQ TCGA-PL-A8LV TCGA-PL-A8LX TCGA-PL-A8LY TCGA-S3-A6ZF TCGA-S3-A6ZH 
       19.73         0.23         0.16         0.26        16.50         8.65 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 
       10.59         7.92         5.56         7.17         6.87         3.91 
TCGA-W8-A86G TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        5.29         9.60         9.14       100.01       105.04 

  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 
            22.935             22.320 
[1] "0.3 - 211.6 (22.9)" "0.0 - 234.3 (22.3)"
[1] "hr=" "1.2"
D32V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18P GAIN MUTATED        10       13        1        0        75        30
  18P GAIN WILD-TYPE      73       67        8        5       267       204
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18P GAIN MUTATED           1         17          6          8        4
  18P GAIN WILD-TYPE         1        125         23         55       14
                    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                  10                 73
  STAGE IA                 13                 67
  STAGE IB                  1                  8
  STAGE II                  0                  5
  STAGE IIA                75                267
  STAGE IIB                30                204
  STAGE III                 1                  1
  STAGE IIIA               17                125
  STAGE IIIB                6                 23
  STAGE IIIC                8                 55
  STAGE IV                  4                 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
  18P GAIN MUTATED    36 105  20   6
  18P GAIN WILD-TYPE 229 489 104  33
D32V4, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1               36                229
  T2              105                489
  T3               20                104
  T4                6                 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
  18P GAIN MUTATED    95  43  15  13
  18P GAIN WILD-TYPE 386 296  98  61
D32V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0               95                386
  N1               43                296
  N2               15                 98
  N3               13                 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
  18P GAIN MUTATED          0 143   4  21
  18P GAIN WILD-TYPE        5 711  15 126
D32V6, multiclass
          clus
vv         18P GAIN MUTATED 18P GAIN WILD-TYPE
  CM0 (I+)                0                  5
  M0                    143                711
  M1                      4                 15
  MX                     21                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"
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED   166   2
  18P GAIN WILD-TYPE 848   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED    166    2
  18P GAIN WILD-TYPE  848    9
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE              166                848
  MALE                  2                  9
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  18P GAIN MUTATED                            0                           141
  18P GAIN WILD-TYPE                          1                           613
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  18P GAIN MUTATED                               13                   2
  18P GAIN WILD-TYPE                            162                   4
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  18P GAIN MUTATED                                  4                  0
  18P GAIN WILD-TYPE                               25                 15
                    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                 141                613
  INFILTRATING LOBULAR CARCINOMA                 13                162
  MEDULLARY CARCINOMA                             2                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                4                 25
  MUCINOUS CARCINOMA                              0                 15
  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    50 118
  18P GAIN WILD-TYPE 232 625
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     50  118
  18P GAIN WILD-TYPE  232  625
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                50                232
  YES              118                625
[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                          43    99
  18P GAIN WILD-TYPE                       115   618
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                      43                115
  WHITE                                          99                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"
D32V12, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     3 133
  18P GAIN WILD-TYPE  33 693
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      3  133
  18P GAIN WILD-TYPE   33  693
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 33
  NOT HISPANIC OR LATINO              133                693
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED   124  17
  18Q GAIN WILD-TYPE 762 102
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
               141                864 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                17                102 
$`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        28.96        12.00        93.04        43.00        33.01 
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-AC-A6NO TCGA-AN-A03Y TCGA-AN-A04C TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT 
        1.68         0.33         1.78         0.33         0.33         0.33 
TCGA-AN-A0FJ TCGA-AN-A0FY TCGA-AN-A0XO TCGA-AO-A03P TCGA-AO-A0JL TCGA-AO-A124 
        7.96         0.33        12.33        84.69        55.33       102.58 
TCGA-AO-A12A TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AQ-A54N TCGA-AR-A0U0 
       90.58        48.36        61.87         0.53         2.56        65.36 
TCGA-AR-A1AJ TCGA-AR-A24K TCGA-AR-A24Q TCGA-AR-A24Z TCGA-AR-A2LH TCGA-B6-A0I2 
       52.77        50.89       101.52        79.00        20.25       143.38 
TCGA-B6-A0IB TCGA-B6-A0IH TCGA-B6-A0IM TCGA-B6-A0IQ TCGA-B6-A0RO TCGA-B6-A0WS 
      129.57       112.37       126.12       140.88       162.05        97.48 
TCGA-B6-A1KC TCGA-B6-A401 TCGA-B6-A408 TCGA-BH-A0BL TCGA-BH-A0C0 TCGA-BH-A0C1 
       43.59        85.35        49.94        44.05        41.75        44.02 
TCGA-BH-A0DD TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0E0 TCGA-BH-A0E6 
       45.83        15.65         2.56        38.47         4.41         9.63 
TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0HB TCGA-BH-A0HY TCGA-BH-A0WA TCGA-BH-A18L 
       46.19        24.49        26.50        50.79        23.05        26.66 
TCGA-BH-A18N TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A208 TCGA-C8-A12L TCGA-C8-A12M 
       37.74        55.63         7.36        57.83        11.93        11.77 
TCGA-C8-A12U TCGA-C8-A1HG TCGA-C8-A1HN TCGA-C8-A27A TCGA-D8-A1JF TCGA-D8-A1JL 
       12.66        11.34         3.25        12.20        12.03        20.09 
TCGA-D8-A1JP TCGA-D8-A1JT TCGA-D8-A1Y2 TCGA-D8-A27H TCGA-E2-A10B TCGA-E2-A14T 
       21.01        13.32        14.24        13.05        37.51        33.30 
TCGA-E2-A14X TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15G TCGA-E2-A1IN TCGA-E2-A1IU 
       31.96        22.82        17.29        18.21        22.19        11.08 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LH TCGA-E2-A2P5 TCGA-E2-A56Z TCGA-E9-A1N6 
       27.42        39.62       106.75        16.93         7.20        13.48 
TCGA-E9-A1N8 TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 
       12.00        20.05         9.86         0.62         2.10         6.12 
TCGA-E9-A1RA TCGA-E9-A1RD TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A249 TCGA-E9-A3HO 
       32.09         0.66        23.51         0.69         0.95        26.07 
TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P5 
       14.40        15.39        28.77        22.82        29.82        23.11 
TCGA-EW-A1PB TCGA-GM-A2DC TCGA-GM-A3XL TCGA-LD-A7W5 TCGA-LL-A5YP TCGA-LL-A7SZ 
       19.99        53.52        69.30         4.08        14.79         5.59 
TCGA-OL-A66I TCGA-S3-A6ZG TCGA-S3-AA10 
       23.47         6.81         7.92 

$`18Q GAIN WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        0.39         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
       47.24        20.88        13.68         7.96        39.32        28.01 
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-A0CO 
       64.04        55.43        36.13       136.73        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-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D3 
       63.45        64.04        56.81        21.14        34.55        28.77 
TCGA-A2-A0D4 TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES 
       25.22        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-A0SX TCGA-A2-A0SY 
       99.19        54.64        27.12        44.88        50.43        44.28 
TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.52        17.13        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-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FW 
       21.67        14.50        19.33        48.46        23.77        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-A25F 
       52.47       107.70        16.31        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        32.75        49.48 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       31.99        38.37         7.30        24.39        21.30        23.21 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH 
       26.96        21.14        21.90        35.31        34.29        35.47 
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-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-A4SE 
       13.41        14.70        11.97        14.93        13.74        21.17 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV 
       17.92        14.73        12.10        10.72        11.05        10.29 
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 
       53.06        29.03        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        43.00        19.99        18.97        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W 
       12.00        17.03         9.99         7.99        24.99         9.99 
TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A08A TCGA-A8-A08B 
       28.04        18.05        15.06        36.95         0.99        38.01 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P 
       33.01        19.96        37.05         9.99        31.00        31.00 
TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 
        0.99        33.01        40.01        30.97        17.95        41.98 
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        50.04        49.05 
TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A09V 
       45.07        33.07         1.02        25.02        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-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-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-A3W5 
        0.99         0.69        14.83        22.19         1.12        16.57 
TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X 
       19.79        23.24        24.79         1.55         0.07         1.12 
TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR 
        1.81         1.18         0.43         1.74         1.12         1.32 
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-A0FD TCGA-AN-A0FF 
        8.02         7.36         6.51         0.16         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-A0FW TCGA-AN-A0FX TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN 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-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        52.18        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        50.24 
TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 
       62.04        71.80        99.25       108.72       106.78        96.10 
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-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-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP 
        5.65        15.62        32.52        32.91         9.99       111.32 
TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW 
       49.32         5.26        74.79        86.66        29.75        98.93 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 
       64.83        55.86        76.14       101.95        83.87       114.02 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM 
       85.97        75.55        61.84        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        37.81 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H 
       76.21        61.28        63.62        62.14        20.22       109.58 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R 
       73.02        96.89        78.51        84.20         0.85        87.22 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A250 
       76.01        53.36        85.35        50.96        83.77        56.15 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE 
       78.48        73.18        72.76        58.92        93.83       128.65 
TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       62.86        42.87         7.36        40.04        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       40.54        20.38        54.74        16.04        20.45        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IE 
       77.62       149.59        12.13       220.90        50.70        65.72 
TCGA-B6-A0IG TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP 
      146.50       176.98        18.77        84.59       110.14       110.93 
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-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY 
      157.41       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-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       103.63 
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-A0BG TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ 
       24.85        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-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI 
       48.13        42.90        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-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EE 
       16.27        15.68        14.30        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-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HI TCGA-BH-A0HK 
       24.56        23.08        41.00        52.96        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-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-A18M TCGA-BH-A18P 
        2.01         7.23        20.12        90.84        72.56        30.28 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO 
       37.55        66.05        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-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-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-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-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK 
        3.75        12.33        10.92        11.34         0.16        12.03 
TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y 
       10.42         2.30         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-A27B 
        8.28         9.67         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-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-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JM 
       12.03        14.01        18.97        20.09        20.12        19.40 
TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 
       20.38        12.20        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-A1XK TCGA-D8-A1XL TCGA-D8-A1XM 
       15.22        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-A1XU 
        7.96        16.41        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-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27I TCGA-D8-A27K 
       14.14        17.42        16.04        13.45        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-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-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-A14Y TCGA-E2-A14Z 
       33.17        43.33        34.26        32.02        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-A159 TCGA-E2-A15A TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15H 
       14.79        25.05        23.34        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-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-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-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LA 
       22.65         3.88        20.98        54.18        19.66        24.59 
TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL 
       40.47        28.90        18.87       102.61         8.75        43.04 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 
        5.52        15.72        30.61        34.92        19.89        19.00 
TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC 
        9.21        19.20        36.82        13.12        36.56        39.55 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R5 
       12.59        35.77        21.57        11.90        14.30         1.38 
TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RF 
        2.76        21.21        20.81        40.24        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-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-A24A TCGA-E9-A295 TCGA-E9-A2JS 
        0.85        27.22         1.94        24.56         0.72        17.75 
TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y 
        0.76        18.41         0.62        15.72        12.33         0.23 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
       14.70         0.26        13.81        12.20        39.72         8.48 
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-A1P3 
       29.95        29.85        40.41        41.13        39.78        52.96 
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-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        43.73        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U 
       72.03        13.55        18.12        11.84        11.57        21.24 
TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
        6.67         4.60         8.75         9.53        11.44        10.95 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP 
        7.59        17.06        15.32        14.70        14.47        11.57 
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-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
        6.21         7.36        27.91         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        31.99        58.62        27.65        34.92        36.36 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J 
       16.87        24.72        22.32        20.38        26.70        65.62 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO 
       33.57        31.07        26.04         7.23        14.07        28.21 
TCGA-OL-A6VQ TCGA-PL-A8LV TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF 
       19.73         0.23         0.16         0.26         3.95        16.50 
TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 
        8.65        10.59         5.56         8.52         7.17         6.87 
TCGA-S3-AA17 TCGA-W8-A86G TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        3.91         5.29         9.60         9.14       100.01       105.04 

  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 
             22.82              22.34 
[1] "0.3 - 162.1 (22.8)" "0.0 - 234.3 (22.3)"
[1] "hr=" "1"  
D33V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18Q GAIN MUTATED         9        9        1        0        64        26
  18Q GAIN WILD-TYPE      74       71        8        5       278       208
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18Q GAIN MUTATED           1         15          4          9        4
  18Q GAIN WILD-TYPE         1        127         25         54       14
                    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                   9                 74
  STAGE IA                  9                 71
  STAGE IB                  1                  8
  STAGE II                  0                  5
  STAGE IIA                64                278
  STAGE IIB                26                208
  STAGE III                 1                  1
  STAGE IIIA               15                127
  STAGE IIIB                4                 25
  STAGE IIIC                9                 54
  STAGE IV                  4                 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
  18Q GAIN MUTATED    29  94  15   5
  18Q GAIN WILD-TYPE 236 500 109  34
D33V4, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1               29                236
  T2               94                500
  T3               15                109
  T4                5                 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
  18Q GAIN MUTATED    77  40  12  13
  18Q GAIN WILD-TYPE 404 299 101  61
D33V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0               77                404
  N1               40                299
  N2               12                101
  N3               13                 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
  18Q GAIN MUTATED          0 128   4  11
  18Q GAIN WILD-TYPE        5 726  15 136
D33V6, multiclass
          clus
vv         18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CM0 (I+)                0                  5
  M0                    128                726
  M1                      4                 15
  MX                     11                136
[1] 4 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   141   2
  18Q GAIN WILD-TYPE 873   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED    141    2
  18Q GAIN WILD-TYPE  873    9
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE              141                873
  MALE                  2                  9
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  18Q GAIN MUTATED                            0                           120
  18Q GAIN WILD-TYPE                          1                           634
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  18Q GAIN MUTATED                               12                   1
  18Q GAIN WILD-TYPE                            163                   5
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  18Q GAIN MUTATED                                  4                  0
  18Q GAIN WILD-TYPE                               25                 15
                    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                 120                634
  INFILTRATING LOBULAR CARCINOMA                 12                163
  MEDULLARY CARCINOMA                             1                  5
  MIXED HISTOLOGY (PLEASE SPECIFY)                4                 25
  MUCINOUS CARCINOMA                              0                 15
  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    43 100
  18Q GAIN WILD-TYPE 239 643
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     43  100
  18Q GAIN WILD-TYPE  239  643
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                43                239
  YES              100                643
[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                          29    90
  18Q GAIN WILD-TYPE                       129   627
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                      29                129
  WHITE                                          90                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"
D33V12, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     3 110
  18Q GAIN WILD-TYPE  33 716
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      3  110
  18Q GAIN WILD-TYPE   33  716
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 33
  NOT HISPANIC OR LATINO              110                716
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED   160  19
  19P GAIN WILD-TYPE 726 100
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               179                826 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                19                100 
$`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        21.14 
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        38.01        43.00 
TCGA-A8-A093 TCGA-A8-A097 TCGA-A8-A09B TCGA-A8-A09E TCGA-A8-A09M TCGA-A8-A0A7 
       17.95        12.00        12.00        49.05        33.07         0.99 
TCGA-A8-A0A9 TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2FO TCGA-AC-A3OD TCGA-AC-A62Y 
       13.02         2.37        10.85        50.70        14.83         1.81 
TCGA-AC-A6IW TCGA-AC-A8OP TCGA-AN-A03Y TCGA-AN-A04C TCGA-AN-A0AK TCGA-AN-A0FK 
        0.69         1.74         0.33         1.78         7.36         7.00 
TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0XN TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03O 
        0.36         0.33         0.33         5.59        80.28        81.63 
TCGA-AO-A0J2 TCGA-AO-A0J7 TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A128 TCGA-AO-A12A 
       32.78        20.32        55.33       102.58       106.78        90.58 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A1KS TCGA-AQ-A54O TCGA-AR-A0U0 TCGA-AR-A1AV 
       77.56        64.04         0.53        32.91        65.36        61.28 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24K TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A255 
       63.62        62.14        50.89        85.35        50.96        58.92 
TCGA-AR-A256 TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-B6-A0IH TCGA-B6-A0IJ 
       93.83        40.54        20.38        54.74       112.37       176.98 
TCGA-B6-A0RU TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A1KC TCGA-B6-A1KI 
      131.21        21.47       113.79       129.57        43.59        73.51 
TCGA-B6-A401 TCGA-BH-A0AU TCGA-BH-A0B6 TCGA-BH-A0BA TCGA-BH-A0BJ TCGA-BH-A0C0 
       85.35        24.53        56.94        37.22        21.70        41.75 
TCGA-BH-A0C1 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DO TCGA-BH-A0E9 TCGA-BH-A0GY 
       44.02        42.90        45.83        17.26        46.19        30.35 
TCGA-BH-A0HQ TCGA-BH-A18K TCGA-BH-A18N TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A18V 
       36.85        90.84        37.74        55.63         7.36        51.16 
TCGA-BH-A1EO TCGA-BH-A208 TCGA-C8-A12L TCGA-C8-A12V TCGA-C8-A130 TCGA-C8-A1HM 
       91.99        57.83        11.93        12.66         3.12         2.30 
TCGA-C8-A275 TCGA-D8-A13Z TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J8 
        0.03        20.88        14.17        13.48        19.20        14.17 
TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JL TCGA-D8-A1JN TCGA-D8-A1X6 TCGA-D8-A1XJ 
       12.03        14.01        20.09        20.38        17.79        21.83 
TCGA-D8-A1XU TCGA-D8-A27N TCGA-D8-A27R TCGA-D8-A27V TCGA-D8-A27W TCGA-E2-A10B 
       12.99         4.80        10.09        12.53        12.26        37.51 
TCGA-E2-A14N TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 
       47.15        38.60        31.96        28.60        17.03        25.41 
TCGA-E2-A153 TCGA-E2-A15M TCGA-E2-A1II TCGA-E2-A1IN TCGA-E2-A1LE TCGA-E2-A1LG 
       23.24         7.73        33.70        22.19        28.90        18.87 
TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NF 
       19.00         9.21        12.00        13.12        36.56        20.05 
TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RD TCGA-E9-A22E TCGA-E9-A243 TCGA-E9-A244 
        2.76        32.09         0.66        12.89        17.06         0.69 
TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A295 TCGA-E9-A3QA TCGA-E9-A5FK TCGA-E9-A5FL 
        1.94         0.95         0.72         0.62        14.70         0.26 
TCGA-E9-A5UP TCGA-EW-A1J6 TCGA-EW-A1P4 TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A423 
       14.40        28.77        29.82        19.99        13.94        10.16 
TCGA-GI-A2C9 TCGA-GM-A2DD TCGA-LD-A7W6 TCGA-LL-A5YN TCGA-LL-A5YP TCGA-LL-A6FQ 
      109.87        43.04         4.60        14.70        14.79         2.63 
TCGA-LL-A73Y TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-OL-A5RW TCGA-PL-A8LZ TCGA-S3-A6ZG 
        4.14         6.21         7.36        36.36         3.95         6.81 
TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA12 TCGA-W8-A86G 
        8.65        10.59         7.92         8.52         5.29 

$`19P GAIN WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SH 
        0.39         8.52        14.37        43.43        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-A04R TCGA-A2-A04T TCGA-A2-A04U 
       18.21       104.81        18.02        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       136.73        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-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D3 TCGA-A2-A0D4 
        5.19        63.45        64.04        56.81        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-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-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 
       44.88        44.28        17.52        17.13         8.38        18.71 
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-A0YH TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL 
       15.42        21.90        21.67        14.50        19.33        48.46 
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-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-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       33.93        83.01        32.75        49.48        38.40        34.98 
TCGA-A2-A3XZ TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 
       31.99         7.30        24.39        21.30        23.21        26.96 
TCGA-A2-A4S3 TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A13D 
       21.90        34.29        35.47        37.45        35.67        31.73 
TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26F TCGA-A7-A26G 
       10.72        12.72        23.61        29.56        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-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-A06Q 
        9.37        10.42         8.75        13.02        13.02         1.02 
TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 
       17.98        53.06        29.03        26.01         1.02        17.03 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G 
       53.98         9.01        43.00        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 
       24.99         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        28.96        33.01        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        33.01 
TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A099 
       93.04        40.01        33.01        30.97        41.98         9.99 
TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09N 
        9.99         1.02        50.04        45.07        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        22.19         1.12        16.57 
TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X 
       19.79        23.24        24.79         1.55         0.07         1.12 
TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AN-A03X 
        1.18         0.43         1.68         1.12         1.32         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-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-A0FT 
        4.64         7.96         7.59         7.17         6.28         6.02 
TCGA-AN-A0FV TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL 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-AO-A03M 
        0.33         0.33         0.33         0.33         5.33        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-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 
       21.40        52.18        24.16        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-A0JM TCGA-AO-A125 TCGA-AO-A126 
       26.24        50.24        62.04        71.80        99.25       108.72 
TCGA-AO-A129 TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
       96.10        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-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-A54N TCGA-AQ-A7U7 
      130.09         5.65        15.62        32.52         2.56         9.99 
TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV 
      111.32        49.32         5.26        74.79        86.66        29.75 
TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 
       98.93        64.83        55.86        76.14       101.95        83.87 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK 
      114.02        85.97        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-A1AY TCGA-AR-A24H TCGA-AR-A24L 
       17.23        37.81        76.21        20.22       109.58        73.02 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R 
       96.89        78.51        84.20         0.85       101.52        87.22 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 
       76.01        53.36        83.77        79.00        56.15        78.48 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK 
       73.18        72.76       128.65        20.25        62.86        42.87 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A5QN TCGA-AR-A5QP 
        7.36        40.04        38.17        39.39        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-A0IK TCGA-B6-A0IM 
      129.57        50.70        65.72       146.50        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-A0RV TCGA-B6-A0WS 
      102.77       140.48       100.70        89.46       157.41        97.48 
TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
      188.68        79.63        17.98       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-A0AW TCGA-BH-A0AY 
       49.94       103.63        55.00        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-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-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-A0C3 
       53.95        45.57        49.94        11.67        49.05        48.13 
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-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-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 
       32.65        24.49        31.00        24.43        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-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-A18L TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S 
       20.12        26.66        72.56        30.28        37.55        66.05 
TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV 
       51.39        69.93       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-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-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-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-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-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-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-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A146 TCGA-D8-A1J9 TCGA-D8-A1JA 
       13.25        20.58        13.97        21.14        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-A1JM TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT 
       20.09        20.12        19.40        21.01        12.20        13.32 
TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA 
       14.70        18.58        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-A1XK 
       18.15         2.66        17.16        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-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-A27M TCGA-D8-A27P 
       13.05        14.43         9.44        16.41        13.48         0.76 
TCGA-D8-A27T TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A107 
       13.08        14.50        18.51         7.33        43.00        34.42 
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-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U 
       44.68        40.96        38.24        33.17        33.30        43.33 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 
       34.26        32.02        27.12        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-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-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-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-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LH 
       27.42        39.62        19.66        24.59        40.47       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        30.61        34.92        19.89        19.20        36.82 
TCGA-E9-A1N6 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NI 
       13.48        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-A1R7 TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG 
       21.21        20.81        40.24        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-A22G TCGA-E9-A22H TCGA-E9-A245 TCGA-E9-A247 
       39.09        22.75        23.51        24.10         0.85        27.22 
TCGA-E9-A24A TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3X8 
       24.56        17.75         0.76        26.07        18.41        15.72 
TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
       12.33         0.23        13.81        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-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-A1PC TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH 
       18.90         6.15        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-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC 
       10.59         7.40        59.57       194.27        53.13        53.52 
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        43.73        69.30 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX 
       66.38        72.03        13.55        18.12        11.84        11.57 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 
       21.24         6.67         4.08         8.75         9.53        11.44 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A6FP 
       10.95         7.59        17.06        15.32        14.47        11.57 
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        27.91 
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        31.99        58.62 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 
       27.65        34.92        16.87        24.72        22.32        20.38 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       26.70        23.47        65.62        33.57        31.07        26.04 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PL-A8LV TCGA-PL-A8LX 
        7.23        14.07        28.21        19.73         0.23         0.16 
TCGA-PL-A8LY TCGA-S3-A6ZF TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 
        0.26        16.50         5.56         7.17         6.87         3.91 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        9.60         9.14       100.01       105.04 

  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 
             21.17              22.82 
[1] "0.0 - 177.0 (21.2)" "0.0 - 234.3 (22.8)"
[1] "hr=" "1"  
D34V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19P GAIN MUTATED        13       12        0        0        77        38
  19P GAIN WILD-TYPE      70       68        9        5       265       196
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19P GAIN MUTATED           0         23          5         11        0
  19P GAIN WILD-TYPE         2        119         24         52       18
                    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                 70
  STAGE IA                 12                 68
  STAGE IB                  0                  9
  STAGE II                  0                  5
  STAGE IIA                77                265
  STAGE IIB                38                196
  STAGE III                 0                  2
  STAGE IIIA               23                119
  STAGE IIIB                5                 24
  STAGE IIIC               11                 52
  STAGE IV                  0                 18
  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    36 116  23   6
  19P GAIN WILD-TYPE 229 478 101  33
D34V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1               36                229
  T2              116                478
  T3               23                101
  T4                6                 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
  19P GAIN MUTATED    99  53  18  11
  19P GAIN WILD-TYPE 382 286  95  63
D34V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0               99                382
  N1               53                286
  N2               18                 95
  N3               11                 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
  19P GAIN MUTATED          0 157   0  24
  19P GAIN WILD-TYPE        5 697  19 123
D34V6, multiclass
          clus
vv         19P GAIN MUTATED 19P GAIN WILD-TYPE
  CM0 (I+)                0                  5
  M0                    157                697
  M1                      0                 19
  MX                     24                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"
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED   177   4
  19P GAIN WILD-TYPE 837   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED    177    4
  19P GAIN WILD-TYPE  837    7
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE              177                837
  MALE                  4                  7
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  19P GAIN MUTATED                            1                           137
  19P GAIN WILD-TYPE                          0                           617
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  19P GAIN MUTATED                               25                   2
  19P GAIN WILD-TYPE                            150                   4
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  19P GAIN MUTATED                                  4                  2
  19P GAIN WILD-TYPE                               25                 13
                    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                 137                617
  INFILTRATING LOBULAR CARCINOMA                 25                150
  MEDULLARY CARCINOMA                             2                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                4                 25
  MUCINOUS CARCINOMA                              2                 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"
D34V9, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    55 126
  19P GAIN WILD-TYPE 227 617
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     55  126
  19P GAIN WILD-TYPE  227  617
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                55                227
  YES              126                617
[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                          32   130
  19P GAIN WILD-TYPE                       126   587
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                      32                126
  WHITE                                         130                587
[1] 4 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     6 149
  19P GAIN WILD-TYPE  30 677
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      6  149
  19P GAIN WILD-TYPE   30  677
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                 30
  NOT HISPANIC OR LATINO              149                677
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED   188  24
  19Q GAIN WILD-TYPE 698  95
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               212                793 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                24                 95 
$`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        21.14 
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        43.00 
TCGA-A8-A07R TCGA-A8-A08B TCGA-A8-A08X TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A097 
        8.98        38.01        43.00        30.97        17.95        12.00 
TCGA-A8-A09B TCGA-A8-A09E TCGA-A8-A09Q TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-AC-A23E 
       12.00        49.05        25.02         0.99        13.02         2.37 
TCGA-AC-A23G TCGA-AC-A2FO TCGA-AC-A3OD TCGA-AC-A62Y TCGA-AC-A6IW TCGA-AN-A03Y 
       10.85        50.70        14.83         1.81         0.69         0.33 
TCGA-AN-A04C TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0FK TCGA-AN-A0FW TCGA-AN-A0FX 
        1.78         7.36         0.16         7.00         0.36         0.33 
TCGA-AN-A0FY TCGA-AN-A0XW TCGA-AO-A03O TCGA-AO-A0J2 TCGA-AO-A0J7 TCGA-AO-A128 
        0.33         5.59        81.63        32.78        20.32       106.78 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A1KR TCGA-AO-A1KS 
       90.58        77.56        64.04        48.36        70.39         0.53 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0TQ TCGA-AR-A0TW TCGA-AR-A0U0 TCGA-AR-A1AV 
        2.56        32.91        49.32        98.93        65.36        61.28 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24K TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24Z 
       63.62        62.14        50.89        85.35        50.96        79.00 
TCGA-AR-A250 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM 
       56.15        58.92        93.83        40.54        20.38        54.74 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IO TCGA-B6-A0IQ TCGA-B6-A0RS TCGA-B6-A0RU 
      112.37       176.98       110.14       140.88       100.70       131.21 
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-A0AW TCGA-BH-A0B3 TCGA-BH-A0B6 TCGA-BH-A0BA TCGA-BH-A0BG TCGA-BH-A0BJ 
       20.45        39.55        56.94        37.22        24.85        21.70 
TCGA-BH-A0BL TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0DO TCGA-BH-A0E9 TCGA-BH-A0GY 
       44.05        44.02        45.83        17.26        46.19        30.35 
TCGA-BH-A0HQ TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18Q TCGA-BH-A18T 
       36.85        90.84        26.66        37.74        55.63         7.36 
TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A208 
       51.16        69.93        91.99        12.00        55.69        57.83 
TCGA-C8-A12L TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A130 TCGA-C8-A1HK TCGA-C8-A1HM 
       11.93        12.66        12.66         3.12        12.03         2.30 
TCGA-C8-A1HN TCGA-C8-A26Z TCGA-C8-A274 TCGA-C8-A275 TCGA-D8-A13Z TCGA-D8-A142 
        3.25         8.28         0.03         0.03        20.88        13.97 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1JF TCGA-D8-A1JG 
       14.17        13.48        19.20        14.17        12.03        12.03 
TCGA-D8-A1JH TCGA-D8-A1JL TCGA-D8-A1JN TCGA-D8-A1JU TCGA-D8-A1X6 TCGA-D8-A1XJ 
       14.01        20.09        20.38        14.70        17.79        21.83 
TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A27N TCGA-D8-A27R TCGA-D8-A27V TCGA-D8-A27W 
       12.99        12.66         4.80        10.09        12.53        12.26 
TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A14N TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Y 
       37.51        40.11        47.15        38.60        31.96        28.60 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A15F TCGA-E2-A15M 
       17.03        25.41        27.12        23.24        21.63         7.73 
TCGA-E2-A1II TCGA-E2-A1IN TCGA-E2-A1LG TCGA-E2-A576 TCGA-E9-A1N8 TCGA-E9-A1N9 
       33.70        22.19        18.87        19.00        12.00        13.12 
TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RD TCGA-E9-A1RI TCGA-E9-A22B TCGA-E9-A22E 
        2.76        32.09         0.66        35.64        22.75        12.89 
TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A295 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A5FK 
        1.94         0.95         0.72         0.62        15.72        14.70 
TCGA-E9-A5FL TCGA-E9-A5UP TCGA-EW-A1J6 TCGA-EW-A1P4 TCGA-EW-A1P8 TCGA-EW-A1PD 
        0.26        14.40        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        14.79         2.63 
TCGA-LL-A73Y TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-MS-A51U TCGA-OL-A5RW TCGA-OL-A66I 
        4.14         6.21         7.36         2.79        36.36        23.47 
TCGA-PL-A8LV TCGA-PL-A8LZ TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 
        0.23         3.95         6.81         8.65        10.59         7.92 
TCGA-S3-AA12 TCGA-W8-A86G 
        8.52         5.29 

$`19Q GAIN WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SH 
        0.39         8.52        14.37        43.43        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ 
       20.88         7.96        39.32        28.01        19.20        18.21 
TCGA-A2-A04N TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W 
      104.81        82.16        73.84        22.06        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       136.73        64.57        24.79       112.08 
TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CV 
       92.48        88.60       107.93        75.55         5.19        63.45 
TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN 
       64.04        56.81        34.55        28.77       101.72        89.36 
TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EV TCGA-A2-A0EW 
       80.28       107.61        74.40        37.05        31.82        29.75 
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-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD 
       17.13        20.52        17.46        20.75        32.55        25.28 
TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK 
       18.21        15.42        21.90        14.50        18.61        19.33 
TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX 
       48.46        31.73        23.77        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-A3XT TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       39.65        83.01        32.75        49.48        38.40        34.98 
TCGA-A2-A3XZ TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 
       31.99         7.30        24.39        21.30        23.21        26.96 
TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DA 
       21.90        35.31        34.29        35.47        37.45        35.67 
TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26F TCGA-A7-A26G 
       10.72        12.72        23.61        29.56        24.26        23.74 
TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J1 
       23.80        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-A4SF 
       13.41        14.70        11.97        14.93        13.74        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-A6VY TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U 
        8.75        13.02         1.02        17.98        53.06        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-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-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z 
        9.99        10.98         7.99        24.99         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        28.96 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O 
       33.01        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        33.01        93.04        40.01        33.01 
TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09I 
       41.98         9.99         9.99         1.02        50.04        45.07 
TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       29.98        33.07         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        22.19 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS 
        1.12        16.57        19.79        23.24        24.79         1.55 
TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OP 
        0.07         1.12         1.18         0.43         1.68         1.74 
TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 
        1.12         1.32         0.33         0.23         0.33         0.62 
TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AS 
        2.96         1.71         8.02         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-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN 
        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-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A03R 
        5.33        80.28        47.84        66.77        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        52.18        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        50.24        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       108.72        96.10 
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-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-A7U7 TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT 
       32.52         9.99       111.32         5.26        74.79        86.66 
TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 
       29.75        64.83        55.86        76.14       101.95        83.87 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK 
      114.02        85.97        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-A1AY TCGA-AR-A24H TCGA-AR-A24L 
       17.23        37.81        76.21        20.22       109.58        73.02 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R 
       96.89        78.51        84.20         0.85       101.52        87.22 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 
       76.01        53.36        83.77        78.48        73.18        72.76 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM 
      128.65        20.25        62.86        42.87         7.36        40.04 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       38.17        39.39        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-A0IP 
       65.72       146.50        18.77       126.12        84.59       110.93 
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-A0RT TCGA-B6-A0RV 
      172.96       162.05       102.77       140.48        89.46       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0X0 
       97.48       188.68        79.63        17.98        21.47       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-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV 
      170.17        54.28        49.94       103.63        55.00        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-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BM 
       56.98        51.68        32.02        18.21        25.71        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-A0C3 TCGA-BH-A0C7 
       49.94        11.67        49.05        41.75        48.13        42.90 
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-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-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 
       32.65        24.49        31.00        24.43        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-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-A18M TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U 
       20.12        72.56        30.28        37.55        66.05        51.39 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 
      113.82        82.85        42.28        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-A12M TCGA-C8-A12N TCGA-C8-A12O 
        0.99       109.28         8.94        11.77        11.77        12.66 
TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12X TCGA-C8-A131 TCGA-C8-A132 
       11.77         0.07        12.66        12.66         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-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A26V TCGA-C8-A26W 
       11.34        11.34         0.16        10.42         0.30         0.23 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B 
        0.36         0.43         9.67         0.03        12.20         0.99 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A146 
        0.03         0.23        11.90        13.25        20.58        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-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JM TCGA-D8-A1JP TCGA-D8-A1JS 
       18.97        20.09        20.12        19.40        21.01        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-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XK 
       18.15         2.66        17.16        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-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-A27P TCGA-D8-A27T 
       14.43         9.44        16.41        13.48         0.76        13.08 
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-A10E TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14P 
       46.59        40.41        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-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-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-A15P TCGA-E2-A15R 
       19.40         9.04        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-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-A1IO 
       32.78        33.73        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-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL 
       40.47        28.90       106.75       102.61         8.75        43.04 
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        30.61        34.92 
TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1NA 
       19.89         9.21        19.20        36.82        13.48        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-A1R7 TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG 
       21.21        20.81        40.24        34.65         6.58        21.27 
TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       34.59        34.13         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-A247 
       23.51        24.10        17.06         0.69         0.85        27.22 
TCGA-E9-A24A TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A54X 
       24.56        17.75         0.76        26.07        18.41        12.33 
TCGA-E9-A54Y TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
        0.23        13.81        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-A1OV 
       18.21        18.90        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-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-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FR TCGA-EW-A2FS 
        6.15        10.52        14.43        34.55        55.00        52.73 
TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 TCGA-GI-A2C8 
       25.91        22.09        21.27        17.49        10.59         7.40 
TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DF 
      109.87        59.57       194.27        53.13        53.52        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        43.73        69.30        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U 
       72.03        13.55        18.12        11.84        11.57        21.24 
TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
        6.67         4.08         8.75         9.53        11.44        10.95 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP 
        7.59        17.06        15.32        14.70        14.47        11.57 
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        27.91 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.10        12.66        46.55        31.99        58.62        27.65 
TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H 
       34.92        16.87        24.72        22.32        20.38        26.70 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P 
       65.62        33.57        31.07        26.04         7.23        14.07 
TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PL-A8LX TCGA-PL-A8LY TCGA-S3-A6ZF TCGA-S3-AA11 
       28.21        19.73         0.16         0.26        16.50         5.56 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
        7.17         6.87         3.91         9.60         9.14       100.01 
TCGA-Z7-A8R6 
      105.04 

  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 
             21.40              23.08 
[1] "0.0 - 177.0 (21.4)" "0.0 - 234.3 (23.1)"
[1] "hr=" "1.1"
D35V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19Q GAIN MUTATED        18       13        2        0        90        43
  19Q GAIN WILD-TYPE      65       67        7        5       252       191
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19Q GAIN MUTATED           0         27          8         10        1
  19Q GAIN WILD-TYPE         2        115         21         53       17
                    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                 65
  STAGE IA                 13                 67
  STAGE IB                  2                  7
  STAGE II                  0                  5
  STAGE IIA                90                252
  STAGE IIB                43                191
  STAGE III                 0                  2
  STAGE IIIA               27                115
  STAGE IIIB                8                 21
  STAGE IIIC               10                 53
  STAGE IV                  1                 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
  19Q GAIN MUTATED    48 131  26   9
  19Q GAIN WILD-TYPE 217 463  98  30
D35V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1               48                217
  T2              131                463
  T3               26                 98
  T4                9                 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
  19Q GAIN MUTATED   116  67  19  11
  19Q GAIN WILD-TYPE 365 272  94  63
D35V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0              116                365
  N1               67                272
  N2               19                 94
  N3               11                 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
  19Q GAIN MUTATED          0 192   1  21
  19Q GAIN WILD-TYPE        5 662  18 126
D35V6, multiclass
          clus
vv         19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CM0 (I+)                0                  5
  M0                    192                662
  M1                      1                 18
  MX                     21                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"
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED   210   4
  19Q GAIN WILD-TYPE 804   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED    210    4
  19Q GAIN WILD-TYPE  804    7
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE              210                804
  MALE                  4                  7
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  19Q GAIN MUTATED                            0                           169
  19Q GAIN WILD-TYPE                          1                           585
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  19Q GAIN MUTATED                               28                   3
  19Q GAIN WILD-TYPE                            147                   3
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  19Q GAIN MUTATED                                  4                  2
  19Q GAIN WILD-TYPE                               25                 13
                    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                 169                585
  INFILTRATING LOBULAR CARCINOMA                 28                147
  MEDULLARY CARCINOMA                             3                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)                4                 25
  MUCINOUS CARCINOMA                              2                 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"
D35V9, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    62 152
  19Q GAIN WILD-TYPE 220 591
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     62  152
  19Q GAIN WILD-TYPE  220  591
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                62                220
  YES              152                591
[1] 2 2
[1] FALSE
D35V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q GAIN MUTATED                                  0    12
  19Q GAIN WILD-TYPE                                1    44
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED                          35   154
  19Q GAIN WILD-TYPE                       123   563
D35V11, multiclass
                                  clus
vv                                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          12                 44
  BLACK OR AFRICAN AMERICAN                      35                123
  WHITE                                         154                563
[1] 4 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     8 175
  19Q GAIN WILD-TYPE  28 651
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      8  175
  19Q GAIN WILD-TYPE   28  651
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    8                 28
  NOT HISPANIC OR LATINO              175                651
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED   343  48
  20P GAIN WILD-TYPE 543  71
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               391                614 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                48                 71 
$`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 
       24.39        21.14        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        24.99         9.99        28.04        13.02 
TCGA-A8-A08B TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S 
       38.01        12.00        37.05        31.00         0.99        33.01 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E 
       30.97        17.95        41.98         1.02        50.04        49.05 
TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A0A1 TCGA-A8-A0A7 
       45.07        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-A6NO 
        2.27         1.55         0.07         1.81         0.69         1.68 
TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A04A TCGA-AN-A04C 
        1.74         1.12         0.33         0.33         2.96         1.78 
TCGA-AN-A0AJ TCGA-AN-A0AS TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XL 
        8.02         0.33         0.33         0.36         0.33         0.33 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O 
       12.33         0.30        80.28        47.84        66.77        81.63 
TCGA-AO-A03P TCGA-AO-A03V TCGA-AO-A0J4 TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A0JD 
       84.69        29.13        52.18        20.32        53.03        72.00 
TCGA-AO-A0JE TCGA-AO-A0JI TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A128 TCGA-AO-A12A 
       76.77        50.24        55.33        71.80       106.78        90.58 
TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS 
       77.56        57.30        48.36        82.62        61.87         0.53 
TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TQ TCGA-AR-A0TT 
      130.09        15.62        32.91         9.99        49.32        86.66 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0U0 TCGA-AR-A0U2 TCGA-AR-A1AI 
       29.75        98.93        64.83        65.36        83.87        61.84 
TCGA-AR-A1AP TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A24H TCGA-AR-A24Q TCGA-AR-A24R 
       39.98        61.28        63.62       109.58       101.52        87.22 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A254 
       85.35        50.96        79.00        56.15        73.18        72.76 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A5QM TCGA-B6-A0I1 
       58.92        93.83        42.87         7.36        54.74        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IO 
      143.38       149.59       129.57        65.72       112.37       110.14 
TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RO TCGA-B6-A0RU TCGA-B6-A0WV TCGA-B6-A0WY 
      211.56       189.01       162.05       131.21        79.63       113.79 
TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B 
       43.59        73.51        85.35        54.28        49.94       103.63 
TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0B2 TCGA-BH-A0B6 TCGA-BH-A0BA TCGA-BH-A0BF 
       24.53        20.45        40.83        56.94        37.22        25.71 
TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BZ 
       24.85        44.05        48.69        45.57        49.94        49.05 
TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0DG TCGA-BH-A0DL TCGA-BH-A0E0 
       41.75        44.02        45.83        23.44        48.23         4.41 
TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY 
       14.30         9.63        46.19        31.00        24.43        30.35 
TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HQ TCGA-BH-A0HX 
       23.08        41.00        26.50        20.38        36.85        27.25 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18K 
       50.79         5.59        42.35        44.81        23.05        90.84 
TCGA-BH-A18N TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO 
       37.74        55.63         7.36        51.39        69.93        91.99 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F2 TCGA-BH-A1F6 
       42.28        12.00        55.69        49.58        31.53        97.48 
TCGA-BH-A1F8 TCGA-BH-A1FH TCGA-BH-A1FN TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A28Q 
       24.66        36.92        72.07         0.72        38.60         6.44 
TCGA-C8-A12L TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V 
       11.93        12.66        11.77         0.07        12.66        12.66 
TCGA-C8-A12W TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A138 TCGA-C8-A1HI 
       12.66         3.12         1.78         1.45         3.75        11.34 
TCGA-C8-A1HM TCGA-C8-A26Z TCGA-C8-A274 TCGA-C8-A278 TCGA-C8-A3M8 TCGA-D8-A13Z 
        2.30         8.28         0.03         0.03         0.23        20.88 
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-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-A1JP TCGA-D8-A1JT TCGA-D8-A1X5 TCGA-D8-A1XB 
       14.01        18.97        21.01        13.32        18.58        18.15 
TCGA-D8-A1XF TCGA-D8-A1XL TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XY 
       15.22        19.92        16.31        12.99        12.66        16.54 
TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A27I TCGA-D8-A27L TCGA-D8-A27M 
       15.32        15.52         3.81        14.43        16.41        13.48 
TCGA-D8-A27W TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14T 
       12.26        37.51        40.11        44.68        40.96        33.30 
TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 
       34.26        31.96        17.03        25.41        27.12        23.24 
TCGA-E2-A154 TCGA-E2-A159 TCGA-E2-A15C TCGA-E2-A15H TCGA-E2-A15K TCGA-E2-A15O 
       19.43        25.05        22.82        12.92         9.04        13.02 
TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IN 
       60.53        53.62        17.10        33.73        33.70        22.19 
TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK 
       20.98        27.42        19.66       106.75       102.61         8.75 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N6 
        7.20        30.61        19.89        19.00         9.21        13.48 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NI 
       12.00        13.12        12.59        35.77        20.05         9.86 
TCGA-E9-A1QZ TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1RA TCGA-E9-A1RB 
       11.90         2.10         6.12         1.38        32.09        20.81 
TCGA-E9-A1RC TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A229 
       40.24         6.58        21.27        34.59        34.13        13.32 
TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A295 
       22.75        12.89        27.22         1.94         0.95         0.72 
TCGA-E9-A2JS TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UP TCGA-EW-A1IY 
       17.75         0.23        14.70         0.26        14.40         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-LD-A7W5 
       53.52        43.04        42.28        69.30        21.24         4.08 
TCGA-LL-A441 TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Z 
       11.44        15.32        14.70        11.57         2.63         4.50 
TCGA-LL-A7SZ TCGA-LQ-A4E4 TCGA-OL-A5RZ TCGA-OL-A66I TCGA-OL-A66N TCGA-PL-A8LV 
        5.59        27.91        22.32        23.47        26.04         0.23 
TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-AA10 TCGA-S3-AA17 TCGA-W8-A86G 
        3.95        16.50         6.81         7.92         3.91         5.29 
TCGA-Z7-A8R6 
      105.04 

$`20P GAIN WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SE TCGA-A1-A0SH TCGA-A1-A0SK TCGA-A1-A0SO 
        0.39         8.52        43.43        47.24        31.79        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-A04W TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CO TCGA-A2-A0CP 
       63.12        64.04        36.13       136.73       112.08        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CW TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0EM 
       88.60       107.93        64.04        34.55        28.77       101.72 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EW 
       89.36        80.28       107.61        74.40        37.05        29.75 
TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 
       24.72        99.19        54.64        44.28        17.52        17.13 
TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YE 
       18.71        20.52        17.46        18.90        32.55        18.21 
TCGA-A2-A0YF TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV 
       15.42        14.50        19.33        48.46        31.73        23.47 
TCGA-A2-A1FZ TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B 
       22.45        19.56        16.47        52.47       107.70        16.31 
TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KD TCGA-A2-A3XU 
       17.19        18.15        91.92        10.59        39.65        29.98 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 
       32.75        49.48        38.40        34.98        31.99        38.37 
TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CE 
        7.30        21.30        23.21        26.96        21.90        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F 
       34.29        35.47        23.61        29.56        31.36        24.26 
TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 
       23.80        21.73        22.32        11.34        10.59        10.29 
TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A426 TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A4SF 
       11.28        13.41        11.97        13.74        21.17        17.92 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P 
       12.10        10.72        11.05        10.42         8.75        13.02 
TCGA-A8-A06Q TCGA-A8-A06T TCGA-A8-A06X TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07B 
        1.02        53.06        31.00         1.02         9.01        43.00 
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-A07S TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A08A 
        9.99         7.99        18.05        15.06        36.95         0.99 
TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08T 
       28.96        33.01        19.96         9.99        31.00        93.04 
TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A 
       43.00        40.01        33.01        12.00         9.99         9.99 
TCGA-A8-A09B TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
       12.00        33.07        25.02        19.04        15.02         0.99 
TCGA-A8-A09X TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0AB TCGA-A8-A0AD 
       14.01        19.04        13.02        21.04        17.03        38.04 
TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2FB TCGA-AC-A2FF 
        0.95         2.37         1.48        38.53        40.57        55.43 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3HN 
       36.99        38.79        50.70         0.92         0.99         0.69 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI 
       14.83        22.19         1.12        16.57        19.79        23.24 
TCGA-AC-A3YJ TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A8OR TCGA-AN-A041 
       24.79         1.12         1.18         0.43         1.32         0.23 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM 
        0.33         0.62         1.71         7.36         6.51         0.16 
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-A0FX TCGA-AN-A0FY 
        7.59         7.17         6.28         6.02         0.33         0.33 
TCGA-AN-A0XN TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV 
        0.33         0.33         0.33         0.33         0.33         5.33 
TCGA-AN-A0XW TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A0J2 TCGA-AO-A0J3 
        5.59        68.75        47.87        59.05        32.78        21.40 
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-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 
       21.37        26.24        62.04       102.58        99.25       108.72 
TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KR 
       96.10        64.04        41.62        28.37        14.73        70.39 
TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A0Y5 TCGA-AQ-A1H3 TCGA-AQ-A54N 
       17.79        24.79        26.93         5.65        32.52         2.56 
TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 
      111.32         5.26        74.79        55.86        76.14       101.95 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL 
      114.02        85.97        75.55        52.77        51.25        48.82 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS 
       62.56        43.73        43.56        43.07        17.23        37.81 
TCGA-AR-A1AU TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M 
       76.21        62.14        20.22        50.89        73.02        96.89 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X 
       78.51        84.20         0.85        76.01        53.36        83.77 
TCGA-AR-A251 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN 
       78.48       128.65        20.25        62.86        40.04        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       39.39        40.54        20.38        16.04        20.45        10.59 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IG TCGA-B6-A0IJ TCGA-B6-A0IK 
       12.13       220.90        50.70       146.50       176.98        18.77 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RI 
      126.12        84.59       110.93       140.88        68.45       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-A1KN TCGA-B6-A2IU TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AY 
      101.52       139.17       170.17        55.00        38.79        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 
       28.50        46.95        39.55        39.16        48.36        56.98 
TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO 
       51.68        32.02        18.21        21.70        61.68        35.67 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BW TCGA-BH-A0C3 TCGA-BH-A0C7 
       27.19        53.69        53.95        11.67        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-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-A0E1 TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0GZ TCGA-BH-A0H0 
       15.68        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-A18F 
       13.61        12.89        51.32        23.93        24.95         8.81 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18P 
        2.01         7.23        20.12        26.66        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-A1FM TCGA-BH-A1FR TCGA-BH-A1FU 
      122.89        63.35        55.00        45.63       144.59        72.07 
TCGA-BH-A201 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A2L8 
        6.90        83.31        57.83       130.16        10.65        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12X 
        0.99       109.28         8.94        11.77        11.77        12.66 
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-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-A273 TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A27B 
        0.36         0.43         9.67         0.03        12.20         0.99 
TCGA-C8-A3M7 TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A1J9 TCGA-D8-A1JA 
        0.03        11.90        13.25        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-A1XA 
       14.70        17.79        16.73        25.74        23.90        27.58 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XM 
        2.66        17.16        14.73        21.83        14.50        17.69 
TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1Y2 
        7.96        16.41        15.85         6.35        15.16        14.24 
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-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-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14Q TCGA-E2-A14R 
       40.41        28.44        28.87        47.15        38.24        38.60 
TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A155 TCGA-E2-A156 
       33.17        43.33        32.02        28.60        21.04        23.87 
TCGA-E2-A158 TCGA-E2-A15A TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G 
       14.79        23.34        17.29        20.71        21.63        18.21 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R 
       17.42        19.40        20.58         7.73        19.56        17.06 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       14.07        14.99        53.03        29.95        32.35        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-A1IU TCGA-E2-A1L6 TCGA-E2-A1L8 TCGA-E2-A1LA TCGA-E2-A1LB 
        3.88        11.08        54.18        39.62        24.59        40.47 
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-A573 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1NG 
       34.92        19.20        36.82        36.56        39.55        21.57 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RD TCGA-E9-A1RE 
       14.30         0.62         2.76        21.21         0.66        34.65 
TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A22A TCGA-E9-A22G TCGA-E9-A22H 
       35.64         0.79        12.53        39.09        23.51        24.10 
TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3HO 
       17.06         0.69         0.85        24.56         0.76        26.07 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5UO TCGA-E9-A6HE 
       18.41         0.62        15.72        12.33        13.81        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-A1OZ TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 
       22.82        29.95        40.41        39.78        52.96        29.82 
TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
       30.08         7.86        18.90        10.52        14.43        34.55 
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-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-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-A3XN TCGA-GM-A4E0 
       53.36       110.50        38.20        43.73        66.38        72.03 
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-LD-A9QF TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YO 
        8.75         9.53        10.95         7.59        17.06        14.47 
TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A740 TCGA-LL-A7T0 TCGA-LL-A8F5 
       14.79         3.88         4.14         4.50         3.22         6.21 
TCGA-LL-A9Q3 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 
        7.36         2.79         2.10        12.66        46.55        31.99 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY 
       58.62        27.65        34.92        36.36        16.87        24.72 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66O 
       20.38        26.70        65.62        33.57        31.07         7.23 
TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PL-A8LX TCGA-PL-A8LY TCGA-S3-A6ZH 
       14.07        28.21        19.73         0.16         0.26         8.65 
TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-XX-A899 
       10.59         5.56         8.52         7.17         6.87         9.60 
TCGA-XX-A89A TCGA-Z7-A8R5 
        9.14       100.01 

  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 
             23.05              22.16 
[1] "0.0 - 211.6 (23.1)" "0.0 - 234.3 (22.2)"
[1] "hr=" "1.2"
D36V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20P GAIN MUTATED        36       26        1        2       137        82
  20P GAIN WILD-TYPE      47       54        8        3       205       152
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20P GAIN MUTATED           1         64         13         19       10
  20P GAIN WILD-TYPE         1         78         16         44        8
                    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                  36                 47
  STAGE IA                 26                 54
  STAGE IB                  1                  8
  STAGE II                  2                  3
  STAGE IIA               137                205
  STAGE IIB                82                152
  STAGE III                 1                  1
  STAGE IIIA               64                 78
  STAGE IIIB               13                 16
  STAGE IIIC               19                 44
  STAGE IV                 10                  8
  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    99 238  40  18
  20P GAIN WILD-TYPE 166 356  84  21
D36V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1               99                166
  T2              238                356
  T3               40                 84
  T4               18                 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
  20P GAIN MUTATED   185 123  59  23
  20P GAIN WILD-TYPE 296 216  54  51
D36V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0              185                296
  N1              123                216
  N2               59                 54
  N3               23                 51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  20P GAIN MUTATED          1 344  10  42
  20P GAIN WILD-TYPE        4 510   9 105
D36V6, multiclass
          clus
vv         20P GAIN MUTATED 20P GAIN WILD-TYPE
  CM0 (I+)                1                  4
  M0                    344                510
  M1                     10                  9
  MX                     42                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"
D36V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   389   8
  20P GAIN WILD-TYPE 625   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    389    8
  20P GAIN WILD-TYPE  625    3
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE              389                625
  MALE                  8                  3
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  20P GAIN MUTATED                            0                           331
  20P GAIN WILD-TYPE                          1                           423
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  20P GAIN MUTATED                               40                   2
  20P GAIN WILD-TYPE                            135                   4
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  20P GAIN MUTATED                                  9                  1
  20P GAIN WILD-TYPE                               20                 14
                    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                 331                423
  INFILTRATING LOBULAR CARCINOMA                 40                135
  MEDULLARY CARCINOMA                             2                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                9                 20
  MUCINOUS CARCINOMA                              1                 14
  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   126 271
  20P GAIN WILD-TYPE 156 472
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    126  271
  20P GAIN WILD-TYPE  156  472
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO               126                156
  YES              271                472
[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                          65   272
  20P GAIN WILD-TYPE                        93   445
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                      65                 93
  WHITE                                         272                445
[1] 4 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    11 321
  20P GAIN WILD-TYPE  25 505
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     11  321
  20P GAIN WILD-TYPE   25  505
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                   11                 25
  NOT HISPANIC OR LATINO              321                505
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED   372  52
  20Q GAIN WILD-TYPE 514  67
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               424                581 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                52                 67 
$`20Q GAIN MUTATED`
TCGA-5T-A9QA TCGA-A1-A0SD TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SI TCGA-A1-A0SJ 
        0.39        14.37        48.10        14.27        20.88        13.68 
TCGA-A1-A0SM TCGA-A1-A0SP TCGA-A2-A04P TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CL 
        7.96        19.20        18.02        64.04        55.43        64.57 
TCGA-A2-A0CM TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CX 
       24.79        75.55        75.25         5.19        63.45        56.81 
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-A0EV TCGA-A2-A0EY TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0T7 TCGA-A2-A0YD 
       31.82        24.16        44.88        50.43        20.75        25.28 
TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YJ TCGA-A2-A0YT TCGA-A2-A1FW 
       18.21        21.90        21.67        18.61        23.77        17.36 
TCGA-A2-A1FX TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A25B TCGA-A2-A25E TCGA-A2-A3KC 
       36.79        20.25        19.20        16.31        91.92        20.88 
TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XX TCGA-A2-A4RX TCGA-A2-A4S2 TCGA-A7-A0CD 
       33.93        83.01        38.40        24.39        21.14        38.30 
TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F 
       30.61        37.45        33.11        31.73        10.72        12.72 
TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SD TCGA-A7-A4SE 
       23.74        20.61        14.70        14.93        14.50        21.17 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A6VV TCGA-A8-A06O TCGA-A8-A06R TCGA-A8-A06U 
       17.92        14.73        10.29        13.02        17.98        29.03 
TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07P TCGA-A8-A07R 
       26.01        17.03        53.98         9.01        10.98         8.98 
TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A086 TCGA-A8-A08B TCGA-A8-A08G 
       24.99         9.99        28.04        13.02        38.01        19.96 
TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08X 
       12.00        37.05        31.00         0.99        33.01        43.00 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E 
       30.97        17.95        41.98         1.02        50.04        49.05 
TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A0A1 
       45.07        29.98        33.07         1.02         8.98        12.00 
TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2BM TCGA-AC-A2FM 
        0.99        13.02        10.85         2.66        38.20        26.04 
TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A3W5 TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y 
        1.02         2.27        16.57         1.55         0.07         1.81 
TCGA-AC-A6IW TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AN-A03X TCGA-AN-A03Y 
        0.69         1.68         1.74         1.12         0.33         0.33 
TCGA-AN-A04C TCGA-AN-A0AJ TCGA-AN-A0AM TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XL 
        1.78         8.02         0.16         0.36         0.33         0.33 
TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N 
        0.33        12.33         0.30        80.28        47.84        66.77 
TCGA-AO-A03O TCGA-AO-A03T TCGA-AO-A03V TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A0JD 
       81.63        47.87        29.13        20.32        53.03        72.00 
TCGA-AO-A0JE TCGA-AO-A0JI TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A128 TCGA-AO-A12A 
       76.77        50.24        55.33        71.80       106.78        90.58 
TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KT 
       77.56        57.30        48.36        82.62        61.87        17.79 
TCGA-AQ-A04H TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A7U7 TCGA-AR-A0TQ TCGA-AR-A0TT 
       24.79       130.09        15.62         9.99        49.32        86.66 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TZ TCGA-AR-A0U2 TCGA-AR-A1AI 
       29.75        98.93        64.83        76.14        83.87        61.84 
TCGA-AR-A1AK TCGA-AR-A1AP TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A24H TCGA-AR-A24L 
       51.25        39.98        61.28        63.62       109.58        73.02 
TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24Z TCGA-AR-A250 
      101.52        87.22        85.35        50.96        79.00        56.15 
TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LR 
       73.18        58.92        93.83        42.87         7.36        20.38 
TCGA-AR-A5QM TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IB 
       54.74        77.62       143.38       149.59        12.13       129.57 
TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IO TCGA-B6-A0RE TCGA-B6-A0RL 
       65.72       112.37       176.98       110.14       211.56        81.17 
TCGA-B6-A0RO TCGA-B6-A0RU TCGA-B6-A0WV TCGA-B6-A0WY TCGA-B6-A1KC TCGA-B6-A1KF 
      162.05       131.21        79.63       113.79        43.59       101.52 
TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B 
       73.51       139.17        85.35        54.28        49.94       103.63 
TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0B6 TCGA-BH-A0BA TCGA-BH-A0BF 
       24.53        20.45        25.55        56.94        37.22        25.71 
TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BZ TCGA-BH-A0C0 
       44.05        48.69        45.57        49.94        49.05        41.75 
TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0DG TCGA-BH-A0DL TCGA-BH-A0DQ TCGA-BH-A0E0 
       44.02        45.83        23.44        48.23         3.22         4.41 
TCGA-BH-A0E2 TCGA-BH-A0E9 TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0H7 
       14.30        46.19        31.00        24.43        30.35        23.08 
TCGA-BH-A0H9 TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HQ TCGA-BH-A0HX TCGA-BH-A0HY 
       41.00        26.50        20.38        36.85        27.25        50.79 
TCGA-BH-A0RX TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18N 
        5.59        42.35        44.81        90.84        26.66        37.74 
TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1EU 
       55.63         7.36        51.39        69.93        91.99        42.28 
TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1F8 
       12.00        55.69        49.58        31.53        97.48        24.66 
TCGA-BH-A1FH TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 
       36.92        45.63        72.07         0.72        38.60        57.83 
TCGA-BH-A28Q TCGA-C8-A12L TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U 
        6.44        11.93        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-A138 
       12.66        12.66         3.12         1.78         1.45         3.75 
TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26Z TCGA-C8-A274 
       11.34        11.34         2.30         3.25         8.28         0.03 
TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A3M8 TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A142 
        0.03        12.20         0.23        20.88        13.25        13.97 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1JB 
       14.17        13.48        21.14        19.20        14.17        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-A1JP TCGA-D8-A1JT TCGA-D8-A1X5 TCGA-D8-A1XA TCGA-D8-A1XB 
       18.97        21.01        13.32        18.58        27.58        18.15 
TCGA-D8-A1XF TCGA-D8-A1XL TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XW 
       15.22        19.92        16.41        16.31        12.99        12.66 
TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A27I TCGA-D8-A27L 
       16.54        15.32        15.52         3.81        14.43        16.41 
TCGA-D8-A27M TCGA-D8-A27R TCGA-D8-A27W TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A14O 
       13.48        10.09        12.26        37.51        40.11        44.68 
TCGA-E2-A14P TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14V TCGA-E2-A14X 
       40.96        38.60        33.17        33.30        34.26        31.96 
TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A159 TCGA-E2-A15A 
       25.41        27.12        23.24        19.43        25.05        23.34 
TCGA-E2-A15C TCGA-E2-A15H TCGA-E2-A15K TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15R 
       22.82        12.92         9.04         7.73        13.02        17.06 
TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IN 
       60.53        53.62        17.10        33.73        33.70        22.19 
TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK 
       20.98        27.42        19.66       106.75       102.61         8.75 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU 
        7.20        30.61        34.92        19.89        19.00         9.21 
TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NE TCGA-E9-A1NI 
       36.82        13.48        12.00        13.12        35.77         9.86 
TCGA-E9-A1QZ TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 
       11.90         0.62         2.10         6.12         1.38         2.76 
TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG 
       32.09        20.81        40.24        34.65         6.58        21.27 
TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A229 TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A244 
       34.59        34.13        13.32        22.75        12.89         0.69 
TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A54Y 
       27.22         1.94         0.95         0.72        17.75         0.23 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UP TCGA-EW-A1IY TCGA-EW-A1J3 TCGA-EW-A1J5 
       14.70         0.26        14.40         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-LD-A7W5 TCGA-LL-A441 TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A6FP 
       21.24         4.08        11.44        15.32        14.70        11.57 
TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LQ-A4E4 TCGA-OL-A5RZ 
        2.63         4.14         5.59         3.22        27.91        22.32 
TCGA-OL-A66I TCGA-OL-A66N TCGA-PL-A8LX TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG 
       23.47        26.04         0.16         3.95        16.50         6.81 
TCGA-S3-AA10 TCGA-S3-AA17 TCGA-W8-A86G TCGA-Z7-A8R6 
        7.92         3.91         5.29       105.04 

$`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       136.73       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        48.46        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        32.75        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        21.30        23.21 
TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0DA 
       26.96        21.90        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        53.06        31.00 
TCGA-A8-A06Z TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I 
        1.02        43.00        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        28.96        33.01         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        33.01        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 
       22.19         1.12        19.79        23.24        24.79         1.12 
TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A8OR TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 
        1.18         0.43         1.32         0.23         0.33         0.62 
TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AS 
        2.96         1.71         7.36         6.51         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-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-A03P TCGA-AO-A03R TCGA-AO-A03U TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 
       84.69        68.75        59.05        32.78        21.40        52.18 
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-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 
       21.37        26.24        62.04       102.58        99.25       108.72 
TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KR 
       96.10        64.04        41.62        28.37        14.73        70.39 
TCGA-AO-A1KS TCGA-AQ-A04J TCGA-AQ-A0Y5 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O 
        0.53        26.93         5.65        32.52         2.56        32.91 
TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TY TCGA-AR-A0U0 TCGA-AR-A0U1 
      111.32         5.26        74.79        55.86        65.36       101.95 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AL TCGA-AR-A1AM 
      114.02        85.97        75.55        52.77        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        37.81        76.21 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       62.14        20.22        50.89        96.89        78.51        84.20 
TCGA-AR-A24P TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A251 TCGA-AR-A254 
        0.85        76.01        53.36        83.77        78.48        72.76 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
      128.65        20.25        62.86        40.04        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0IA TCGA-B6-A0IC 
       40.54        16.04        20.45        10.59       220.90        50.70 
TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ 
      146.50        18.77       126.12        84.59       110.93       140.88 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RP 
       68.45       189.01       234.28        78.02       172.96       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-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-A2IU TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AZ 
       68.94        58.88       170.17        55.00        38.79        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-A0BC TCGA-BH-A0BD TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BM 
       51.68        32.02        18.21        24.85        21.70        61.68 
TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BW TCGA-BH-A0C3 
       35.67        27.19        53.69        53.95        11.67        48.13 
TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO 
       42.90        31.17        38.01        22.13        13.91        17.26 
TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ 
       15.65         2.56        38.47        45.17        47.41        16.27 
TCGA-BH-A0E1 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0GZ 
       15.68         9.63        44.81        32.65        24.49        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0HA TCGA-BH-A0HK 
       15.16        37.78        35.51        24.56        52.96         5.85 
TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0W3 TCGA-BH-A0W4 
        2.50        13.61        12.89        51.32        23.93        24.95 
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-A18V TCGA-BH-A1ES TCGA-BH-A1ET 
       30.28        37.55        66.05        51.16       113.82        82.85 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F5 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD 
       17.69        25.81        89.16       120.62       114.15        33.17 
TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FR TCGA-BH-A1FU 
       74.73       122.89        63.35        55.00       144.59        72.07 
TCGA-BH-A201 TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A2L8 TCGA-BH-A42T 
        6.90        83.31       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-A1HJ TCGA-C8-A1HK 
        0.62         3.85        12.33        10.92         0.16        12.03 
TCGA-C8-A1HL TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A273 
       10.42         0.30         0.23         0.36         0.43         9.67 
TCGA-C8-A275 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-D8-A13Y TCGA-D8-A141 TCGA-D8-A1J9 
        0.03         0.99         0.03        11.90        20.58        17.49 
TCGA-D8-A1JA TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN 
       16.50        20.09        20.12        20.09        19.40        20.38 
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-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XM 
        2.66        17.16        14.73        21.83        14.50        17.69 
TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1Y2 TCGA-D8-A1Y3 
        7.96        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-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-A109 TCGA-E2-A10A TCGA-E2-A10E 
       43.00        34.42        27.52        46.59        40.41        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14Q TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14Y 
       28.87        47.15        38.24        43.33        32.02        28.60 
TCGA-E2-A14Z TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15D TCGA-E2-A15E 
       17.03        21.04        23.87        14.79        17.29        20.71 
TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15L TCGA-E2-A15P 
       21.63        18.21        17.42        19.40        20.58        19.56 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       14.07        14.99        53.03        29.95        32.35        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-A1IU TCGA-E2-A1L6 TCGA-E2-A1L8 TCGA-E2-A1LA TCGA-E2-A1LB 
        3.88        11.08        54.18        39.62        24.59        40.47 
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-E9-A1N4 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1NG 
       19.20        36.56        39.55        12.59        20.05        21.57 
TCGA-E9-A1R0 TCGA-E9-A1R7 TCGA-E9-A1RD TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 
       14.30        21.21         0.66        35.64         0.79        12.53 
TCGA-E9-A22A TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A245 TCGA-E9-A24A 
       39.09        23.51        24.10        17.06         0.85        24.56 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X 
        0.76        26.07        18.41         0.62        15.72        12.33 
TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J1 
       13.81        15.39        12.20        39.72        18.21        18.90 
TCGA-EW-A1J2 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1P1 TCGA-EW-A1P3 
       13.25        25.94        22.82        29.95        39.78        52.96 
TCGA-EW-A1P4 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PE TCGA-EW-A1PF 
       29.82        30.08         7.86        18.90        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 
       34.55        19.96        55.00        25.91        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-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        43.73        66.38        72.03        13.55 
TCGA-GM-A5PX TCGA-JL-A3YX TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 
       18.12        11.57         6.67         4.60         8.75         9.53 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FR 
       10.95         7.59        17.06        14.47        14.79         3.88 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-MS-A51U TCGA-OK-A5Q2 
        4.50         4.50         6.21         7.36         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        31.99        58.62        27.65        34.92 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J 
       36.36        16.87        24.72        20.38        26.70        65.62 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ 
       33.57        31.07         7.23        14.07        28.21        19.73 
TCGA-PL-A8LV TCGA-PL-A8LY TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA12 
        0.23         0.26         8.65        10.59         5.56         8.52 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
        7.17         6.87         9.60         9.14       100.01 

  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 
            22.785             22.320 
[1] "0.0 - 211.6 (22.8)" "0.0 - 234.3 (22.3)"
[1] "hr=" "1.2"
D37V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20Q GAIN MUTATED        35       28        2        2       147        94
  20Q GAIN WILD-TYPE      48       52        7        3       195       140
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20Q GAIN MUTATED           1         68         15         24        9
  20Q GAIN WILD-TYPE         1         74         14         39        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                  35                 48
  STAGE IA                 28                 52
  STAGE IB                  2                  7
  STAGE II                  2                  3
  STAGE IIA               147                195
  STAGE IIB                94                140
  STAGE III                 1                  1
  STAGE IIIA               68                 74
  STAGE IIIB               15                 14
  STAGE IIIC               24                 39
  STAGE IV                  9                  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   100 265  42  22
  20Q GAIN WILD-TYPE 165 329  82  17
D37V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1              100                165
  T2              265                329
  T3               42                 82
  T4               22                 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
  20Q GAIN MUTATED   197 137  61  28
  20Q GAIN WILD-TYPE 284 202  52  46
D37V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0              197                284
  N1              137                202
  N2               61                 52
  N3               28                 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
  20Q GAIN MUTATED          1 372  10  48
  20Q GAIN WILD-TYPE        4 482   9  99
D37V6, multiclass
          clus
vv         20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CM0 (I+)                1                  4
  M0                    372                482
  M1                     10                  9
  MX                     48                 99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   424   7
  20Q GAIN WILD-TYPE 590   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    424    7
  20Q GAIN WILD-TYPE  590    4
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE              424                590
  MALE                  7                  4
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  20Q GAIN MUTATED                            0                           361
  20Q GAIN WILD-TYPE                          1                           393
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  20Q GAIN MUTATED                               44                   1
  20Q GAIN WILD-TYPE                            131                   5
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  20Q GAIN MUTATED                                  9                  1
  20Q GAIN WILD-TYPE                               20                 14
                    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                 361                393
  INFILTRATING LOBULAR CARCINOMA                 44                131
  MEDULLARY CARCINOMA                             1                  5
  MIXED HISTOLOGY (PLEASE SPECIFY)                9                 20
  MUCINOUS CARCINOMA                              1                 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"
D37V9, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   130 301
  20Q GAIN WILD-TYPE 152 442
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    130  301
  20Q GAIN WILD-TYPE  152  442
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO               130                152
  YES              301                442
[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                          73   290
  20Q GAIN WILD-TYPE                        85   427
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                      73                 85
  WHITE                                         290                427
[1] 4 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    11 351
  20Q GAIN WILD-TYPE  25 475
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     11  351
  20Q GAIN WILD-TYPE   25  475
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   11                 25
  NOT HISPANIC OR LATINO              351                475
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED   156  32
  21Q GAIN WILD-TYPE 730  87
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               188                817 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                32                 87 
$`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        26.96        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        24.99         9.99        28.04        38.01 
TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08X TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 
        9.99        31.00        43.00        33.01        30.97        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       106.78 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A1KT TCGA-AQ-A54O TCGA-AR-A0TW TCGA-AR-A0TY 
       77.56        64.04        17.79        32.91        98.93        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        61.28        62.14        50.89 
TCGA-AR-A24R TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A2LR TCGA-AR-A5QM TCGA-B6-A0I1 
       87.22        79.00        78.48        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-E2-A9RU 
       19.66        28.90         8.75        16.93        34.92         9.21 
TCGA-E9-A1R7 TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RH TCGA-E9-A244 TCGA-E9-A2JS 
       21.21         0.66        34.65        34.59         0.69        17.75 
TCGA-E9-A3X8 TCGA-E9-A5UP TCGA-EW-A1OZ TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P8 
       15.72        14.40        40.41        29.82        23.11         7.86 
TCGA-EW-A1PC TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A423 TCGA-GM-A2DC 
        6.15        19.96        55.00        25.91        10.16        53.52 
TCGA-GM-A2DF TCGA-LD-A7W5 TCGA-LL-A441 TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A73Y 
       42.71         4.08        11.44        14.47        14.79         4.14 
TCGA-LL-A73Z TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-S3-AA0Z 
        4.50         3.22         6.21        36.36        20.38        10.59 
TCGA-S3-AA10 TCGA-W8-A86G 
        7.92         5.29 

$`21Q GAIN WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        0.39         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A1-A0SQ 
       47.24        31.79         7.96        39.32        19.20        18.21 
TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04V TCGA-A2-A04W 
      104.81        41.95        82.16        73.84        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       136.73        64.57       112.08        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CW 
       88.60       107.93        75.55        75.25        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-A0SU 
       35.05        34.29        31.82        29.75        24.72        54.64 
TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T4 TCGA-A2-A0T5 
       44.88        50.43        44.28        17.52        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-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FV 
       14.50        18.61        19.33        48.46        23.77        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-A3XS TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XY 
       10.59        20.88        33.93        83.01        32.75        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        24.39        21.30        23.21 
TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH 
       21.14        21.90        38.30        35.31        34.29        35.47 
TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       30.61        37.45        33.11        23.61        29.56        31.36 
TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ 
       24.26        23.74        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-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-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        53.06 
TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E 
       29.03        31.00         1.02         9.01        43.00        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-A082 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 
       10.98         7.99        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        28.96        33.01        19.96        12.00        37.05 
TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A095 
       31.00         0.99        33.01        93.04        40.01        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        50.04 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T 
       49.05        45.07        33.07        25.02         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-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23H 
        0.99        13.02        38.04         0.95         2.37         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-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 
       22.19         1.12        16.57        19.79        23.24        24.79 
TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO 
        1.55         0.07         1.12         1.18         0.43         1.68 
TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 
        1.74         1.12         1.32         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-A0AT TCGA-AN-A0FD TCGA-AN-A0FF 
        6.51         0.16         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-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-A03M TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T 
        5.59        80.28        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        52.18        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        50.24 
TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 
       62.04        55.33       102.58        99.25       108.72        96.10 
TCGA-AO-A12A TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
       90.58        57.30        48.36        41.62        28.37        14.73 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04J 
       82.62        61.87        70.39         0.53        24.79        26.93 
TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A7U7 
      130.09         5.65        15.62        32.52         2.56         9.99 
TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV 
      111.32        49.32         5.26        74.79        86.66        29.75 
TCGA-AR-A0TX TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 
       64.83        76.14       101.95        83.87       114.02        85.97 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
       75.55        61.84        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-A1AW 
       43.56        39.98        43.07        37.81        76.21        63.62 
TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       20.22       109.58        73.02        96.89        78.51        84.20 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W 
        0.85       101.52        76.01        53.36        85.35        50.96 
TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
       83.77        56.15        73.18        72.76        58.92        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM 
      128.65        20.25        62.86        42.87         7.36        40.04 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       38.17        39.39        40.54        16.04        20.45        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-A0IJ TCGA-B6-A0IM TCGA-B6-A0IP TCGA-B6-A0RG 
       65.72       146.50       176.98       126.12       110.93        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-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-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-A1KN TCGA-B6-A2IU 
       28.27        68.94        58.88        43.59       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       103.63        55.00        24.53        38.79 
TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 
       20.45        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-A0BM TCGA-BH-A0BO TCGA-BH-A0BP 
       25.71        24.85        21.70        61.68        35.67        48.69 
TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0C0 TCGA-BH-A0C3 
       27.19        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-A0DT 
       13.91        48.23        17.26        15.65         3.22        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-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 
       44.81        46.19        32.65        24.43        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-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-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-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-A1EY TCGA-BH-A1F0 
      113.82        82.85        42.28        55.69        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-A201 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 
       72.07       144.59         6.90        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-A12U 
       11.93        11.77        11.77        12.66         0.07        12.66 
TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A138 
       12.66        12.66        12.66         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-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Z 
       10.42         3.25         0.30         0.23         0.36         8.28 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 
        9.67         0.03        12.20         0.99         0.03         0.23 
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-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-A1JI TCGA-D8-A1JJ TCGA-D8-A1JL TCGA-D8-A1JM 
       18.90        12.03        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-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-A1XF TCGA-D8-A1XG TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO 
        2.66        15.22        14.73        19.92        17.69         7.96 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XY 
       16.41        15.85        16.31         6.35        15.16        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-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-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-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V 
       47.15        38.24        33.17        33.30        43.33        34.26 
TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A155 
       32.02        28.60        25.41        27.12        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-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-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B1 
       20.58        19.56        17.06        14.07        14.99        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-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-A1LA TCGA-E2-A1LB TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LL 
       24.59        40.47        18.87       106.75       102.61        43.04 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A574 TCGA-E2-A576 
        5.52        15.72         7.20        30.61        19.89        19.00 
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-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-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RF TCGA-E9-A1RG 
        2.76        32.09        20.81        40.24         6.58        21.27 
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-A245 
       22.75        12.89        23.51        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        24.56         0.72         0.76 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK 
       26.07        18.41         0.62        12.33         0.23        14.70 
TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
        0.26        13.81        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        43.73 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW 
       69.30        66.38        72.03        13.55        18.12        11.84 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 
       11.57        21.24         6.67         4.60         8.75         9.53 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A6FP 
       10.95         7.59        17.06        15.32        14.70        11.57 
TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A9Q3 TCGA-LQ-A4E4 
        2.63         3.88         4.50         5.59         7.36        27.91 
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        31.99        58.62 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H 
       27.65        34.92        16.87        24.72        22.32        26.70 
TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O 
       23.47        65.62        33.57        31.07        26.04         7.23 
TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PL-A8LV TCGA-PL-A8LX TCGA-PL-A8LY 
       14.07        28.21        19.73         0.23         0.16         0.26 
TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA11 TCGA-S3-AA12 
        3.95        16.50         6.81         8.65         5.56         8.52 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
        7.17         6.87         3.91         9.60         9.14       100.01 
TCGA-Z7-A8R6 
      105.04 

  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 
            22.125             22.450 
[1] "0.0 - 211.6 (22.1)" "0.0 - 234.3 (22.4)"
[1] "hr=" "1.7"
D38V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  21Q GAIN MUTATED        12       11        1        1        70        38
  21Q GAIN WILD-TYPE      71       69        8        4       272       196
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  21Q GAIN MUTATED           0         31          3         16        4
  21Q GAIN WILD-TYPE         2        111         26         47       14
                    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                 71
  STAGE IA                 11                 69
  STAGE IB                  1                  8
  STAGE II                  1                  4
  STAGE IIA                70                272
  STAGE IIB                38                196
  STAGE III                 0                  2
  STAGE IIIA               31                111
  STAGE IIIB                3                 26
  STAGE IIIC               16                 47
  STAGE IV                  4                 14
  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    44 119  22   5
  21Q GAIN WILD-TYPE 221 475 102  34
D38V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1               44                221
  T2              119                475
  T3               22                102
  T4                5                 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
  21Q GAIN MUTATED    83  65  21  17
  21Q GAIN WILD-TYPE 398 274  92  57
D38V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0               83                398
  N1               65                274
  N2               21                 92
  N3               17                 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
  21Q GAIN MUTATED          0 167   4  20
  21Q GAIN WILD-TYPE        5 687  15 127
D38V6, multiclass
          clus
vv         21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CM0 (I+)                0                  5
  M0                    167                687
  M1                      4                 15
  MX                     20                127
[1] 4 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   189   2
  21Q GAIN WILD-TYPE 825   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED    189    2
  21Q GAIN WILD-TYPE  825    9
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE              189                825
  MALE                  2                  9
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  21Q GAIN MUTATED                            0                           164
  21Q GAIN WILD-TYPE                          1                           590
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  21Q GAIN MUTATED                               15                   2
  21Q GAIN WILD-TYPE                            160                   4
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  21Q GAIN MUTATED                                  0                  1
  21Q GAIN WILD-TYPE                               29                 14
                    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                 164                590
  INFILTRATING LOBULAR CARCINOMA                 15                160
  MEDULLARY CARCINOMA                             2                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                0                 29
  MUCINOUS CARCINOMA                              1                 14
  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    64 127
  21Q GAIN WILD-TYPE 218 616
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     64  127
  21Q GAIN WILD-TYPE  218  616
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                64                218
  YES              127                616
[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                          39   118
  21Q GAIN WILD-TYPE                       119   599
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                      39                119
  WHITE                                         118                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"
D38V12, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     9 147
  21Q GAIN WILD-TYPE  27 679
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      9  147
  21Q GAIN WILD-TYPE   27  679
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    9                 27
  NOT HISPANIC OR LATINO              147                679
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    81  14
  22Q GAIN WILD-TYPE 805 105
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                95                910 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                14                105 
$`22Q GAIN MUTATED`
TCGA-5T-A9QA TCGA-A1-A0SK TCGA-A1-A0SP TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A0CL 
        0.39        31.79        19.20        22.06        64.04        64.57 
TCGA-A2-A0CX TCGA-A2-A0D2 TCGA-A2-A0T1 TCGA-A2-A1FV TCGA-A2-A1G1 TCGA-A7-A0CD 
       56.81        33.76        17.13        23.47        19.20        38.30 
TCGA-A7-A13F TCGA-A7-A6VV TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A079 TCGA-A8-A08B 
       12.72        10.29        10.42        13.02         9.01        38.01 
TCGA-A8-A08R TCGA-A8-A091 TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09X TCGA-AC-A23H 
        0.99        33.01        29.98        33.07        14.01         2.66 
TCGA-AC-A2QJ TCGA-AC-A3W5 TCGA-AC-A62V TCGA-AC-A8OQ TCGA-AN-A0AL TCGA-AN-A0AM 
        2.27        16.57         0.07         1.12         6.51         0.16 
TCGA-AN-A0AS TCGA-AN-A0FL TCGA-AN-A0FX TCGA-AN-A0XN TCGA-AO-A12B TCGA-AO-A12F 
        0.33         7.59         0.33         0.33        77.56        48.36 
TCGA-AO-A12G TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AR-A0TP TCGA-AR-A0TV TCGA-AR-A0U1 
       41.62       130.09         5.65       111.32        29.75       101.95 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A2LR TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WV 
       53.36        85.35        20.38       100.70       131.21        79.63 
TCGA-B6-A1KC TCGA-B6-A402 TCGA-BH-A0BG TCGA-BH-A0C0 TCGA-BH-A0DL TCGA-BH-A0E2 
       43.59        54.28        24.85        41.75        48.23        14.30 
TCGA-BH-A0HY TCGA-BH-A18Q TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EV TCGA-BH-A1FU 
       50.79        55.63        51.39        69.93        12.00        72.07 
TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 TCGA-C8-A12L TCGA-C8-A12O TCGA-C8-A12P 
        0.72        38.60        57.83        11.93        12.66        11.77 
TCGA-C8-A12W TCGA-C8-A1HG TCGA-D8-A142 TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JK 
       12.66        11.34        13.97        15.78        18.90        20.12 
TCGA-D8-A1XJ TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A27M TCGA-D8-A27W TCGA-E2-A14X 
       21.83        12.66        15.32        13.48        12.26        31.96 
TCGA-E2-A152 TCGA-E2-A1B0 TCGA-E9-A1NC TCGA-E9-A22B TCGA-E9-A243 TCGA-E9-A5UP 
       27.12        53.62        39.55        22.75        17.06        14.40 
TCGA-EW-A1OZ TCGA-EW-A424 TCGA-GI-A2C9 TCGA-GM-A2DF TCGA-GM-A3XL TCGA-LL-A5YM 
       40.41        10.59       109.87        42.71        69.30        15.32 
TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-PL-A8LV 
       14.79         3.88         5.59         6.21         0.23 

$`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       136.73        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        48.46        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        32.75        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        24.39        21.30        23.21        26.96 
TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ 
       21.14        21.90        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        53.06 
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 
       43.00        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        24.99 
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        28.96        33.01        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        33.01        93.04        43.00 
TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 
       40.01        30.97        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        50.04        49.05        45.07 
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        22.19         1.12        19.79        23.24        24.79 
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-A6NO TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 
        1.68         1.74         1.32         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-A0AR TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ 
        7.36         0.33         0.33         6.44         4.64         7.96 
TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW 
        7.00         7.17         6.28         6.02         0.33         0.36 
TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL 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-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        52.18        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        50.24 
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       108.72 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12H 
      106.78        96.10        90.58        64.04        57.30        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        32.52         2.56        32.91 
TCGA-AQ-A7U7 TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TW 
        9.99        49.32         5.26        74.79        86.66        98.93 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U2 TCGA-AR-A0U3 
       64.83        55.86        76.14        65.36        83.87       114.02 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL 
       85.97        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 
       37.81        76.21        61.28        63.62        62.14        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        96.89        78.51        84.20 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24W TCGA-AR-A24X 
        0.85       101.52        87.22        76.01        50.96        83.77 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 
       79.00        56.15        78.48        73.18        72.76        58.92 
TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL 
       93.83       128.65        20.25        62.86        42.87         7.36 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN 
       40.04        38.17        39.39        40.54        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-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-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-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-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 
      103.63        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-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-A0BT TCGA-BH-A0BV TCGA-BH-A0BW 
       27.19        53.69        53.95        45.57        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-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-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-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-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-A18V TCGA-BH-A1EO TCGA-BH-A1ES 
       37.55        66.05         7.36        51.16        91.99       113.82 
TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 
       82.85        42.28        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-A201 TCGA-BH-A204 TCGA-BH-A209 
       45.63        72.07       144.59         6.90        83.31       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-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12X 
       11.77        11.77         0.07        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-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK 
        3.75        12.33        10.92        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-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-A1JD TCGA-D8-A1JF 
       14.17        17.49        16.50        18.71        18.15        12.03 
TCGA-D8-A1JG 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-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-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-A1XU TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 
       12.99        15.16        16.54        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-A27R TCGA-D8-A27T 
        9.44        16.41         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-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-A14Y 
       33.17        33.30        43.33        34.26        32.02        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-A15E 
       14.79        25.05        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-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-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-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        30.61 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1N5 
       34.92        19.89        19.00         9.21        19.20        36.82 
TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1ND TCGA-E9-A1NE 
       13.48        12.00        13.12        36.56        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-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A244 TCGA-E9-A245 
       39.09        12.89        23.51        24.10         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        24.56         0.72        17.75 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X 
        0.76        26.07        18.41         0.62        15.72        12.33 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW 
        0.23        14.70         0.26        13.81        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-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-A1PB TCGA-EW-A1PC TCGA-EW-A1PD 
       30.08         7.86        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-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-GI-A2C8 
       25.91        22.09        21.27        17.49        10.16         7.40 
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-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV 
      110.50        38.20        43.73        66.38        72.03        13.55 
TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 
       18.12        11.84        11.57        21.24         6.67         4.08 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y 
        4.60         8.75         9.53        11.44        10.95         7.59 
TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Y 
       17.06        14.70        14.47        11.57         2.63         4.14 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
        4.50         4.50         3.22         7.36        27.91         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        31.99        58.62        27.65 
TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 
       34.92        36.36        16.87        24.72        22.32        20.38 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       26.70        23.47        65.62        33.57        31.07        26.04 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PL-A8LX TCGA-PL-A8LY 
        7.23        14.07        28.21        19.73         0.16         0.26 
TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 
        3.95        16.50         6.81         8.65        10.59         7.92 
TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-W8-A86G 
        5.56         8.52         7.17         6.87         3.91         5.29 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        9.60         9.14       100.01       105.04 

  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              22.82 
[1] "0.1 - 131.2 (20.1)" "0.0 - 234.3 (22.8)"
[1] "hr=" "1.4"
D39V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  22Q GAIN MUTATED         7        4        1        1        41        19
  22Q GAIN WILD-TYPE      76       76        8        4       301       215
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  22Q GAIN MUTATED           0         13          7          3        1
  22Q GAIN WILD-TYPE         2        129         22         60       17
                    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                 76
  STAGE IA                  4                 76
  STAGE IB                  1                  8
  STAGE II                  1                  4
  STAGE IIA                41                301
  STAGE IIB                19                215
  STAGE III                 0                  2
  STAGE IIIA               13                129
  STAGE IIIB                7                 22
  STAGE IIIC                3                 60
  STAGE IV                  1                 17
  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  64   9   7
  22Q GAIN WILD-TYPE 248 530 115  32
D39V4, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1               17                248
  T2               64                530
  T3                9                115
  T4                7                 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
  22Q GAIN MUTATED    52  27  10   4
  22Q GAIN WILD-TYPE 429 312 103  70
D39V5, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0               52                429
  N1               27                312
  N2               10                103
  N3                4                 70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  22Q GAIN MUTATED          0  84   1  12
  22Q GAIN WILD-TYPE        5 770  18 135
D39V6, multiclass
          clus
vv         22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CM0 (I+)                0                  5
  M0                     84                770
  M1                      1                 18
  MX                     12                135
[1] 4 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    96   1
  22Q GAIN WILD-TYPE 918  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     96    1
  22Q GAIN WILD-TYPE  918   10
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               96                918
  MALE                  1                 10
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  22Q GAIN MUTATED                            0                            80
  22Q GAIN WILD-TYPE                          1                           674
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  22Q GAIN MUTATED                                4                   1
  22Q GAIN WILD-TYPE                            171                   5
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  22Q GAIN MUTATED                                  2                  1
  22Q GAIN WILD-TYPE                               27                 14
                    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                  80                674
  INFILTRATING LOBULAR CARCINOMA                  4                171
  MEDULLARY CARCINOMA                             1                  5
  MIXED HISTOLOGY (PLEASE SPECIFY)                2                 27
  MUCINOUS CARCINOMA                              1                 14
  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  76
  22Q GAIN WILD-TYPE 261 667
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     21   76
  22Q GAIN WILD-TYPE  261  667
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                21                261
  YES               76                667
[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                          20    57
  22Q GAIN WILD-TYPE                       138   660
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                      20                138
  WHITE                                          57                660
[1] 4 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  82
  22Q GAIN WILD-TYPE  33 744
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      3   82
  22Q GAIN WILD-TYPE   33  744
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 33
  NOT HISPANIC OR LATINO               82                744
[1] 2 2
[1] FALSE

Clustering(40) Variable = XQ GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED   123  12
  XQ GAIN WILD-TYPE 763 107
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              135               870 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               12               107 
$`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 
       21.14        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 
       24.99         9.99        28.04        13.02        38.01        28.96 
TCGA-A8-A08F TCGA-A8-A08T TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 
       33.01        93.04        33.01        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 
       52.18        71.80       106.78        77.56        48.36        70.39 
TCGA-AR-A0TW TCGA-AR-A1AV TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24Z TCGA-AR-A254 
       98.93        61.28       101.52        87.22        79.00        72.76 
TCGA-AR-A255 TCGA-AR-A5QM TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0WZ TCGA-B6-A0X1 
       58.92        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-C8-A12L TCGA-C8-A12M TCGA-C8-A1HG TCGA-C8-A274 TCGA-C8-A275 
        0.72        11.93        11.77        11.34         0.03         0.03 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A1JD TCGA-D8-A1JT TCGA-D8-A1X5 TCGA-D8-A1XQ 
       13.97        14.17        18.15        13.32        18.58        16.41 
TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z6 TCGA-E2-A10B 
       12.66        15.32        12.53        12.26        18.51        37.51 
TCGA-E2-A14P TCGA-E2-A14S TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A15D 
       40.96        33.17        34.26        31.96        28.60        17.29 
TCGA-E2-A1B0 TCGA-E2-A56Z TCGA-E2-A9RU TCGA-E9-A1N6 TCGA-E9-A1RC TCGA-E9-A2JS 
       53.62         7.20         9.21        13.48        40.24        17.75 
TCGA-E9-A54X TCGA-E9-A5FL TCGA-EW-A1IY TCGA-EW-A1P5 TCGA-EW-A1PB TCGA-GI-A2C9 
       12.33         0.26         8.48        23.11        19.99       109.87 
TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-OL-A5S0 TCGA-OL-A66I TCGA-PL-A8LV TCGA-PL-A8LZ 
        2.63         4.14        20.38        23.47         0.23         3.95 
TCGA-S3-A6ZF TCGA-S3-AA0Z TCGA-Z7-A8R6 
       16.50        10.59       105.04 

$`XQ GAIN WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        0.39         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP 
       47.24        20.88        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-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       136.73        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-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D3 
        5.19        63.45        64.04        21.14        34.55        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-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-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 
       17.52        17.13        20.52        17.46        18.90        20.75 
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-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX 
       19.33        48.46        23.77        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-A25C TCGA-A2-A25D TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS 
       17.19        18.15        10.59        20.88        39.65        33.93 
TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XZ TCGA-A2-A3Y0 
       83.01        29.98        32.75        49.48        31.99        38.37 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S3 
        7.30        24.39        21.30        23.21        26.96        21.90 
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-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-A3IY 
       24.26        23.74        23.80        21.73        20.61        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB 
       10.59        11.28        13.41        11.97        14.93        13.74 
TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV 
       21.17        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-A06Q 
        9.37        10.42         8.75        13.02        13.02         1.02 
TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z 
       17.98        53.06        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        43.00        19.99        18.97        18.97 
TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07O TCGA-A8-A07S TCGA-A8-A082 TCGA-A8-A084 
       14.01        12.00         9.99         7.99        18.05        15.06 
TCGA-A8-A085 TCGA-A8-A08A TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L 
       36.95         0.99        19.96        12.00        37.05         9.99 
TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08X TCGA-A8-A08Z 
       31.00        31.00         0.99        33.01        43.00        40.01 
TCGA-A8-A092 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D 
       30.97         9.99         9.99        12.00         1.02        50.04 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R 
       49.05        45.07        29.98        33.07         1.02         8.98 
TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 
       19.04        15.02        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-A2BM TCGA-AC-A2FB 
        2.37        10.85         2.66         1.48        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-A3QP TCGA-AC-A3TN 
        0.92         2.27         0.99         0.69        22.19         1.12 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V 
       16.57        19.79        23.24        24.79         1.55         0.07 
TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OP 
        1.81         1.18         0.69         0.43         1.68         1.74 
TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 
        1.12         1.32         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-A0AL 
        2.96         1.78         1.71         8.02         7.36         6.51 
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-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-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-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U 
       80.28        47.84        84.69        68.75        47.87        59.05 
TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 
       29.13        21.40        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-A124 
       21.37        26.24        50.24        62.04        55.33       102.58 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12D TCGA-AO-A12E 
       99.25       108.72        96.10        90.58        64.04        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 
       32.52         2.56        32.91         9.99       111.32        49.32 
TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY 
        5.26        74.79        86.66        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       101.95        83.87       114.02        85.97 
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        37.81 
TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K 
       76.21        63.62        62.14        20.22       109.58        50.89 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24T 
       73.02        96.89        78.51        84.20         0.85        76.01 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A251 
       53.36        85.35        50.96        83.77        56.15        78.48 
TCGA-AR-A252 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK 
       73.18        93.83       128.65        20.25        62.86        42.87 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
        7.36        40.04        38.17        39.39        40.54        20.38 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I9 TCGA-B6-A0IA 
       16.04        20.45        10.59        77.62        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-A0WV TCGA-B6-A0WW 
      131.21       157.41        97.48       188.68        79.63        17.98 
TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
       21.47       113.79       129.70        28.27        68.94        58.88 
TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 
       43.59        73.51       139.17       170.17        85.35        54.28 
TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AZ 
       49.94       103.63        55.00        24.53        38.79        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-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-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ 
       27.19        53.95        45.57        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-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-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB 
       15.68        14.30        44.81        46.19        32.65        24.49 
TCGA-BH-A0EE TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       31.00        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-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX 
        2.50        13.61        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-A18P 
        7.23        20.12        90.84        26.66        72.56        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-A1ES TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY 
      113.82        42.28        12.00        55.69        49.58        17.69 
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-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-A42T 
       57.83       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-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-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-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 
        9.67         0.03        12.20         0.99         0.03         0.23 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A145 TCGA-D8-A146 
       11.90        20.88        13.25        20.58        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-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-A1JU TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA 
       14.70        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-A1XJ 
       18.15         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-A1XV TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 
        6.35        12.99        15.16        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-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-A3Z5 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A107 
       10.09        13.08        14.50         7.33        43.00        34.42 
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-A14O TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14T TCGA-E2-A14U 
       47.15        44.68        38.24        38.60        33.30        43.33 
TCGA-E2-A14W TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 
       32.02        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-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-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       14.07        14.99        60.53        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-A570 
        8.75        43.04        16.93         5.52        15.72        30.61 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 
       34.92        19.89        19.00        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        24.56         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        14.70 
TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ 
       13.81        14.40        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-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-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-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       10.16        10.59         7.40        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 
       43.73        69.30        66.38        72.03        13.55        18.12 
TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 
       11.84        11.57        21.24         6.67         4.08         4.60 
TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL 
        8.75         9.53        11.44        10.95         7.59        17.06 
TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FR 
       15.32        14.70        14.47        14.79        11.57         3.88 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 
        4.50         4.50         5.59         3.22         6.21         7.36 
TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 
       27.91         2.79         2.10        12.66        46.55        31.99 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY 
       58.62        27.65        34.92        36.36        16.87        24.72 
TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       22.32        26.70        65.62        33.57        31.07        26.04 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PL-A8LX TCGA-PL-A8LY 
        7.23        14.07        28.21        19.73         0.16         0.26 
TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 
        6.81         8.65         7.92         5.56         8.52         7.17 
TCGA-S3-AA15 TCGA-S3-AA17 TCGA-W8-A86G TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
        6.87         3.91         5.29         9.60         9.14       100.01 

  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 
            24.43             22.16 
[1] "0.0 - 186.5 (24.4)" "0.0 - 234.3 (22.2)"
[1] "hr=" "1.6"
D40V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XQ GAIN MUTATED         9        8        2        1        53        28
  XQ GAIN WILD-TYPE      74       72        7        4       289       206
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XQ GAIN MUTATED           0         17          5          9        5
  XQ GAIN WILD-TYPE         2        125         24         54       13
                   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                74
  STAGE IA                 8                72
  STAGE IB                 2                 7
  STAGE II                 1                 4
  STAGE IIA               53               289
  STAGE IIB               28               206
  STAGE III                0                 2
  STAGE IIIA              17               125
  STAGE IIIB               5                24
  STAGE IIIC               9                54
  STAGE IV                 5                13
  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  90  13   5
  XQ GAIN WILD-TYPE 236 504 111  34
D40V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1              29               236
  T2              90               504
  T3              13               111
  T4               5                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
  XQ GAIN MUTATED    68  40  17  11
  XQ GAIN WILD-TYPE 413 299  96  63
D40V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              68               413
  N1              40               299
  N2              17                96
  N3              11                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
  XQ GAIN MUTATED          0 117   5  15
  XQ GAIN WILD-TYPE        5 737  14 132
D40V6, multiclass
          clus
vv         XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CM0 (I+)               0                 5
  M0                   117               737
  M1                     5                14
  MX                    15               132
[1] 4 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   136   1
  XQ GAIN WILD-TYPE 878  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED    136    1
  XQ GAIN WILD-TYPE  878   10
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE             136               878
  MALE                 1                10
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  XQ GAIN MUTATED                            1                           116
  XQ GAIN WILD-TYPE                          0                           638
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  XQ GAIN MUTATED                                9                   2
  XQ GAIN WILD-TYPE                            166                   4
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  XQ GAIN MUTATED                                  1                  3
  XQ GAIN WILD-TYPE                               28                 12
                   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                116               638
  INFILTRATING LOBULAR CARCINOMA                 9               166
  MEDULLARY CARCINOMA                            2                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               1                28
  MUCINOUS CARCINOMA                             3                12
  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  91
  XQ GAIN WILD-TYPE 236 652
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     46   91
  XQ GAIN WILD-TYPE  236  652
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO               46               236
  YES              91               652
[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                          29    82
  XQ GAIN WILD-TYPE                       129   635
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                     29               129
  WHITE                                         82               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"
D40V12, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     3 103
  XQ GAIN WILD-TYPE  33 723
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      3  103
  XQ GAIN WILD-TYPE   33  723
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                33
  NOT HISPANIC OR LATINO             103               723
[1] 2 2
[1] FALSE

Clustering(41) Variable = 1P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED   192  37
  1P LOSS WILD-TYPE 694  82
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              229               776 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               37                82 
$`1P LOSS MUTATED`
TCGA-5T-A9QA TCGA-A1-A0SN TCGA-A2-A04R TCGA-A2-A0CS TCGA-A2-A0CW TCGA-A2-A0D4 
        0.39        39.32        82.16        75.55        64.04        25.22 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EQ TCGA-A2-A0ET TCGA-A2-A0EY TCGA-A2-A0SV 
       89.36        80.28        79.76        35.05        24.16        27.12 
TCGA-A2-A0T4 TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A1FW 
       20.52        18.21        15.42        21.90        21.67        17.36 
TCGA-A2-A1FX TCGA-A2-A25C TCGA-A2-A3KC TCGA-A2-A3XU TCGA-A2-A4S3 TCGA-A7-A0CJ 
       36.79        17.19        20.88        29.98        21.90        30.61 
TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A8-A06O TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Y 
       14.73        12.10        13.02        53.06        29.03        26.01 
TCGA-A8-A075 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07R 
       17.03         9.01        43.00        18.97        18.97         8.98 
TCGA-A8-A084 TCGA-A8-A08B TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A092 
       15.06        38.01        37.05        31.00        33.01        30.97 
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        50.04        49.05 
TCGA-A8-A09I TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09X TCGA-A8-A0A2 TCGA-A8-A0A6 
       45.07         1.02        25.02        14.01        19.04        21.04 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-AC-A23E TCGA-AC-A2BK TCGA-AC-A2FM TCGA-AC-A3BB 
       13.02        17.03         2.37        38.53        26.04         0.99 
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-A0AL TCGA-AN-A0AR TCGA-AN-A0FD TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0XP 
        6.51         0.33         6.44         7.00         7.17         0.30 
TCGA-AN-A0XS TCGA-AN-A0XU TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A0J5 
        0.33         0.33        80.28        66.77        84.69        24.16 
TCGA-AO-A0J7 TCGA-AO-A0JA TCGA-AO-A0JI TCGA-AO-A12A TCGA-AO-A1KP TCGA-AO-A1KQ 
       20.32        21.53        50.24        90.58        82.62        61.87 
TCGA-AO-A1KS TCGA-AQ-A0Y5 TCGA-AR-A0TQ TCGA-AR-A0U2 TCGA-AR-A1AP TCGA-AR-A1AW 
        0.53         5.65        49.32        83.87        39.98        63.62 
TCGA-AR-A24H TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A250 TCGA-AR-A254 TCGA-AR-A2LK 
      109.58        87.22        76.01        56.15        72.76        42.87 
TCGA-AR-A2LO TCGA-AR-A5QN TCGA-B6-A0I9 TCGA-B6-A0IB TCGA-B6-A0IG TCGA-B6-A0IJ 
       39.39        16.04        12.13       129.57       146.50       176.98 
TCGA-B6-A0IO TCGA-B6-A0RE TCGA-B6-A0RL TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RS 
      110.14       211.56        81.17       162.05       102.77       100.70 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A1KF TCGA-B6-A1KI 
       79.63        17.98        21.47       113.79       101.52        73.51 
TCGA-B6-A1KN TCGA-B6-A40B TCGA-BH-A0B2 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0BA 
      139.17       103.63        40.83        48.36        56.94        37.22 
TCGA-BH-A0BV TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0E2 TCGA-BH-A0E9 TCGA-BH-A0EB 
       49.94        41.75        44.02        14.30        46.19        24.49 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H7 TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0W3 
       30.35        10.78        23.08        12.89        51.32        23.93 
TCGA-BH-A18F TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18P TCGA-BH-A18T TCGA-BH-A18U 
        8.81        90.84        26.66        30.28         7.36        51.39 
TCGA-BH-A1EN TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1F8 TCGA-BH-A1FC TCGA-BH-A1FE 
       69.93        42.28        12.00        24.66       114.15        74.73 
TCGA-BH-A1FM TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A42T TCGA-C8-A12P TCGA-C8-A12W 
       45.63        83.31       130.16         0.99        11.77        12.66 
TCGA-C8-A131 TCGA-C8-A138 TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A26X TCGA-C8-A26Z 
        1.78         3.75        12.03        10.42         0.36         8.28 
TCGA-C8-A274 TCGA-C8-A27A TCGA-C8-A3M7 TCGA-D8-A142 TCGA-D8-A146 TCGA-D8-A1JE 
        0.03        12.20         0.03        13.97        21.14        18.90 
TCGA-D8-A1JF TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JM TCGA-D8-A1XF TCGA-D8-A1XG 
       12.03        18.97        20.09        19.40        15.22        14.73 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XZ 
       16.41        15.85        16.31        12.99        15.16        15.32 
TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27I TCGA-D8-A27T TCGA-D8-A27W TCGA-E2-A107 
        3.81        14.14        14.43        13.08        12.26        34.42 
TCGA-E2-A10E TCGA-E2-A14O TCGA-E2-A14V TCGA-E2-A15R TCGA-E2-A1IH TCGA-E2-A1LG 
       28.44        44.68        34.26        17.06        33.73        18.87 
TCGA-E2-A2P5 TCGA-E2-A576 TCGA-E9-A1NA TCGA-E9-A1ND TCGA-E9-A1NI TCGA-E9-A1R3 
       16.93        19.00        36.56        12.59         9.86         2.10 
TCGA-E9-A1R5 TCGA-E9-A1RC TCGA-E9-A1RG TCGA-E9-A22A TCGA-E9-A22E TCGA-E9-A244 
        1.38        40.24        21.27        39.09        12.89         0.69 
TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A54Y TCGA-E9-A5FK 
       27.22         0.95         0.72        17.75         0.23        14.70 
TCGA-E9-A5UP TCGA-EW-A1J6 TCGA-EW-A1OY TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1PC 
       14.40        28.77        29.85        52.96        23.11         6.15 
TCGA-EW-A1PE TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A2FW TCGA-GI-A2C8 
       10.52        19.96        55.00        25.91        22.09         7.40 
TCGA-GM-A3NW TCGA-JL-A3YX TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A6FP TCGA-LL-A9Q3 
      110.50        11.57        17.06        15.32        11.57         7.36 
TCGA-OK-A5Q2 TCGA-OL-A5RZ TCGA-OL-A66K TCGA-OL-A66N TCGA-PL-A8LX TCGA-S3-A6ZF 
        2.10        22.32        33.57        26.04         0.16        16.50 
TCGA-Z7-A8R5 
      100.01 

$`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       136.73        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        48.46        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        32.75        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        24.39        21.30        23.21 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH 
       26.96        21.14        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-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W 
       17.03         9.99        10.98         7.99        24.99         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        28.96 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R 
       33.01        19.96        12.00         9.99        31.00         0.99 
TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 
       93.04        43.00        40.01        33.01        17.95        41.98 
TCGA-A8-A097 TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       12.00        29.98        33.07         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        22.19         1.12        16.57        19.79 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y 
       23.24        24.79         1.55         0.07         1.12         1.81 
TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OQ TCGA-AC-A8OR 
        1.18         0.69         0.43         1.68         1.12         1.32 
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-A0AS TCGA-AN-A0AT TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FS 
        0.33         0.33         4.64         7.96         7.59         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-A0XR TCGA-AN-A0XT TCGA-AN-A0XV 
        0.33         0.33        12.33         0.33         0.33         5.33 
TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U 
        5.59        47.84        81.63        68.75        47.87        59.05 
TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J6 TCGA-AO-A0J8 
       29.13        32.78        21.40        52.18        37.48        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF 
       53.03        50.70        50.86        72.00        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 
      108.72       106.78        96.10        77.56        64.04        57.30 
TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KR TCGA-AO-A1KT 
       48.36        41.62        28.37        14.73        70.39        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        32.52         2.56 
TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT 
       32.91         9.99       111.32         5.26        74.79        86.66 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 
       29.75        98.93        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 
      101.95       114.02        85.97        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-A1AU TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A1AY 
       17.23        37.81        76.21        61.28        62.14        20.22 
TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
       50.89        73.02        96.89        78.51        84.20         0.85 
TCGA-AR-A24Q TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
      101.52        53.36        85.35        50.96        83.77        79.00 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH 
       78.48        73.18        58.92        93.83       128.65        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ TCGA-AR-A2LR 
       62.86         7.36        40.04        38.17        40.54        20.38 
TCGA-AR-A5QM TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 
       54.74        20.45        10.59        77.62       143.38       149.59 
TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IK TCGA-B6-A0IM 
      220.90        50.70        65.72       112.37        18.77       126.12 
TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
       84.59       110.93       140.88        68.45       189.01       234.28 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV 
       78.02       172.96       140.48        89.46       131.21       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
       97.48       188.68       129.57       129.70       186.48        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 
       68.94        58.88        43.59       170.17        85.35        54.28 
TCGA-B6-A408 TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY 
       49.94        55.00        24.53        38.79        20.45        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B7 TCGA-BH-A0B9 
       28.50        46.95        39.55        39.16        56.98        51.68 
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-A0BW TCGA-BH-A0BZ TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD 
       45.57        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-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E6 TCGA-BH-A0E7 
       47.41        16.27         4.41        15.68         9.63        44.81 
TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       32.65        31.00        24.43        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-A0HX TCGA-BH-A0HY TCGA-BH-A0RX 
        2.50        13.61        36.85        27.25        50.79         5.59 
TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18I 
       24.95        42.35        44.81        23.05         2.01         7.23 
TCGA-BH-A18J TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S 
       20.12        72.56        37.74        55.63        37.55        66.05 
TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EW TCGA-BH-A1EX 
       51.16        91.99       113.82        82.85        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-A1FD TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN 
       33.17       122.89        36.92        63.35        55.00        72.07 
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-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V 
       11.77        11.77        12.66         0.07        12.66        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-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HM 
       12.33        10.92        11.34        11.34         0.16         2.30 
TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A275 
        3.25         0.30         0.23         0.43         9.67         0.03 
TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 
        0.03         0.99         0.23        11.90        20.88        13.25 
TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 
       20.58        14.17        13.48        19.20        14.17        17.49 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JG TCGA-D8-A1JH 
       16.50        18.71        15.78        18.15        12.03        14.01 
TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT 
       20.12        20.09        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-A1XJ TCGA-D8-A1XK 
       27.58        18.15         2.66        17.16        21.83        14.50 
TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XT TCGA-D8-A1XW TCGA-D8-A1XY 
       19.92        17.69         7.96         6.35        12.66        16.54 
TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H 
       15.52        14.24        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-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-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10F TCGA-E2-A14N 
       46.59        40.41        37.51        40.11        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-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-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-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 
       13.02        19.56        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-A1II TCGA-E2-A1IJ TCGA-E2-A1IK 
       38.30        37.41        32.78        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-A1LH 
       39.62        19.66        24.59        40.47        28.90       106.75 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z 
      102.61         8.75        43.04         5.52        15.72         7.20 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1N5 
       30.61        34.92        19.89         9.21        19.20        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-A1NG TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R6 
       21.57        11.90        14.30         0.62         6.12         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-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-A22B TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A245 TCGA-E9-A248 
       22.75        23.51        24.10        17.06         0.85         1.94 
TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
       24.56         0.76        26.07        18.41         0.62        15.72 
TCGA-E9-A54X TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
       12.33         0.26        13.81        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-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 
       25.94        22.82        29.95        40.41        41.13        39.78 
TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB 
       29.82        18.48        30.08         7.86        18.90        19.99 
TCGA-EW-A1PD TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FS TCGA-EW-A3E8 TCGA-EW-A3U0 
       13.94        14.43        34.55        52.73        21.27        17.49 
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-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-A3NY TCGA-GM-A3XG 
       90.84        76.64        77.33        53.36        38.20        43.73 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW 
       69.30        66.38        72.03        13.55        18.12        11.84 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 
       21.24         6.67         4.08         4.60         8.75         9.53 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP 
       11.44        10.95         7.59        14.70        14.47        14.79 
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-OL-A5D6 TCGA-OL-A5D7 
        3.22         6.21        27.91         2.79        12.66        46.55 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX 
       31.99        58.62        27.65        34.92        36.36        16.87 
TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66L 
       24.72        20.38        26.70        23.47        65.62        31.07 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PL-A8LV TCGA-PL-A8LY 
        7.23        14.07        28.21        19.73         0.23         0.26 
TCGA-PL-A8LZ TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 
        3.95         6.81         8.65        10.59         7.92         5.56 
TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-W8-A86G TCGA-XX-A899 
        8.52         7.17         6.87         3.91         5.29         9.60 
TCGA-XX-A89A TCGA-Z7-A8R6 
        9.14       105.04 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.03              0.03 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           211.56            234.28 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           21.270            23.225 
[1] "0.0 - 211.6 (21.3)" "0.0 - 234.3 (23.2)"
[1] "hr=" "1.4"
D41V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1P LOSS MUTATED        12       12        2        1        75        40
  1P LOSS WILD-TYPE      71       68        7        4       267       194
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1P LOSS MUTATED           1         42         17         19        7
  1P LOSS WILD-TYPE         1        100         12         44       11
                   vv
clus                STAGE TIS STAGE X
  1P LOSS MUTATED           0       5
  1P LOSS WILD-TYPE         1      11
D41V3, multiclass
            clus
vv           1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                 12                71
  STAGE IA                12                68
  STAGE IB                 2                 7
  STAGE II                 1                 4
  STAGE IIA               75               267
  STAGE IIB               40               194
  STAGE III                1                 1
  STAGE IIIA              42               100
  STAGE IIIB              17                12
  STAGE IIIC              19                44
  STAGE IV                 7                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
  1P LOSS MUTATED    48 135  27  22
  1P LOSS WILD-TYPE 217 459  97  17
D41V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1              48               217
  T2             135               459
  T3              27                97
  T4              22                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
  1P LOSS MUTATED    90  77  36  24
  1P LOSS WILD-TYPE 391 262  77  50
D41V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0              90               391
  N1              77               262
  N2              36                77
  N3              24                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
  1P LOSS MUTATED          0 195   7  31
  1P LOSS WILD-TYPE        5 659  12 116
D41V6, multiclass
          clus
vv         1P LOSS MUTATED 1P LOSS WILD-TYPE
  CM0 (I+)               0                 5
  M0                   195               659
  M1                     7                12
  MX                    31               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"
D41V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED   231   2
  1P LOSS WILD-TYPE 783   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED    231    2
  1P LOSS WILD-TYPE  783    9
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE             231               783
  MALE                 2                 9
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  1P LOSS MUTATED                            1                           174
  1P LOSS WILD-TYPE                          0                           580
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  1P LOSS MUTATED                               41                   2
  1P LOSS WILD-TYPE                            134                   4
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  1P LOSS MUTATED                                  5                  2
  1P LOSS WILD-TYPE                               24                 13
                   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                174               580
  INFILTRATING LOBULAR CARCINOMA                41               134
  MEDULLARY CARCINOMA                            2                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               5                24
  MUCINOUS CARCINOMA                             2                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"
D41V9, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    61 172
  1P LOSS WILD-TYPE 221 571
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     61  172
  1P LOSS WILD-TYPE  221  571
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO               61               221
  YES             172               571
[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                          33   152
  1P LOSS WILD-TYPE                       125   565
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                     33               125
  WHITE                                        152               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"
D41V12, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     6 178
  1P LOSS WILD-TYPE  30 648
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      6  178
  1P LOSS WILD-TYPE   30  648
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                30
  NOT HISPANIC OR LATINO             178               648
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    39   9
  1Q LOSS WILD-TYPE 847 110
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               48               957 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                9               110 
$`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        21.90 
TCGA-A8-A06U TCGA-A8-A079 TCGA-A8-A08J TCGA-A8-A08S TCGA-A8-A09N TCGA-AC-A3BB 
       29.03         9.01        37.05        33.01         1.02         0.99 
TCGA-AN-A04A TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0XS TCGA-AN-A0XU TCGA-AO-A03N 
        2.96         6.51         0.33         0.33         0.33        66.77 
TCGA-AO-A03P TCGA-AO-A1KP TCGA-AO-A1KS TCGA-AR-A0TQ TCGA-AR-A0U2 TCGA-AR-A24H 
       84.69        82.62         0.53        49.32        83.87       109.58 
TCGA-AR-A24T TCGA-B6-A0IG TCGA-B6-A0RL TCGA-BH-A0B6 TCGA-BH-A0BV TCGA-BH-A0E2 
       76.01       146.50        81.17        56.94        49.94        14.30 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0HW TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A204 
       30.35        10.78        51.32       114.15        74.73        83.31 
TCGA-BH-A42T TCGA-C8-A138 TCGA-C8-A27A TCGA-D8-A1XQ TCGA-D8-A1XU TCGA-D8-A1XZ 
        0.99         3.75        12.20        16.41        12.99        15.32 
TCGA-E2-A15R TCGA-E9-A1ND TCGA-E9-A1RC TCGA-E9-A247 TCGA-EW-A1J6 TCGA-OL-A5RZ 
       17.06        12.59        40.24        27.22        28.77        22.32 

$`1Q LOSS WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        0.39         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN 
       47.24        20.88        13.68        31.79         7.96        39.32 
TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q 
       28.01        19.20        18.21       104.81        18.02        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-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
       36.13       136.73        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-A0CV 
       88.60       107.93        75.55        75.25         5.19        63.45 
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-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-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX 
       24.16        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-A0YG 
       17.46        18.90        20.75        32.55        25.28        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        48.46        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-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        32.75        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        24.39        21.30        23.21        26.96 
TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ 
       21.14        38.30        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-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-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW 
       14.50        21.17        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-A06O 
       11.05        10.29         9.37        10.42         8.75        13.02 
TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06X TCGA-A8-A06Y 
       13.02         1.02        17.98        53.06        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        43.00        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        24.99         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        38.01        28.96 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P 
       33.01        19.96        12.00         9.99        31.00        31.00 
TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 
        0.99        93.04        43.00        40.01        33.01        30.97 
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        50.04        49.05        45.07        29.98        33.07 
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-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ 
       38.79        26.04        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        22.19         1.12        16.57        19.79 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y 
       23.24        24.79         1.55         0.07         1.12         1.81 
TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OQ 
        1.18         0.69         0.43         1.68         1.74         1.12 
TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 
        1.32         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        52.18        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        50.24        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       108.72       106.78        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        32.52         2.56        32.91 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV 
        9.99       111.32         5.26        74.79        86.66        29.75 
TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 
       98.93        64.83        55.86        76.14        65.36       101.95 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK 
      114.02        85.97        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        37.81        76.21        61.28        63.62        62.14 
TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       20.22        50.89        73.02        96.89        78.51        84.20 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W 
        0.85       101.52        87.22        53.36        85.35        50.96 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 
       83.77        79.00        56.15        78.48        73.18        72.76 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK 
       58.92        93.83       128.65        20.25        62.86        42.87 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
        7.36        40.04        38.17        39.39        40.54        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       103.63 
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-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N4 
       30.61        34.92        19.89        19.00         9.21        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-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-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG 
       32.09        20.81         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-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
        0.69         0.85         1.94         0.95        24.56         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-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP 
       12.33         0.23        14.70         0.26        13.81        14.40 
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-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-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-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        43.73        69.30        66.38        72.03        13.55 
TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 
       18.12        11.84        11.57        21.24         6.67         4.08 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y 
        4.60         8.75         9.53        11.44        10.95         7.59 
TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP 
       17.06        15.32        14.70        14.47        14.79        11.57 
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-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 
        3.22         6.21         7.36        27.91         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        31.99        58.62        27.65        34.92 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I 
       36.36        16.87        24.72        20.38        26.70        23.47 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P 
       65.62        33.57        31.07        26.04         7.23        14.07 
TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PL-A8LV TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ 
       28.21        19.73         0.23         0.16         0.26         3.95 
TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 
       16.50         6.81         8.65        10.59         7.92         5.56 
TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-W8-A86G TCGA-XX-A899 
        8.52         7.17         6.87         3.91         5.29         9.60 
TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        9.14       100.01       105.04 

  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 
            24.77             22.36 
[1] "0.3 - 146.5 (24.8)" "0.0 - 234.3 (22.4)"
[1] "hr=" "1.4"
D42V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1Q LOSS MUTATED         2        5        0        0        15        11
  1Q LOSS WILD-TYPE      81       75        9        5       327       223
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1Q LOSS MUTATED           0         10          2          3        1
  1Q LOSS WILD-TYPE         2        132         27         60       17
                   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                81
  STAGE IA                 5                75
  STAGE IB                 0                 9
  STAGE II                 0                 5
  STAGE IIA               15               327
  STAGE IIB               11               223
  STAGE III                0                 2
  STAGE IIIA              10               132
  STAGE IIIB               2                27
  STAGE IIIC               3                60
  STAGE IV                 1                17
  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    13  27   5   4
  1Q LOSS WILD-TYPE 252 567 119  35
D42V4, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1              13               252
  T2              27               567
  T3               5               119
  T4               4                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
  1Q LOSS MUTATED    16  19   9   5
  1Q LOSS WILD-TYPE 465 320 104  69
D42V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0              16               465
  N1              19               320
  N2               9               104
  N3               5                69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  1Q LOSS MUTATED          0  45   1   3
  1Q LOSS WILD-TYPE        5 809  18 144
D42V6, multiclass
          clus
vv         1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CM0 (I+)               0                 5
  M0                    45               809
  M1                     1                18
  MX                     3               144
[1] 4 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    49   0
  1Q LOSS WILD-TYPE 965  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     49    0
  1Q LOSS WILD-TYPE  965   11
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              49               965
  MALE                 0                11
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  1Q LOSS MUTATED                            0                            42
  1Q LOSS WILD-TYPE                          1                           712
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  1Q LOSS MUTATED                                5                   1
  1Q LOSS WILD-TYPE                            170                   5
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  1Q LOSS MUTATED                                  1                  0
  1Q LOSS WILD-TYPE                               28                 15
                   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                 42               712
  INFILTRATING LOBULAR CARCINOMA                 5               170
  MEDULLARY CARCINOMA                            1                 5
  MIXED HISTOLOGY (PLEASE SPECIFY)               1                28
  MUCINOUS CARCINOMA                             0                15
  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    15  34
  1Q LOSS WILD-TYPE 267 709
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     15   34
  1Q LOSS WILD-TYPE  267  709
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO               15               267
  YES              34               709
[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    31
  1Q LOSS WILD-TYPE                       149   686
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               149
  WHITE                                         31               686
[1] 4 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  36
  1Q LOSS WILD-TYPE  35 790
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1   36
  1Q LOSS WILD-TYPE   35  790
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                35
  NOT HISPANIC OR LATINO              36               790
[1] 2 2
[1] FALSE

Clustering(43) Variable = 2P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED   150  18
  2P LOSS WILD-TYPE 736 101
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
              168               837 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               18               101 
$`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        24.39 
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        43.00        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        38.01        33.01        37.05        31.00        33.01 
TCGA-A8-A092 TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09T 
       30.97        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        50.24 
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        32.91        76.14 
TCGA-AR-A0U3 TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AS TCGA-AR-A24H TCGA-AR-A24K 
      114.02        62.56        43.73        37.81       109.58        50.89 
TCGA-AR-A24R TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A2LK TCGA-B6-A0IH TCGA-B6-A0IJ 
       87.22        85.35        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-E9-A5UP TCGA-EW-A1J1 TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1OY 
        0.23        14.40        18.90        28.77        22.82        29.85 
TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PE TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A423 
       23.11         7.86        10.52        25.91        22.09        10.16 
TCGA-GI-A2C8 TCGA-LL-A6FR TCGA-LL-A73Y TCGA-PL-A8LX TCGA-S3-A6ZH TCGA-XX-A89A 
        7.40         3.88         4.14         0.16         8.65         9.14 

$`2P LOSS WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        0.39         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN 
       47.24        20.88        13.68        31.79         7.96        39.32 
TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q 
       28.01        19.20        18.21       104.81        18.02        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-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
       36.13       136.73        64.57        24.79       112.08        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 
       88.60       107.93         5.19        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-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EV TCGA-A2-A0EW 
      107.61        79.76        74.40        37.05        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-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-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL 
       15.42        21.90        14.50        18.61        19.33        48.46 
TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 
       31.73        23.77        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-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        32.75        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        21.30        23.21        26.96        21.14 
TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 
       21.90        38.30        34.29        35.47        30.61        37.45 
TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H 
       35.67        33.11        31.73        10.72        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-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-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-A06U TCGA-A8-A06X 
       13.02         1.02        17.98        53.06        29.03        31.00 
TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07I 
       17.03        53.98         9.01        19.99        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07Z 
       12.00        17.03         9.99         7.99        24.99        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        28.96 
TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08P 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 
       43.00        40.01        33.01        17.95        41.98        12.00 
TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K 
        9.99         9.99        50.04        49.05        45.07        29.98 
TCGA-A8-A09M TCGA-A8-A09R TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 
       33.07         8.98        15.02         0.99        14.01        12.00 
TCGA-A8-A0A4 TCGA-A8-A0A7 TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A23H 
       13.02         0.99        38.04         0.95        10.85         2.66 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2FB TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO 
        1.48        38.53        40.57        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 
       22.19         1.12        16.57        19.79        23.24        24.79 
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-A6NO TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A041 
        1.68         1.74         1.12         1.32         0.33         0.23 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AK 
        0.33         0.62         2.96         1.78         1.71         7.36 
TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR 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-A0FN TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0FY 
        7.96         7.17         6.28         0.33         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XU 
        0.33         0.33        12.33         0.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T 
        5.33         5.59        66.77        81.63        68.75        47.87 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       59.05        29.13        32.78        52.18        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-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       108.72       106.78        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-A1KR TCGA-AQ-A04H TCGA-AQ-A04J 
       14.73        82.62        61.87        70.39        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        32.52         2.56         9.99       111.32 
TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW 
       49.32         5.26        74.79        86.66        29.75        98.93 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U4 
       64.83        55.86        65.36       101.95        83.87        85.97 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AO 
       75.55        61.84        52.77        51.25        48.82        43.56 
TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       39.98        43.07        17.23        76.21        61.28        63.62 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       62.14        20.22        73.02        96.89        78.51        84.20 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A24Z 
        0.85       101.52        76.01        53.36        83.77        79.00 
TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
       56.15        78.48        73.18        72.76        58.92        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN 
      128.65        20.25        62.86         7.36        40.04        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP 
       39.39        40.54        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-A0IG TCGA-B6-A0IK TCGA-B6-A0IM 
      129.57        50.70        65.72       146.50        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-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-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-A1KF 
      129.70       186.48        28.27        68.94        58.88       101.52 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A40B TCGA-B6-A40C 
      139.17       170.17        85.35        54.28       103.63        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-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-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-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0DD 
       11.67        49.05        41.75        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-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-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 
       47.41        16.27        15.68         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-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       35.51        24.56        26.50        20.38         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 
       13.61        36.85         5.59        23.93        24.95        42.35 
TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18J TCGA-BH-A18K 
       44.81        23.05         8.81         2.01        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-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-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-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-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-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A130 TCGA-C8-A131 
       11.77         0.07        12.66        12.66         3.12         1.78 
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-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-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-A143 TCGA-D8-A145 
       11.90        20.88        13.25        20.58        14.17        13.48 
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-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JJ TCGA-D8-A1JK 
       18.90        12.03        12.03        14.01        20.09        20.12 
TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU 
       20.09        19.40        20.38        12.20        13.32        14.70 
TCGA-D8-A1X5 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XC TCGA-D8-A1XD 
       18.58        16.73        25.74        23.90         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-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XZ 
       16.41        16.31         6.35        12.99        12.66        15.32 
TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H 
       15.52        14.24        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-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 
       10.09        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-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-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 
       28.60        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-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-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-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-A573 TCGA-E2-A574 
        5.52        15.72         7.20        30.61        34.92        19.89 
TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA 
       19.00         9.21        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        24.56         0.72 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54X TCGA-E9-A5FK 
       17.75         0.76        18.41         0.62        12.33        14.70 
TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
        0.26        13.81        15.39        12.20        39.72         8.48 
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-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-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PF 
       30.08        18.90        19.99         6.15        13.94        14.43 
TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A3E8 TCGA-EW-A3U0 
       34.55        19.96        55.00        52.73        21.27        17.49 
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-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        43.73 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW 
       69.30        66.38        72.03        13.55        18.12        11.84 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF 
       11.57        21.24         6.67         4.08         4.60         8.75 
TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM 
        9.53        11.44        10.95         7.59        17.06        15.32 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Z 
       14.70        14.47        14.79        11.57         2.63         4.50 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
        4.50         5.59         3.22         6.21         7.36        27.91 
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        31.99        58.62 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       27.65        34.92        36.36        16.87        24.72        22.32 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L 
       20.38        26.70        23.47        65.62        33.57        31.07 
TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PL-A8LV 
       26.04         7.23        14.07        28.21        19.73         0.23 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA10 
        0.26         3.95        16.50         6.81        10.59         7.92 
TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-W8-A86G 
        5.56         8.52         7.17         6.87         3.91         5.29 
TCGA-XX-A899 TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        9.60       100.01       105.04 

  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 
           21.335            23.210 
[1] "0.0 - 177.0 (21.3)" "0.0 - 234.3 (23.2)"
[1] "hr=" "1.2"
D43V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2P LOSS MUTATED        11       11        0        1        54        36
  2P LOSS WILD-TYPE      72       69        9        4       288       198
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2P LOSS MUTATED           1         30          6         13        7
  2P LOSS WILD-TYPE         1        112         23         50       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                72
  STAGE IA                11                69
  STAGE IB                 0                 9
  STAGE II                 1                 4
  STAGE IIA               54               288
  STAGE IIB               36               198
  STAGE III                1                 1
  STAGE IIIA              30               112
  STAGE IIIB               6                23
  STAGE IIIC              13                50
  STAGE IV                 7                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    37 105  21   9
  2P LOSS WILD-TYPE 228 489 103  30
D43V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1              37               228
  T2             105               489
  T3              21               103
  T4               9                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
  2P LOSS MUTATED    76  51  28  16
  2P LOSS WILD-TYPE 405 288  85  58
D43V5, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0              76               405
  N1              51               288
  N2              28                85
  N3              16                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
  2P LOSS MUTATED          1 138   8  25
  2P LOSS WILD-TYPE        4 716  11 122
D43V6, multiclass
          clus
vv         2P LOSS MUTATED 2P LOSS WILD-TYPE
  CM0 (I+)               1                 4
  M0                   138               716
  M1                     8                11
  MX                    25               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"
D43V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED   170   2
  2P LOSS WILD-TYPE 844   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED    170    2
  2P LOSS WILD-TYPE  844    9
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE             170               844
  MALE                 2                 9
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  2P LOSS MUTATED                            0                           137
  2P LOSS WILD-TYPE                          1                           617
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  2P LOSS MUTATED                               20                   0
  2P LOSS WILD-TYPE                            155                   6
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  2P LOSS MUTATED                                  7                  2
  2P LOSS WILD-TYPE                               22                 13
                   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                137               617
  INFILTRATING LOBULAR CARCINOMA                20               155
  MEDULLARY CARCINOMA                            0                 6
  MIXED HISTOLOGY (PLEASE SPECIFY)               7                22
  MUCINOUS CARCINOMA                             2                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"
D43V9, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    60 112
  2P LOSS WILD-TYPE 222 631
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     60  112
  2P LOSS WILD-TYPE  222  631
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO               60               222
  YES             112               631
[1] 2 2
[1] FALSE
D43V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P LOSS MUTATED                                  0    11
  2P LOSS WILD-TYPE                                1    45
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED                          18   118
  2P LOSS WILD-TYPE                       140   599
D43V11, multiclass
                                  clus
vv                                 2P LOSS MUTATED 2P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         11                45
  BLACK OR AFRICAN AMERICAN                     18               140
  WHITE                                        118               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"
D43V12, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    10 121
  2P LOSS WILD-TYPE  26 705
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     10  121
  2P LOSS WILD-TYPE   26  705
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                  10                26
  NOT HISPANIC OR LATINO             121               705
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2Q LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED   172  24
  2Q LOSS WILD-TYPE 714  95
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
              196               809 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               24                95 
$`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        24.39 
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-A06Q TCGA-A8-A06T TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A07B TCGA-A8-A07F 
        1.02        53.06        26.01         1.02        43.00        18.97 
TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07W TCGA-A8-A08B TCGA-A8-A08F TCGA-A8-A08I 
       10.98         8.98         9.99        38.01        33.01        12.00 
TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08S TCGA-A8-A092 TCGA-A8-A09B TCGA-A8-A09C 
       37.05        31.00        33.01        30.97        12.00         1.02 
TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A0A2 TCGA-A8-A0A6 TCGA-A8-A0A9 
        1.02        25.02        19.04        19.04        21.04        13.02 
TCGA-A8-A0AB TCGA-AC-A23E TCGA-AC-A2BM TCGA-AC-A2FF TCGA-AC-A2FM TCGA-AC-A62V 
       17.03         2.37        38.20        55.43        26.04         0.07 
TCGA-AC-A6IW TCGA-AN-A03Y TCGA-AN-A0AJ TCGA-AN-A0AS TCGA-AN-A0FK TCGA-AN-A0FL 
        0.69         0.33         8.02         0.33         7.00         7.59 
TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FZ TCGA-AN-A0XP TCGA-AN-A0XT 
        6.02         0.36         0.33         0.33         0.30         0.33 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03P TCGA-AO-A0J3 TCGA-AO-A0JD TCGA-AO-A0JI 
       80.28        47.84        84.69        21.40        72.00        50.24 
TCGA-AO-A12A TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AQ-A54O 
       90.58         0.53        17.79         5.65         2.56        32.91 
TCGA-AR-A0TS TCGA-AR-A0TV TCGA-AR-A0U3 TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AS 
       74.79        29.75       114.02        62.56        43.73        37.81 
TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24R TCGA-AR-A24V TCGA-AR-A24W 
       20.22       109.58        50.89        87.22        85.35        50.96 
TCGA-AR-A2LK TCGA-B6-A0I9 TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0RL TCGA-B6-A0RU 
       42.87        12.13       112.37       176.98        81.17       131.21 
TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A408 TCGA-BH-A0B2 TCGA-BH-A0BA 
       43.59        73.51       139.17        49.94        40.83        37.22 
TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0C7 TCGA-BH-A0E0 TCGA-BH-A0E2 TCGA-BH-A0E6 
       45.57        49.94        42.90         4.41        14.30         9.63 
TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HU 
       24.49        31.00        23.08        41.00        52.96        12.89 
TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A18I TCGA-BH-A18Q TCGA-BH-A1ES TCGA-BH-A1EU 
       51.32        27.25         7.23        55.63       113.82        42.28 
TCGA-BH-A1EV TCGA-BH-A1F6 TCGA-BH-A1FC TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A202 
       12.00        97.48       114.15        45.63        72.07         0.72 
TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HK 
       12.66        12.66         3.75        10.92        11.34        12.03 
TCGA-C8-A26Z TCGA-C8-A3M7 TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A146 TCGA-D8-A1JI 
        8.28         0.03        20.88        13.97        21.14        18.97 
TCGA-D8-A1X6 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XJ TCGA-D8-A1XR TCGA-D8-A1XV 
       17.79        27.58        18.15        21.83        15.85        15.16 
TCGA-D8-A1XY TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27T TCGA-E2-A14O TCGA-E2-A14R 
       16.54         3.81        14.14        13.08        44.68        38.60 
TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15H 
       31.96        17.03        27.12        20.71        18.21        12.92 
TCGA-E2-A15S TCGA-E2-A1AZ TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IN 
       14.07        60.53        17.10        33.73        33.70        22.19 
TCGA-E2-A2P5 TCGA-E9-A1N4 TCGA-E9-A1N6 TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1R6 
       16.93        19.20        13.48        20.05         9.86         2.76 
TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A228 
       32.09        20.81        34.65        21.27        35.64        12.53 
TCGA-E9-A22G TCGA-E9-A249 TCGA-E9-A3HO TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5UP 
       23.51         0.95        26.07        15.72         0.23        14.40 
TCGA-EW-A1J1 TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1P5 TCGA-EW-A1P8 
       18.90        28.77        22.82        29.85        23.11         7.86 
TCGA-EW-A1PE TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A423 TCGA-GM-A2DF TCGA-GM-A4E0 
       10.52        25.91        22.09        10.16        42.71        72.03 
TCGA-LL-A6FR TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-OL-A5RZ TCGA-OL-A6VO TCGA-PL-A8LV 
        3.88         5.59         3.22        22.32        28.21         0.23 
TCGA-PL-A8LX TCGA-S3-A6ZH TCGA-S3-AA14 TCGA-XX-A89A 
        0.16         8.65         7.17         9.14 

$`2Q LOSS WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        0.39         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN 
       47.24        20.88        13.68        31.79         7.96        39.32 
TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q 
       28.01        19.20        18.21       104.81        18.02        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-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
       36.13       136.73        64.57        24.79       112.08        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 
       88.60       107.93         5.19        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-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EV TCGA-A2-A0EW 
      107.61        79.76        74.40        37.05        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-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-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL 
       15.42        21.90        14.50        18.61        19.33        48.46 
TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 
       31.73        23.77        23.47        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        32.75        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        21.30        23.21        26.96        21.14 
TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 
       21.90        38.30        34.29        35.47        30.61        37.45 
TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       35.67        33.11        31.73        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-A3RF TCGA-A7-A425 TCGA-A7-A426 
       11.34        10.59        10.29        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-A06R TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A076 
       13.02        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        24.99        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        28.96        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        43.00        40.01        33.01 
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        50.04 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09R TCGA-A8-A09V 
       49.05        45.07        29.98        33.07         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        22.19         1.12        16.57 
TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62X TCGA-AC-A62Y 
       19.79        23.24        24.79         1.55         1.12         1.81 
TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR 
        1.18         0.43         1.68         1.74         1.12         1.32 
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-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XR TCGA-AN-A0XS 
        0.33         0.33         0.33        12.33         0.33         0.33 
TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03R 
        0.33         5.33         5.59        66.77        81.63        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        52.18        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-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A0JL 
       50.86        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       108.72       106.78        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-A1KR TCGA-AQ-A04H TCGA-AQ-A04J 
       14.73        82.62        61.87        70.39        24.79        26.93 
TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ 
      130.09        15.62        32.52         9.99       111.32        49.32 
TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
        5.26        86.66        98.93        64.83        55.86        76.14 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
       65.36       101.95        83.87        85.97        75.55        61.84 
TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ 
       52.77        51.25        48.82        43.56        39.98        43.07 
TCGA-AR-A1AR TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24L 
       17.23        76.21        61.28        63.62        62.14        73.02 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24T 
       96.89        78.51        84.20         0.85       101.52        76.01 
TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 
       53.36        83.77        79.00        56.15        78.48        73.18 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       72.76        58.92        93.83       128.65        20.25        62.86 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
        7.36        40.04        38.17        39.39        40.54        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-A0IE TCGA-B6-A0IG 
      149.59       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-A0RV 
      162.05       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-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-A1KF TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A40B TCGA-B6-A40C 
      101.52       170.17        85.35        54.28       103.63        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-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-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-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0DD 
       11.67        49.05        41.75        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-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-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA 
       47.41        16.27        15.68        44.81        46.19        32.65 
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-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       24.56        26.50        20.38         5.85         2.50        13.61 
TCGA-BH-A0HQ TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 
       36.85        50.79         5.59        23.93        24.95        42.35 
TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18J TCGA-BH-A18K 
       44.81        23.05         8.81         2.01        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-A1EO TCGA-BH-A1ET 
        7.36        51.39        51.16        69.93        91.99        82.85 
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-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-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A203 
       63.35        55.00       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-A130 
       12.66        11.77         0.07        12.66        12.66         3.12 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE 
        1.78         1.45         0.69         0.62         3.85        12.33 
TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V 
       11.34         0.16        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-A3M8 TCGA-D8-A13Y TCGA-D8-A140 
        0.03        12.20         0.99         0.23        11.90        13.25 
TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 
       20.58        14.17        13.48        19.20        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-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM 
       12.03        14.01        20.09        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-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-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ 
       14.73        14.50        19.92        17.69         7.96        16.41 
TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y0 
       16.31         6.35        12.99        12.66        15.32        15.52 
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-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-A10C 
       34.42        27.52        46.59        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-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-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-A15F TCGA-E2-A15I TCGA-E2-A15J 
       23.34        22.82        17.29        21.63        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-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-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-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-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z 
      102.61         8.75        43.04         5.52        15.72         7.20 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N5 
       30.61        34.92        19.89        19.00         9.21        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-A1NG TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 
       21.57        11.90        14.30         0.62         2.10         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RF TCGA-E9-A1RH 
        1.38        21.21        40.24         0.66         6.58        34.59 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E 
       34.13         0.79        13.32        39.09        22.75        12.89 
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-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA 
       24.56         0.72        17.75         0.76        18.41         0.62 
TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW 
       12.33        14.70         0.26        13.81        15.39        12.20 
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-A1OV TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 
       25.94        29.95        40.41        41.13        39.78        52.96 
TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC 
       29.82        18.48        30.08        18.90        19.99         6.15 
TCGA-EW-A1PD TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS 
       13.94        14.43        34.55        19.96        55.00        52.73 
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-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-A3XL TCGA-GM-A3XN TCGA-GM-A5PV TCGA-GM-A5PX 
       38.20        43.73        69.30        66.38        13.55        18.12 
TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 
       11.84        11.57        21.24         6.67         4.08         4.60 
TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL 
        8.75         9.53        11.44        10.95         7.59        17.06 
TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ 
       15.32        14.70        14.47        14.79        11.57         2.63 
TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
        4.14         4.50         4.50         6.21         7.36        27.91 
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        31.99        58.62 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5S0 
       27.65        34.92        36.36        16.87        24.72        20.38 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       26.70        23.47        65.62        33.57        31.07        26.04 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF 
        7.23        14.07        19.73         0.26         3.95        16.50 
TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA15 
        6.81        10.59         7.92         5.56         8.52         6.87 
TCGA-S3-AA17 TCGA-W8-A86G TCGA-XX-A899 TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        3.91         5.29         9.60       100.01       105.04 

  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 
           21.205            23.240 
[1] "0.0 - 177.0 (21.2)" "0.0 - 234.3 (23.2)"
[1] "hr=" "1.3"
D44V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2Q LOSS MUTATED        13       13        0        2        63        39
  2Q LOSS WILD-TYPE      70       67        9        3       279       195
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2Q LOSS MUTATED           1         35          7         14        8
  2Q LOSS WILD-TYPE         1        107         22         49       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                 13                70
  STAGE IA                13                67
  STAGE IB                 0                 9
  STAGE II                 2                 3
  STAGE IIA               63               279
  STAGE IIB               39               195
  STAGE III                1                 1
  STAGE IIIA              35               107
  STAGE IIIB               7                22
  STAGE IIIC              14                49
  STAGE IV                 8                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    44 117  27  11
  2Q LOSS WILD-TYPE 221 477  97  28
D44V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1              44               221
  T2             117               477
  T3              27                97
  T4              11                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
  2Q LOSS MUTATED    88  60  32  17
  2Q LOSS WILD-TYPE 393 279  81  57
D44V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0              88               393
  N1              60               279
  N2              32                81
  N3              17                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
  2Q LOSS MUTATED          2 161   8  28
  2Q LOSS WILD-TYPE        3 693  11 119
D44V6, multiclass
          clus
vv         2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CM0 (I+)               2                 3
  M0                   161               693
  M1                     8                11
  MX                    28               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"
D44V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED   197   2
  2Q LOSS WILD-TYPE 817   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED    197    2
  2Q LOSS WILD-TYPE  817    9
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE             197               817
  MALE                 2                 9
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  2Q LOSS MUTATED                            0                           159
  2Q LOSS WILD-TYPE                          1                           595
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  2Q LOSS MUTATED                               21                   2
  2Q LOSS WILD-TYPE                            154                   4
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  2Q LOSS MUTATED                                  8                  2
  2Q LOSS WILD-TYPE                               21                 13
                   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                159               595
  INFILTRATING LOBULAR CARCINOMA                21               154
  MEDULLARY CARCINOMA                            2                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               8                21
  MUCINOUS CARCINOMA                             2                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"
D44V9, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    64 135
  2Q LOSS WILD-TYPE 218 608
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     64  135
  2Q LOSS WILD-TYPE  218  608
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO               64               218
  YES             135               608
[1] 2 2
[1] FALSE
D44V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q LOSS MUTATED                                  0    14
  2Q LOSS WILD-TYPE                                1    42
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED                          27   130
  2Q LOSS WILD-TYPE                       131   587
D44V11, multiclass
                                  clus
vv                                 2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         14                42
  BLACK OR AFRICAN AMERICAN                     27               131
  WHITE                                        130               587
[1] 4 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    11 142
  2Q LOSS WILD-TYPE  25 684
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     11  142
  2Q LOSS WILD-TYPE   25  684
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                  11                25
  NOT HISPANIC OR LATINO             142               684
[1] 2 2
[1] FALSE

Clustering(45) Variable = 3P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED   148  25
  3P LOSS WILD-TYPE 738  94
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              173               832 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               25                94 
$`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 
       26.96        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        33.07        38.53        50.70 
TCGA-AC-A3OD TCGA-AC-A8OQ TCGA-AN-A041 TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AR 
       14.83         1.12         0.23         1.78         1.71         0.33 
TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FT TCGA-AN-A0XU TCGA-AO-A03L TCGA-AO-A03M 
        7.96         7.59         6.02         0.33        80.28        47.84 
TCGA-AO-A03P TCGA-AO-A03T TCGA-AO-A0J3 TCGA-AO-A0JA TCGA-AO-A0JG TCGA-AO-A124 
       84.69        47.87        21.40        21.53        26.24       102.58 
TCGA-AO-A1KS TCGA-AQ-A04L TCGA-AR-A0TP TCGA-AR-A0TT TCGA-AR-A0TX TCGA-AR-A0U1 
        0.53       130.09       111.32        86.66        64.83       101.95 
TCGA-AR-A0U2 TCGA-AR-A1AH TCGA-AR-A1AQ TCGA-AR-A24T TCGA-AR-A251 TCGA-AR-A255 
       83.87        75.55        43.07        76.01        78.48        58.92 
TCGA-AR-A256 TCGA-AR-A2LO TCGA-B6-A0IB TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ 
       93.83        39.39       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-A135 TCGA-C8-A137 TCGA-C8-A1HF 
       57.83         0.99        11.93         0.62         3.85        10.92 
TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A26W TCGA-D8-A1J8 
       11.34         0.16        12.03         2.30         0.23        14.17 
TCGA-D8-A1J9 TCGA-D8-A1JD TCGA-D8-A1JG TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JM 
       17.49        18.15        12.03        20.09        20.12        19.40 
TCGA-D8-A1X5 TCGA-D8-A1XB TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XT 
       18.58        18.15        21.83        14.50        19.92         6.35 
TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A27M TCGA-D8-A27N 
       12.99        16.54        15.32         3.81        13.48         4.80 
TCGA-E2-A10C TCGA-E2-A14R TCGA-E2-A14V TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A159 
       40.11        38.60        34.26        25.41        27.12        25.05 
TCGA-E2-A15A TCGA-E2-A1II TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A1LE TCGA-E2-A574 
       23.34        33.70        20.98        27.42        28.90        19.89 
TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N8 TCGA-E9-A1NC TCGA-E9-A1NF TCGA-E9-A1R4 
       19.00         9.21        12.00        39.55        20.05         6.12 
TCGA-E9-A226 TCGA-E9-A229 TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A295 TCGA-E9-A2JS 
       34.13        13.32        23.51         0.69         0.72        17.75 
TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1PC TCGA-EW-A2FS TCGA-EW-A423 
       22.82        29.82        23.11         6.15        52.73        10.16 
TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2DB TCGA-GM-A2DH TCGA-JL-A3YX TCGA-LD-A7W5 
        7.40       109.87        53.13        42.28        11.57         4.08 
TCGA-LL-A5YL TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66K 
       17.06         3.22         6.21        24.72        20.38        33.57 
TCGA-OL-A66N TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-XX-A89A TCGA-Z7-A8R5 
       26.04         6.81         8.65         9.14       100.01 

$`3P LOSS WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        0.39         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
       47.24        20.88        13.68         7.96        39.32        28.01 
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-A0CM TCGA-A2-A0CO 
       64.04        55.43        36.13       136.73        24.79       112.08 
TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CV 
       92.48        88.60       107.93        75.55         5.19        63.45 
TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0ER 
       33.76        28.77       101.72        89.36       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-A0SV TCGA-A2-A0SW TCGA-A2-A0SX 
       24.16        99.19        54.64        27.12        44.88        50.43 
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-A0YF TCGA-A2-A0YG 
       18.90        20.75        32.55        25.28        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        48.46        31.73 
TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 
       23.47        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-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 
       29.98        32.75        49.48        34.98        31.99        38.37 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 
        7.30        24.39        21.30        23.21        21.14        21.90 
TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB 
       38.30        34.29        35.47        37.45        35.67        33.11 
TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26G 
       10.72        12.72        23.61        29.56        31.36        23.74 
TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 
       23.80        21.73        20.61        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-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T 
       10.29        13.02        13.02         1.02        17.98        53.06 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B 
       31.00        26.01        17.03        53.98         9.01        43.00 
TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P 
       19.99        18.97        14.01        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        24.99         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        38.01        28.96 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08P 
       33.01        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        33.01        93.04        43.00        40.01        33.01 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A 
       30.97        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        50.04        49.05        45.07        29.98 
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-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG 
        2.66         1.48        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        22.19         1.12        16.57        19.79        23.24 
TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV 
       24.79         1.55         0.07         1.12         1.81         1.18 
TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AN-A03X 
        0.69         0.43         1.68         1.74         1.32         0.33 
TCGA-AN-A03Y TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A0AJ TCGA-AN-A0AK 
        0.33         0.33         0.62         2.96         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-A0FN TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX 
        7.00         7.17         6.28         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-A0XV TCGA-AN-A0XW TCGA-AO-A03N 
        0.33         0.33         0.33         5.33         5.59        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        52.18 
TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JB 
       24.16        37.48        20.32        22.36        53.03        50.70 
TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JI TCGA-AO-A0JJ 
       50.86        72.00        76.77        21.37        50.24        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       108.72       106.78        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-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N 
       24.79        26.93         5.65        15.62        32.52         2.56 
TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TV 
       32.91         9.99        49.32         5.26        74.79        29.75 
TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U3 TCGA-AR-A0U4 
       98.93        55.86        76.14        65.36       114.02        85.97 
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-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
       43.56        39.98        17.23        37.81        76.21        61.28 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L 
       63.62        62.14        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 
       96.89        78.51        84.20         0.85       101.52        87.22 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 
       53.36        85.35        50.96        83.77        79.00        56.15 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK 
       73.18        72.76       128.65        20.25        62.86        42.87 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM 
        7.36        40.04        38.17        40.54        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-A0IK TCGA-B6-A0IM 
       12.13       220.90        50.70        65.72        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-A0WT TCGA-B6-A0WV TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 
      188.68        79.63        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-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       103.63        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-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BL TCGA-BH-A0BM 
       37.22        32.02        18.21        25.71        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-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE 
       49.94        41.75        48.13        42.90        45.83        31.17 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ 
       23.44        38.01        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-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-A0HB TCGA-BH-A0HI 
       35.51        24.56        23.08        41.00        26.50        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HX TCGA-BH-A0HY 
        5.85         2.50        13.61        36.85        27.25        50.79 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18G 
       23.93        24.95        42.35        44.81        23.05         2.01 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P 
        7.23        20.12        90.84        72.56        37.74        30.28 
TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EO 
       55.63        37.55        66.05        51.39        51.16        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-A1FB 
       17.69        25.81        31.53        89.16        97.48       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-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42U 
       83.31       130.16        10.65         6.44        20.12       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-A132 TCGA-C8-A134 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HI TCGA-C8-A1HL 
        1.45         0.69         3.75        12.33        11.34        10.42 
TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 
        3.25         0.30         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-A140 TCGA-D8-A141 TCGA-D8-A142 
        0.23        11.90        20.88        13.25        20.58        13.97 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1JA TCGA-D8-A1JB 
       14.17        13.48        21.14        19.20        16.50        18.71 
TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JL 
       15.78        18.90        12.03        14.01        18.97        20.09 
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-A1XF TCGA-D8-A1XG TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR 
       15.22        14.73        17.69         7.96        16.41        15.85 
TCGA-D8-A1XS TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A1Y3 
       16.31        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-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W 
       16.41         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-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-A14S TCGA-E2-A14T TCGA-E2-A14U 
       44.68        40.96        38.24        33.17        33.30        43.33 
TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A153 TCGA-E2-A154 
       32.02        31.96        28.60        17.03        23.24        19.43 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E 
       21.04        23.87        14.79        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-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-A1IN TCGA-E2-A1IU 
       33.73        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-A1LG 
       54.18        39.62        19.66        24.59        40.47        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        30.61        34.92        19.20        36.82 
TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG 
       13.48        13.12        36.56        12.59        35.77        21.57 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R5 
        9.86        11.90        14.30         0.62         2.10         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-A227 
       34.65         6.58        21.27        34.59        35.64         0.79 
TCGA-E9-A228 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 
       12.53        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-A2JT 
        0.85        27.22         1.94         0.95        24.56         0.76 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y 
       26.07        18.41         0.62        15.72        12.33         0.23 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW 
       14.70         0.26        13.81        14.40        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-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ 
       15.68        28.77        25.94        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-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-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 
       19.96        55.00        25.91        22.09        21.27        17.49 
TCGA-EW-A424 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF 
       10.59        59.57       194.27        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-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 
      110.50        38.20        43.73        69.30        66.38        72.03 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 
       13.55        18.12        11.84        21.24         6.67         4.60 
TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YM 
        8.75         9.53        11.44        10.95         7.59        15.32 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR 
       14.70        14.47        14.79        11.57         2.63         3.88 
TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A9Q3 TCGA-LQ-A4E4 
        4.14         4.50         4.50         5.59         7.36        27.91 
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        31.99        58.62 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RZ TCGA-OL-A66H 
       27.65        34.92        36.36        16.87        22.32        26.70 
TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO 
       23.47        65.62        31.07         7.23        14.07        28.21 
TCGA-OL-A6VQ TCGA-PL-A8LV TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF 
       19.73         0.23         0.16         0.26         3.95        16.50 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 
       10.59         7.92         5.56         8.52         7.17         6.87 
TCGA-S3-AA17 TCGA-W8-A86G TCGA-XX-A899 TCGA-Z7-A8R6 
        3.91         5.29         9.60       105.04 

  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 
            22.13             22.55 
[1] "0.2 - 177.0 (22.1)" "0.0 - 234.3 (22.5)"
[1] "hr=" "1.3"
D45V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3P LOSS MUTATED        10       13        1        0        62        50
  3P LOSS WILD-TYPE      73       67        8        5       280       184
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3P LOSS MUTATED           0         21          3         11        3
  3P LOSS WILD-TYPE         2        121         26         52       15
                   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                73
  STAGE IA                13                67
  STAGE IB                 1                 8
  STAGE II                 0                 5
  STAGE IIA               62               280
  STAGE IIB               50               184
  STAGE III                0                 2
  STAGE IIIA              21               121
  STAGE IIIB               3                26
  STAGE IIIC              11                52
  STAGE IV                 3                15
  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    29 124  20   3
  3P LOSS WILD-TYPE 236 470 104  36
D45V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1              29               236
  T2             124               470
  T3              20               104
  T4               3                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
  3P LOSS MUTATED    86  58  17  13
  3P LOSS WILD-TYPE 395 281  96  61
D45V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0              86               395
  N1              58               281
  N2              17                96
  N3              13                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
  3P LOSS MUTATED          0 141   3  32
  3P LOSS WILD-TYPE        5 713  16 115
D45V6, multiclass
          clus
vv         3P LOSS MUTATED 3P LOSS WILD-TYPE
  CM0 (I+)               0                 5
  M0                   141               713
  M1                     3                16
  MX                    32               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"
D45V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED   176   0
  3P LOSS WILD-TYPE 838  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED    176    0
  3P LOSS WILD-TYPE  838   11
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE             176               838
  MALE                 0                11
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  3P LOSS MUTATED                            0                           147
  3P LOSS WILD-TYPE                          1                           607
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  3P LOSS MUTATED                               18                   1
  3P LOSS WILD-TYPE                            157                   5
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  3P LOSS MUTATED                                  2                  0
  3P LOSS WILD-TYPE                               27                 15
                   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                147               607
  INFILTRATING LOBULAR CARCINOMA                18               157
  MEDULLARY CARCINOMA                            1                 5
  MIXED HISTOLOGY (PLEASE SPECIFY)               2                27
  MUCINOUS CARCINOMA                             0                15
  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    62 114
  3P LOSS WILD-TYPE 220 629
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     62  114
  3P LOSS WILD-TYPE  220  629
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               62               220
  YES             114               629
[1] 2 2
[1] FALSE
D45V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P LOSS MUTATED                                  0    14
  3P LOSS WILD-TYPE                                1    42
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED                          35   118
  3P LOSS WILD-TYPE                       123   599
D45V11, multiclass
                                  clus
vv                                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         14                42
  BLACK OR AFRICAN AMERICAN                     35               123
  WHITE                                        118               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"
D45V12, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     2 154
  3P LOSS WILD-TYPE  34 672
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      2  154
  3P LOSS WILD-TYPE   34  672
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                34
  NOT HISPANIC OR LATINO             154               672
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    82  15
  3Q LOSS WILD-TYPE 804 104
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               97               908 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               15               104 
$`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        26.96        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-AC-A8OQ TCGA-AN-A04C TCGA-AN-A0AR TCGA-AN-A0FJ TCGA-AN-A0FT TCGA-AN-A0XU 
        1.12         1.78         0.33         7.96         6.02         0.33 
TCGA-AO-A03P TCGA-AO-A0JA TCGA-AO-A124 TCGA-AO-A1KS TCGA-AR-A0TT TCGA-AR-A0U2 
       84.69        21.53       102.58         0.53        86.66        83.87 
TCGA-AR-A1AH TCGA-AR-A1AQ TCGA-AR-A251 TCGA-B6-A0IG TCGA-B6-A1KI TCGA-BH-A0B9 
       75.55        43.07        78.48       146.50        73.51        51.68 
TCGA-BH-A0BJ TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0HW TCGA-BH-A18F TCGA-BH-A18L 
       21.70        49.05        44.02        51.32         8.81        26.66 
TCGA-BH-A18T TCGA-BH-A1EN TCGA-BH-A1FM TCGA-BH-A1FU TCGA-BH-A208 TCGA-C8-A12L 
        7.36        69.93        45.63        72.07        57.83        11.93 
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-E2-A576 TCGA-E2-A9RU TCGA-E9-A1R4 TCGA-E9-A226 TCGA-E9-A22G 
       19.89        19.00         9.21         6.12        34.13        23.51 
TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A295 TCGA-EW-A1P5 TCGA-GI-A2C9 TCGA-JL-A3YX 
        0.69        27.22         0.72        23.11       109.87        11.57 
TCGA-LD-A7W5 TCGA-LL-A7T0 TCGA-OL-A66K TCGA-OL-A66N TCGA-S3-A6ZG TCGA-XX-A89A 
        4.08         3.22        33.57        26.04         6.81         9.14 
TCGA-Z7-A8R5 
      100.01 

$`3Q LOSS WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        0.39         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
       47.24        20.88        13.68         7.96        39.32        28.01 
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       136.73        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-A0CU TCGA-A2-A0CV TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM 
        5.19        63.45        21.14        33.76        28.77       101.72 
TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU 
       89.36       107.61        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-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-A0YH TCGA-A2-A0YI 
       32.55        25.28        15.42        21.90        21.67        14.50 
TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FW 
       18.61        19.33        48.46        31.73        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-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 
       32.75        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 
       24.39        21.30        23.21        21.14        21.90        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-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A3IY 
       31.36        23.74        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-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZV 
       14.93        13.74        14.50        21.17        14.73        12.10 
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-A06X TCGA-A8-A06Y 
       13.02         1.02        17.98        53.06        31.00        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        43.00        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-A082 TCGA-A8-A084 
        7.99        24.99         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        38.01        28.96        33.01 
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 
       33.01        93.04        43.00        40.01        33.01        30.97 
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        50.04        49.05        45.07        29.98        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-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-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 
        0.99         0.69        22.19         1.12        16.57        19.79 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y 
       23.24        24.79         1.55         0.07         1.12         1.81 
TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OR 
        1.18         0.69         0.43         1.68         1.74         1.32 
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-A0AS 
        1.71         8.02         7.36         6.51         0.16         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-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ 
        6.28         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-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        52.18        24.16        37.48        20.32        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF 
       53.03        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        50.24        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 
      108.72       106.78        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        32.52         2.56        32.91         9.99 
TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TV TCGA-AR-A0TW 
      111.32        49.32         5.26        74.79        29.75        98.93 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 
       64.83        55.86        76.14        65.36       101.95       114.02 
TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM 
       85.97        61.84        52.77        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        37.81        76.21 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K 
       61.28        63.62        62.14        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        96.89        78.51        84.20         0.85       101.52 
TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X 
       87.22        76.01        53.36        85.35        50.96        83.77 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
       79.00        56.15        73.18        72.76        58.92        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM 
      128.65        20.25        62.86        42.87         7.36        40.04 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN 
       38.17        39.39        40.54        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-A0IH TCGA-B6-A0IJ 
      220.90       129.57        50.70        65.72       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-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-A1KN TCGA-B6-A2IU 
       68.94        58.88        43.59       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       103.63        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-A0BA 
       39.55        39.16        48.36        56.94        56.98        37.22 
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-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD 
       49.94        11.67        41.75        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-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-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-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-A0HX TCGA-BH-A0HY 
        2.50        13.61        36.85        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-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-A18U TCGA-BH-A18V 
       30.28        55.63        37.55        66.05        51.39        51.16 
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-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-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-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-A137 
       12.66         3.12         1.78         1.45         0.69         3.85 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A1HN 
        3.75        12.33        11.34         0.16        10.42         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-A140 TCGA-D8-A141 TCGA-D8-A142 
        0.23        11.90        20.88        13.25        20.58        13.97 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1JA TCGA-D8-A1JB 
       14.17        13.48        21.14        19.20        16.50        18.71 
TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JK 
       15.78        18.90        12.03        14.01        18.97        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-A1XA 
       18.58        17.79        16.73        25.74        23.90        27.58 
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-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-A27K 
       17.42        16.04        13.45        13.05        14.43         9.44 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V 
       16.41        13.48         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-A14U 
       47.15        44.68        40.96        38.24        33.17        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-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-A15G TCGA-E2-A15H 
       22.82        17.29        20.71        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-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-A1IU TCGA-E2-A1L6 TCGA-E2-A1L8 
       22.65         3.88        22.19        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-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        30.61        34.92        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-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-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-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       35.64         0.79        12.53        13.32        39.09        22.75 
TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A245 TCGA-E9-A248 TCGA-E9-A249 
       12.89        24.10        17.06         0.85         1.94         0.95 
TCGA-E9-A24A TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA 
       24.56        17.75         0.76        26.07        18.41         0.62 
TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO 
       15.72        12.33         0.23        14.70         0.26        13.81 
TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
       14.40        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        43.73        69.30        66.38        72.03        13.55 
TCGA-GM-A5PX TCGA-JL-A3YW TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LD-A9QF 
       18.12        11.84        21.24         6.67         4.60         8.75 
TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM 
        9.53        11.44        10.95         7.59        17.06        15.32 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR 
       14.70        14.47        14.79        11.57         2.63         3.88 
TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-LL-A9Q3 
        4.14         4.50         4.50         5.59         6.21         7.36 
TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 
       27.91         2.79         2.10        12.66        46.55        31.99 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY 
       58.62        27.65        34.92        36.36        16.87        24.72 
TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66L 
       22.32        20.38        26.70        23.47        65.62        31.07 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PL-A8LV TCGA-PL-A8LX 
        7.23        14.07        28.21        19.73         0.23         0.16 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 
        0.26         3.95        16.50         8.65        10.59         7.92 
TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-W8-A86G 
        5.56         8.52         7.17         6.87         3.91         5.29 
TCGA-XX-A899 TCGA-Z7-A8R6 
        9.60       105.04 

  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 
           22.320            22.405 
[1] "0.3 - 146.5 (22.3)" "0.0 - 234.3 (22.4)"
[1] "hr=" "1.5"
D46V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3Q LOSS MUTATED         2        9        0        0        37        28
  3Q LOSS WILD-TYPE      81       71        9        5       305       206
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3Q LOSS MUTATED           0         14          1          5        2
  3Q LOSS WILD-TYPE         2        128         28         58       16
                   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                81
  STAGE IA                 9                71
  STAGE IB                 0                 9
  STAGE II                 0                 5
  STAGE IIA               37               305
  STAGE IIB               28               206
  STAGE III                0                 2
  STAGE IIIA              14               128
  STAGE IIIB               1                28
  STAGE IIIC               5                58
  STAGE IV                 2                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
  3Q LOSS MUTATED    13  75   9   1
  3Q LOSS WILD-TYPE 252 519 115  38
D46V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1              13               252
  T2              75               519
  T3               9               115
  T4               1                38
[1] 4 2
[1] 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    48  31  12   6
  3Q LOSS WILD-TYPE 433 308 101  68
D46V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0              48               433
  N1              31               308
  N2              12               101
  N3               6                68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  3Q LOSS MUTATED          0  82   2  14
  3Q LOSS WILD-TYPE        5 772  17 133
D46V6, multiclass
          clus
vv         3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CM0 (I+)               0                 5
  M0                    82               772
  M1                     2                17
  MX                    14               133
[1] 4 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    98   0
  3Q LOSS WILD-TYPE 916  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     98    0
  3Q LOSS WILD-TYPE  916   11
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              98               916
  MALE                 0                11
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  3Q LOSS MUTATED                            0                            83
  3Q LOSS WILD-TYPE                          1                           671
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  3Q LOSS MUTATED                               11                   0
  3Q LOSS WILD-TYPE                            164                   6
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  3Q LOSS MUTATED                                  0                  0
  3Q LOSS WILD-TYPE                               29                 15
                   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                 83               671
  INFILTRATING LOBULAR CARCINOMA                11               164
  MEDULLARY CARCINOMA                            0                 6
  MIXED HISTOLOGY (PLEASE SPECIFY)               0                29
  MUCINOUS CARCINOMA                             0                15
  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  62
  3Q LOSS WILD-TYPE 246 681
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     36   62
  3Q LOSS WILD-TYPE  246  681
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO               36               246
  YES              62               681
[1] 2 2
[1] FALSE
D46V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q LOSS MUTATED                                  0     9
  3Q LOSS WILD-TYPE                                1    47
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED                          17    66
  3Q LOSS WILD-TYPE                       141   651
D46V11, multiclass
                                  clus
vv                                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          9                47
  BLACK OR AFRICAN AMERICAN                     17               141
  WHITE                                         66               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"
D46V12, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     0  88
  3Q LOSS WILD-TYPE  36 738
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0   88
  3Q LOSS WILD-TYPE   36  738
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                36
  NOT HISPANIC OR LATINO              88               738
[1] 2 2
[1] FALSE

Clustering(47) Variable = 4P LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED   283  46
  4P LOSS WILD-TYPE 603  73
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              329               676 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               46                73 
$`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        24.39        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        53.06        31.00        26.01        43.00 
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        38.01        33.01 
TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A092 TCGA-A8-A09C 
       12.00         9.99         0.99        43.00        30.97         1.02 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09X TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A2BK 
       49.05        45.07        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-AC-A8OQ TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A 
        0.69         1.12         0.23         0.33         0.62         2.96 
TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT 
        1.71         8.02         0.16         0.33         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW 
        6.44         7.96         7.00         6.02         0.33         0.36 
TCGA-AN-A0FX TCGA-AN-A0XN 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-A0XW TCGA-AO-A03N TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 
        0.33         5.59        66.77        32.78        21.40        52.18 
TCGA-AO-A0J7 TCGA-AO-A0JE TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A129 TCGA-AO-A12A 
       20.32        76.77        71.80       102.58        96.10        90.58 
TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04J 
       64.04        48.36        61.87         0.53        17.79        26.93 
TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TY TCGA-AR-A0U0 
      130.09         5.65       111.32         5.26        55.86        65.36 
TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AM TCGA-AR-A1AN 
      101.95       114.02        75.55        61.84        62.56        43.73 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24O 
       43.07        17.23        20.22       109.58        50.89        84.20 
TCGA-AR-A24Q TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A251 TCGA-AR-A255 TCGA-AR-A256 
      101.52        85.35        50.96        78.48        58.92        93.83 
TCGA-AR-A2LO TCGA-AR-A5QN TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0IA TCGA-B6-A0IB 
       39.39        16.04        10.59        77.62       220.90       129.57 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IN TCGA-B6-A0IO 
      146.50       112.37       176.98        18.77        84.59       110.14 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RL TCGA-B6-A0RS TCGA-B6-A0RU 
      140.88       211.56       189.01        81.17       100.70       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-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-BH-A0AW TCGA-BH-A0B0 TCGA-BH-A0B3 
       54.28        49.94       103.63        20.45        46.95        39.55 
TCGA-BH-A0B5 TCGA-BH-A0BA TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL 
       48.36        37.22        25.71        24.85        21.70        44.05 
TCGA-BH-A0BP TCGA-BH-A0BR TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0C0 TCGA-BH-A0C1 
       48.69        53.69        45.57        49.94        41.75        44.02 
TCGA-BH-A0C7 TCGA-BH-A0DX TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EB 
       42.90        47.41         4.41         9.63        46.19        24.49 
TCGA-BH-A0H7 TCGA-BH-A0HI TCGA-BH-A0HU TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 
       23.08        20.38        12.89        50.79         5.59        23.93 
TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V 
       23.05         8.81        55.63         7.36        51.39        51.16 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1F0 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FD 
       42.28        12.00        25.81        97.48        24.66        33.17 
TCGA-BH-A1FU TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A209 TCGA-C8-A12L TCGA-C8-A12P 
       72.07        38.60        57.83       130.16        11.93        11.77 
TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM 
        0.62         3.75         0.16        12.03        10.42         2.30 
TCGA-C8-A26Y TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B TCGA-D8-A13Y TCGA-D8-A13Z 
        0.43         0.03         0.03         0.99        11.90        20.88 
TCGA-D8-A142 TCGA-D8-A147 TCGA-D8-A1JA TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JJ 
       13.97        19.20        16.50        18.90        12.03        20.09 
TCGA-D8-A1JK TCGA-D8-A1JM TCGA-D8-A1XA TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ 
       20.12        19.40        27.58        15.22        14.73        21.83 
TCGA-D8-A1XK TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1Y3 
       14.50         7.96        15.85        12.99        12.66        14.14 
TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27T TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P 
       16.04        13.05        13.08        47.15        44.68        40.96 
TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A154 TCGA-E2-A158 
       38.24        38.60        17.03        25.41        19.43        14.79 
TCGA-E2-A159 TCGA-E2-A15H TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1BD TCGA-E2-A1IH 
       25.05        12.92        60.53        53.62        17.10        33.73 
TCGA-E2-A1II TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI 
       33.70        27.42        39.62        18.87       106.75       102.61 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1NC 
       34.92        19.89         9.21        13.48        12.00        39.55 
TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1R3 TCGA-E9-A1R7 TCGA-E9-A1RA 
       12.59        20.05         9.86         2.10        21.21        32.09 
TCGA-E9-A1RB TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A249 
       20.81        12.89        23.51         0.69         1.94         0.95 
TCGA-E9-A3HO TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-EW-A1IX 
       26.07        15.72         0.23        14.70         0.26        39.72 
TCGA-EW-A1J1 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P5 
       18.90        25.94        22.82        29.85        40.41        23.11 
TCGA-EW-A1P8 TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A2FR TCGA-EW-A3U0 
        7.86         6.15        13.94        10.52        55.00        17.49 
TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2DB TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI 
        7.40       109.87        53.13        42.71        42.28        61.91 
TCGA-GM-A2DL TCGA-GM-A3XL TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LL-A441 TCGA-LL-A5YM 
       90.84        69.30        11.84        11.57        11.44        15.32 
TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Z TCGA-LL-A8F5 TCGA-OL-A5D7 TCGA-OL-A5RW 
       14.79         3.88         4.50         6.21        46.55        36.36 
TCGA-OL-A5S0 TCGA-OL-A66I TCGA-OL-A66K TCGA-OL-A6VO TCGA-PL-A8LV TCGA-PL-A8LX 
       20.38        23.47        33.57        28.21         0.23         0.16 
TCGA-PL-A8LZ TCGA-S3-A6ZH TCGA-S3-AA10 TCGA-S3-AA14 TCGA-S3-AA17 
        3.95         8.65         7.92         7.17         3.91 

$`4P LOSS WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        0.39         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N 
       47.24        13.68         7.96        19.20        18.21       104.81 
TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W 
       41.95        82.16        73.84        22.06        63.12        64.04 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
       55.43        36.13       136.73       112.08        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D2 
      107.93        75.25         5.19        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-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-A0T0 TCGA-A2-A0T2 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       44.28        17.52         8.38        20.52        17.46        18.90 
TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YI TCGA-A2-A0YK 
       32.55        25.28        15.42        21.90        14.50        19.33 
TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ 
       48.46        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-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-A3Y0 TCGA-A2-A4RY 
       32.75        49.48        38.40        34.98        38.37        21.30 
TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CG 
       23.21        26.96        21.14        21.90        38.30        34.29 
TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       35.47        37.45        33.11        23.61        29.56        31.36 
TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 
       24.26        23.80        20.61        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-A4SF TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A8-A06O TCGA-A8-A06P 
       21.17        17.92        10.72        11.05        13.02        13.02 
TCGA-A8-A06R TCGA-A8-A06U TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 
       17.98        29.03         1.02        17.03        53.98         9.01 
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-A07P TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 
       10.98         7.99        24.99         9.99        28.04        18.05 
TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08O 
       13.02         0.99        28.96        19.96        37.05        31.00 
TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A093 
       31.00        33.01        93.04        40.01        33.01        17.95 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09D 
       41.98        12.00         9.99         9.99        12.00        50.04 
TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T 
       29.98        33.07         1.02        25.02         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-A23G TCGA-AC-A23H 
        0.99        13.02        17.03        38.04        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-A2QJ TCGA-AC-A3HN TCGA-AC-A3OD 
       26.04        50.70         1.02         2.27         0.69        14.83 
TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ 
       22.19         1.12        16.57        19.79        23.24        24.79 
TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AN-A03X 
        1.18         0.43         1.68         1.74         1.32         0.33 
TCGA-AN-A03Y TCGA-AN-A04C TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0FF TCGA-AN-A0FL 
        0.33         1.78         7.36         6.51         4.64         7.59 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XR 
        7.17         6.28         0.33         0.33         0.33         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-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 
       47.87        59.05        29.13        24.16        37.48        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JF 
       53.03        21.53        50.70        50.86        72.00        21.37 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A125 TCGA-AO-A126 
       26.24        50.24        62.04        55.33        99.25       108.72 
TCGA-AO-A128 TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
      106.78        77.56        57.30        41.62        28.37        14.73 
TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AQ-A04H TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N 
       82.62        70.39        24.79        15.62        32.52         2.56 
TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV 
       32.91         9.99        49.32        74.79        86.66        29.75 
TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TZ TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AJ 
       98.93        64.83        76.14        83.87        85.97        52.77 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AU 
       51.25        48.82        43.56        39.98        37.81        76.21 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       61.28        63.62        62.14        73.02        96.89        78.51 
TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A24Z 
        0.85        87.22        76.01        53.36        83.77        79.00 
TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       56.15        73.18        72.76       128.65        20.25        62.86 
TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ TCGA-AR-A2LR 
       42.87         7.36        40.04        38.17        40.54        20.38 
TCGA-AR-A5QM TCGA-AR-A5QP TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IC 
       54.74        20.45       143.38       149.59        12.13        50.70 
TCGA-B6-A0IE TCGA-B6-A0IM TCGA-B6-A0IP TCGA-B6-A0RG TCGA-B6-A0RI TCGA-B6-A0RM 
       65.72       126.12       110.93        68.45       234.28        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV 
      172.96       162.05       102.77       140.48        89.46       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 
       97.48       188.68        17.98       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-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B2 
       55.00        24.53        38.79        25.55        28.50        40.83 
TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD 
       39.16        56.94        56.98        51.68        32.02        18.21 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BW TCGA-BH-A0BZ 
       61.68        35.67        27.19        53.95        11.67        49.05 
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-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 
       38.47        45.17        16.27        15.68        14.30        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-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB 
       37.78        35.51        24.56        41.00        52.96        26.50 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HW TCGA-BH-A0HX 
        5.85         2.50        13.61        36.85        51.32        27.25 
TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J 
       24.95        42.35        44.81         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-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EW 
       66.05        69.93        91.99       113.82        82.85        55.69 
TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1FB TCGA-BH-A1FC 
       49.58        17.69        31.53        89.16       120.62       114.15 
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-A201 TCGA-BH-A202 TCGA-BH-A204 TCGA-BH-A28O 
       72.07       144.59         6.90         0.72        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-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-A12X TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 
       12.66         3.12         1.78         1.45         0.69         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-A27A 
        0.23         0.36         8.28         9.67         0.03        12.20 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A145 
        0.03         0.23        13.25        20.58        14.17        13.48 
TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD 
       21.14        14.17        17.49        18.71        15.78        18.15 
TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JL TCGA-D8-A1JN TCGA-D8-A1JP 
       12.03        14.01        18.97        20.09        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-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XL 
       25.74        23.90        18.15         2.66        17.16        19.92 
TCGA-D8-A1XM TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XY 
       17.69        16.41        16.31         6.35        15.16        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-A27R TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 
       10.09        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-A14S TCGA-E2-A14T TCGA-E2-A14U 
       40.11        28.44        28.87        33.17        33.30        43.33 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A152 TCGA-E2-A153 
       34.26        32.02        31.96        28.60        27.12        23.24 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E 
       21.04        23.87        23.34        22.82        17.29        20.71 
TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       21.63        18.21        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-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-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB 
       20.98        11.08        54.18        19.66        24.59        40.47 
TCGA-E2-A1LE TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX 
       28.90         8.75        43.04        16.93         5.52        15.72 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A576 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N9 
        7.20        30.61        19.00        19.20        36.82        13.12 
TCGA-E9-A1NA TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       36.56        35.77        21.57        11.90        14.30         0.62 
TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE 
        6.12         1.38         2.76        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-A22H TCGA-E9-A243 
       12.53        13.32        39.09        22.75        24.10        17.06 
TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT 
        0.85        27.22        24.56         0.72        17.75         0.76 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54X TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE 
       18.41         0.62        12.33        13.81        14.40        15.39 
TCGA-EW-A1IW TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
       12.20         8.48        18.21        13.25        16.57        15.68 
TCGA-EW-A1J6 TCGA-EW-A1OX TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 
       28.77        29.95        41.13        39.78        52.96        29.82 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PF TCGA-EW-A1PG 
       18.48        30.08        18.90        19.99        14.43        34.55 
TCGA-EW-A1PH TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A423 
       19.96        52.73        25.91        22.09        21.27        10.16 
TCGA-EW-A424 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DK 
       10.59        59.57       194.27        53.52        43.04        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        43.73 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-LD-A66U TCGA-LD-A74U 
       66.38        72.03        13.55        18.12        21.24         6.67 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y 
        4.08         4.60         8.75         9.53        10.95         7.59 
TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Y 
       17.06        14.70        14.47        11.57         2.63         4.14 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
        4.50         5.59         3.22         7.36        27.91         2.79 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
        2.10        12.66        31.99        58.62        27.65        34.92 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66L 
       16.87        24.72        22.32        26.70        65.62        31.07 
TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ TCGA-PL-A8LY TCGA-S3-A6ZF 
       26.04         7.23        14.07        19.73         0.26        16.50 
TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA15 TCGA-W8-A86G 
        6.81        10.59         5.56         8.52         6.87         5.29 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        9.60         9.14       100.01       105.04 

  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 
           21.470            23.225 
[1] "0.0 - 220.9 (21.5)" "0.0 - 234.3 (23.2)"
[1] "hr=" "1.2"
D47V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4P LOSS MUTATED        25       16        1        1       120        78
  4P LOSS WILD-TYPE      58       64        8        4       222       156
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4P LOSS MUTATED           0         50         10         20        7
  4P LOSS WILD-TYPE         2         92         19         43       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                 25                58
  STAGE IA                16                64
  STAGE IB                 1                 8
  STAGE II                 1                 4
  STAGE IIA              120               222
  STAGE IIB               78               156
  STAGE III                0                 2
  STAGE IIIA              50                92
  STAGE IIIB              10                19
  STAGE IIIC              20                43
  STAGE IV                 7                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    69 214  36  15
  4P LOSS WILD-TYPE 196 380  88  24
D47V4, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1              69               196
  T2             214               380
  T3              36                88
  T4              15                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   154 112  43  22
  4P LOSS WILD-TYPE 327 227  70  52
D47V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0             154               327
  N1             112               227
  N2              43                70
  N3              22                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
  4P LOSS MUTATED          2 286   7  40
  4P LOSS WILD-TYPE        3 568  12 107
D47V6, multiclass
          clus
vv         4P LOSS MUTATED 4P LOSS WILD-TYPE
  CM0 (I+)               2                 3
  M0                   286               568
  M1                     7                12
  MX                    40               107
[1] 4 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   331   4
  4P LOSS WILD-TYPE 683   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED    331    4
  4P LOSS WILD-TYPE  683    7
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE             331               683
  MALE                 4                 7
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  4P LOSS MUTATED                            1                           281
  4P LOSS WILD-TYPE                          0                           473
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  4P LOSS MUTATED                               27                   3
  4P LOSS WILD-TYPE                            148                   3
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  4P LOSS MUTATED                                  7                  0
  4P LOSS WILD-TYPE                               22                 15
                   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                281               473
  INFILTRATING LOBULAR CARCINOMA                27               148
  MEDULLARY CARCINOMA                            3                 3
  MIXED HISTOLOGY (PLEASE SPECIFY)               7                22
  MUCINOUS CARCINOMA                             0                15
  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    95 240
  4P LOSS WILD-TYPE 187 503
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     95  240
  4P LOSS WILD-TYPE  187  503
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               95               187
  YES             240               503
[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                          69   222
  4P LOSS WILD-TYPE                        89   495
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                     69                89
  WHITE                                        222               495
[1] 4 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    10 276
  4P LOSS WILD-TYPE  26 550
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     10  276
  4P LOSS WILD-TYPE   26  550
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                  10                26
  NOT HISPANIC OR LATINO             276               550
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4Q LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED   251  38
  4Q LOSS WILD-TYPE 635  81
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              289               716 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               38                81 
$`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        24.39 
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        53.06        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        43.00        19.99         8.98        15.06 
TCGA-A8-A08B TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08R TCGA-A8-A08X 
       38.01        33.01        12.00         9.99         0.99        43.00 
TCGA-A8-A092 TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09R TCGA-A8-A09X TCGA-AC-A23E 
       30.97         1.02        49.05         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-AC-A8OQ TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 
        1.81         0.69         1.12         0.23         0.33         0.62 
TCGA-AN-A04A TCGA-AN-A0AJ TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD 
        2.96         8.02         0.33         0.33         0.33         6.44 
TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0XN 
        7.96         7.00         0.33         0.36         0.33         0.33 
TCGA-AN-A0XP TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XW TCGA-AO-A03N TCGA-AO-A0J2 
        0.30         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 
       52.18        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 
      101.95       114.02        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-A24V 
       20.22       109.58        50.89        84.20       101.52        85.35 
TCGA-AR-A24W TCGA-AR-A251 TCGA-AR-A256 TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0IA 
       50.96        78.48        93.83        10.59        77.62       220.90 
TCGA-B6-A0IB TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IN TCGA-B6-A0IO 
      129.57       112.37       176.98        18.77        84.59       110.14 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RL TCGA-B6-A0RU TCGA-B6-A0WV 
      140.88       211.56       189.01        81.17       131.21        79.63 
TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A401 TCGA-B6-A408 
       21.47       113.79        43.59        73.51        85.35        49.94 
TCGA-B6-A40B TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B5 
      103.63        38.79        20.45        46.95        39.55        48.36 
TCGA-BH-A0BA TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0BR 
       37.22        25.71        21.70        44.05        48.69        53.69 
TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0E0 TCGA-BH-A0E6 
       45.57        49.94        41.75        44.02         4.41         9.63 
TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0GZ TCGA-BH-A0H7 TCGA-BH-A0HI TCGA-BH-A0HU 
       46.19        24.49        10.78        23.08        20.38        12.89 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18Q 
       50.79         5.59        23.93        23.05         8.81        55.63 
TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1F6 
       51.39        51.16        69.93        42.28        12.00        97.48 
TCGA-BH-A1F8 TCGA-BH-A1FD TCGA-BH-A1FU TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A209 
       24.66        33.17        72.07        38.60        57.83       130.16 
TCGA-C8-A12L TCGA-C8-A12P TCGA-C8-A138 TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL 
       11.93        11.77         3.75         0.16        12.03        10.42 
TCGA-C8-A1HM TCGA-C8-A26Y TCGA-C8-A278 TCGA-C8-A27B TCGA-D8-A13Y TCGA-D8-A13Z 
        2.30         0.43         0.03         0.99        11.90        20.88 
TCGA-D8-A1JA TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JM 
       16.50        18.90        12.03        20.09        20.12        19.40 
TCGA-D8-A1JP TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XO TCGA-D8-A1XR 
       21.01        14.73        21.83        14.50         7.96        15.85 
TCGA-D8-A1XU TCGA-D8-A27H TCGA-D8-A27T TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14Q 
       12.99        13.05        13.08        47.15        44.68        38.24 
TCGA-E2-A14R TCGA-E2-A150 TCGA-E2-A154 TCGA-E2-A159 TCGA-E2-A15H TCGA-E2-A15S 
       38.60        25.41        19.43        25.05        12.92        14.07 
TCGA-E2-A1B0 TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1L7 TCGA-E2-A1L8 
       53.62        17.10        33.73        33.70        27.42        39.62 
TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A9RU 
       18.87       106.75       102.61        34.92        19.89         9.21 
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-A1R4 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A226 TCGA-E9-A22E 
        2.10         6.12        32.09        20.81        34.13        12.89 
TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A3HO TCGA-E9-A3X8 
       23.51         0.69         1.94         0.95        26.07        15.72 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-EW-A1IX TCGA-EW-A1J1 TCGA-EW-A1OV 
        0.23        14.70         0.26        39.72        18.90        25.94 
TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PC 
       22.82        29.85        40.41        23.11         7.86         6.15 
TCGA-EW-A1PE TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A3U0 TCGA-GI-A2C8 TCGA-GM-A2DF 
       10.52        19.96        55.00        17.49         7.40        42.71 
TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A3XL TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LL-A441 
       42.28        61.91        69.30        11.84        11.57        11.44 
TCGA-LL-A5YM TCGA-LL-A6FR TCGA-LL-A73Z TCGA-LL-A8F5 TCGA-OL-A5D7 TCGA-OL-A5RW 
       15.32         3.88         4.50         6.21        46.55        36.36 
TCGA-OL-A5S0 TCGA-OL-A66K TCGA-PL-A8LV TCGA-PL-A8LX TCGA-S3-A6ZH TCGA-S3-AA14 
       20.38        33.57         0.23         0.16         8.65         7.17 
TCGA-S3-AA17 
        3.91 

$`4Q LOSS WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        0.39         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N 
       47.24        13.68         7.96        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-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
       36.13       136.73        24.79       112.08        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D2 
      107.93        75.25         5.19        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-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-A0SY 
       24.72        24.16        99.19        54.64        44.88        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-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-A1FX 
       19.33        48.46        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-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD 
       16.31        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        32.75        49.48        38.40        34.98 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 
       38.37         7.30        21.30        23.21        26.96        21.14 
TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB 
       21.90        38.30        34.29        35.47        37.45        33.11 
TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H 
       10.72        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-A5ZV 
       13.41        14.70        11.97        14.93        13.74        12.10 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06R 
       10.72        11.05         8.75        13.02        13.02        17.98 
TCGA-A8-A06U TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I 
       29.03        53.98         9.01        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        24.99 
TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A 
        9.99        28.04        18.05        36.95        13.02         0.99 
TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08S 
       28.96        19.96        37.05        31.00        31.00        33.01 
TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 
       93.04        40.01        33.01        17.95        41.98        12.00 
TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09I TCGA-A8-A09K 
        9.99         9.99        12.00        50.04        45.07        29.98 
TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
       33.07         1.02        25.02        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-A2QJ TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
       50.70         1.02         2.27         0.69        14.83        22.19 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A6IV 
        1.12        16.57        19.79        23.24        24.79         1.18 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y 
        0.43         1.68         1.74         1.32         0.33         0.33 
TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0FF 
        1.78         1.71         7.36         6.51         0.16         4.64 
TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FY TCGA-AN-A0FZ 
        7.59         7.17         6.28         6.02         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XO TCGA-AN-A0XR TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AO-A03L 
        0.33        12.33         0.33         0.33         5.33        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-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 
       29.13        21.40        24.16        37.48        22.36        53.03 
TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI 
       21.53        50.70        50.86        21.37        26.24        50.24 
TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12B 
       62.04        55.33        99.25       108.72       106.78        77.56 
TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR 
       57.30        41.62        28.37        14.73        82.62        70.39 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O 
       24.79        26.93        15.62        32.52         2.56        32.91 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV 
        9.99       111.32        49.32        74.79        86.66        29.75 
TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TZ TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AI 
       98.93        64.83        76.14        83.87        85.97        61.84 
TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AR 
       52.77        51.25        48.82        43.56        39.98        17.23 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24L 
       37.81        76.21        61.28        63.62        62.14        73.02 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24U 
       96.89        78.51         0.85        87.22        76.01        53.36 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 
       83.77        79.00        56.15        73.18        72.76        58.92 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM 
      128.65        20.25        62.86        42.87         7.36        40.04 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN 
       38.17        39.39        40.54        20.38        54.74        16.04 
TCGA-AR-A5QP TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IC TCGA-B6-A0IE 
       20.45       143.38       149.59        12.13        50.70        65.72 
TCGA-B6-A0IG TCGA-B6-A0IM TCGA-B6-A0IP TCGA-B6-A0RG TCGA-B6-A0RI TCGA-B6-A0RM 
      146.50       126.12       110.93        68.45       234.28        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-A0WW TCGA-B6-A0WZ TCGA-B6-A0X0 
      157.41        97.48       188.68        17.98       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-A402 TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AY TCGA-BH-A0AZ 
      170.17        54.28        55.00        24.53        25.55        28.50 
TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC 
       40.83        39.16        56.94        56.98        51.68        32.02 
TCGA-BH-A0BD TCGA-BH-A0BG TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BS 
       18.21        24.85        61.68        35.67        27.19        53.95 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE 
       11.67        49.05        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-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EE 
       16.27        15.68        14.30        44.81        32.65        31.00 
TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       24.43        30.35        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-A18T TCGA-BH-A1EO 
       37.74        30.28        37.55        66.05         7.36        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-A1FB TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FG 
       31.53        89.16       120.62       114.15        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-A201 TCGA-BH-A202 TCGA-BH-A204 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
        6.90         0.72        83.31        10.65         6.44        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O 
        0.99       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-A135 TCGA-C8-A137 TCGA-C8-A1HE 
        1.78         1.45         0.69         0.62         3.85        12.33 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W 
       10.92        11.34        11.34         3.25         0.30         0.23 
TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A27A 
        0.36         8.28         9.67         0.03         0.03        12.20 
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-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JB 
       13.48        21.14        19.20        14.17        17.49        18.71 
TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JL 
       15.78        18.15        12.03        14.01        18.97        20.09 
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-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-A1XL TCGA-D8-A1XM TCGA-D8-A1XQ TCGA-D8-A1XS 
       17.16        15.22        19.92        17.69        16.41        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-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-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 
       10.09        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-A14P TCGA-E2-A14S TCGA-E2-A14T 
       40.11        28.44        28.87        40.96        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-A152 TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15A 
       27.12        23.24        21.04        23.87        14.79        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-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       17.06        14.99        60.53        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-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LK TCGA-E2-A1LL 
       19.66        24.59        40.47        28.90         8.75        43.04 
TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A576 
       16.93         5.52        15.72         7.20        30.61        19.00 
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-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 
       11.90        14.30         0.62         1.38         2.76        21.21 
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-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       35.64         0.79        12.53        13.32        39.09        22.75 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A24A TCGA-E9-A295 
       24.10        17.06         0.85        27.22        24.56         0.72 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54X TCGA-E9-A5UO 
       17.75         0.76        18.41         0.62        12.33        13.81 
TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J2 
       14.40        15.39        12.20         8.48        18.21        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OX TCGA-EW-A1P0 TCGA-EW-A1P1 
       16.57        15.68        28.77        29.95        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-A1PD TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW 
       13.94        14.43        34.55        52.73        25.91        22.09 
TCGA-EW-A3E8 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       21.27        10.16        10.59       109.87        59.57       194.27 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       53.13        53.52        43.04        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        43.73        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 
       72.03        13.55        18.12        21.24         6.67         4.08 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL 
        4.60         8.75         9.53        10.95         7.59        17.06 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Y 
       14.70        14.47        14.79        11.57         2.63         4.14 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
        4.50         5.59         3.22         7.36        27.91         2.79 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
        2.10        12.66        31.99        58.62        27.65        34.92 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J 
       16.87        24.72        22.32        26.70        23.47        65.62 
TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ 
       31.07        26.04         7.23        14.07        28.21        19.73 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA10 
        0.26         3.95        16.50         6.81        10.59         7.92 
TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA15 TCGA-W8-A86G TCGA-XX-A899 TCGA-XX-A89A 
        5.56         8.52         6.87         5.29         9.60         9.14 
TCGA-Z7-A8R5 TCGA-Z7-A8R6 
      100.01       105.04 

  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 
           21.470            22.785 
[1] "0.0 - 220.9 (21.5)" "0.0 - 234.3 (22.8)"
[1] "hr=" "1.1"
D48V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4Q LOSS MUTATED        21       17        0        1       103        67
  4Q LOSS WILD-TYPE      62       63        9        4       239       167
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4Q LOSS MUTATED           0         46          9         17        7
  4Q LOSS WILD-TYPE         2         96         20         46       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                 21                62
  STAGE IA                17                63
  STAGE IB                 0                 9
  STAGE II                 1                 4
  STAGE IIA              103               239
  STAGE IIB               67               167
  STAGE III                0                 2
  STAGE IIIA              46                96
  STAGE IIIB               9                20
  STAGE IIIC              17                46
  STAGE IV                 7                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    60 183  36  15
  4Q LOSS WILD-TYPE 205 411  88  24
D48V4, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1              60               205
  T2             183               411
  T3              36                88
  T4              15                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
  4Q LOSS MUTATED   134  99  37  20
  4Q LOSS WILD-TYPE 347 240  76  54
D48V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0             134               347
  N1              99               240
  N2              37                76
  N3              20                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
  4Q LOSS MUTATED          2 252   7  34
  4Q LOSS WILD-TYPE        3 602  12 113
D48V6, multiclass
          clus
vv         4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CM0 (I+)               2                 3
  M0                   252               602
  M1                     7                12
  MX                    34               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"
D48V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED   293   2
  4Q LOSS WILD-TYPE 721   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    293    2
  4Q LOSS WILD-TYPE  721    9
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE             293               721
  MALE                 2                 9
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  4Q LOSS MUTATED                            0                           246
  4Q LOSS WILD-TYPE                          1                           508
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  4Q LOSS MUTATED                               24                   2
  4Q LOSS WILD-TYPE                            151                   4
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  4Q LOSS MUTATED                                  7                  0
  4Q LOSS WILD-TYPE                               22                 15
                   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                246               508
  INFILTRATING LOBULAR CARCINOMA                24               151
  MEDULLARY CARCINOMA                            2                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               7                22
  MUCINOUS CARCINOMA                             0                15
  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    87 208
  4Q LOSS WILD-TYPE 195 535
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     87  208
  4Q LOSS WILD-TYPE  195  535
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO               87               195
  YES             208               535
[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                          60   193
  4Q LOSS WILD-TYPE                        98   524
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                     60                98
  WHITE                                        193               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"
D48V12, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     9 235
  4Q LOSS WILD-TYPE  27 591
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      9  235
  4Q LOSS WILD-TYPE   27  591
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   9                27
  NOT HISPANIC OR LATINO             235               591
[1] 2 2
[1] FALSE

Clustering(49) Variable = 5P LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED   109  22
  5P LOSS WILD-TYPE 777  97
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              131               874 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               22                97 
$`5P LOSS MUTATED`
TCGA-5T-A9QA TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A04T TCGA-A2-A04U 
        0.39        31.79        28.01        18.02        73.84        22.06 
TCGA-A2-A0CM TCGA-A2-A0D0 TCGA-A2-A0EY TCGA-A2-A0SX TCGA-A2-A0YH TCGA-A2-A0YJ 
       24.79        21.14        24.16        50.43        21.67        18.61 
TCGA-A2-A0YM TCGA-A2-A1G1 TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XX TCGA-A2-A3XY 
       31.73        19.20        33.93        83.01        38.40        34.98 
TCGA-A7-A0DA TCGA-A7-A13E TCGA-A7-A26I TCGA-A7-A4SE TCGA-A7-A6VY TCGA-A8-A06T 
       35.67        10.72        21.73        21.17         8.75        53.06 
TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A084 TCGA-A8-A08X 
       17.03        53.98         9.99         8.98        15.06        43.00 
TCGA-AC-A2BK TCGA-AC-A6IW TCGA-AN-A041 TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR 
       38.53         0.69         0.23         7.36         6.51         0.33 
TCGA-AN-A0AT TCGA-AN-A0FL TCGA-AN-A0FT TCGA-AN-A0FZ TCGA-AO-A0J4 TCGA-AO-A0J5 
        0.33         7.59         6.02         0.33        52.18        24.16 
TCGA-AO-A0JB TCGA-AO-A124 TCGA-AO-A129 TCGA-AO-A12F TCGA-AQ-A04J TCGA-AQ-A04L 
       50.70       102.58        96.10        48.36        26.93       130.09 
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-A24K TCGA-AR-A24Q TCGA-AR-A250 TCGA-AR-A251 TCGA-B6-A0IB TCGA-B6-A0IG 
       50.89       101.52        56.15        78.48       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-A0BT TCGA-BH-A0C0 TCGA-BH-A0E0 TCGA-BH-A0HA TCGA-BH-A0WA TCGA-BH-A18T 
       45.57        41.75         4.41        52.96        23.05         7.36 
TCGA-BH-A18V TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FN TCGA-BH-A1FU TCGA-BH-A209 
       51.16       114.15        74.73        72.07        72.07       130.16 
TCGA-C8-A12O TCGA-C8-A134 TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A26W TCGA-C8-A26X 
       12.66         0.69         3.75        10.92         0.23         0.36 
TCGA-C8-A278 TCGA-C8-A27A TCGA-D8-A147 TCGA-D8-A1JB TCGA-D8-A1JF TCGA-D8-A1XF 
        0.03        12.20        19.20        18.71        12.03        15.22 
TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XQ TCGA-D8-A1XZ TCGA-D8-A1Y3 TCGA-D8-A27R 
       21.83        14.50        16.41        15.32        14.14        10.09 
TCGA-E2-A14N TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A1AZ TCGA-E2-A1B6 TCGA-E2-A1L7 
       47.15        25.05        23.34        60.53        28.50        27.42 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A573 TCGA-E9-A1N8 TCGA-E9-A1NC 
      102.61         8.75        43.04        34.92        12.00        39.55 
TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A3QA TCGA-EW-A1OW 
       12.59        20.05        23.51         0.69         0.62        22.82 
TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P8 TCGA-EW-A2FV TCGA-GM-A2DD TCGA-GM-A2DF 
       29.85        41.13         7.86        25.91        43.04        42.71 
TCGA-GM-A3XL TCGA-JL-A3YW TCGA-LD-A7W5 TCGA-LL-A441 TCGA-OL-A5D7 TCGA-OL-A5RW 
       69.30        11.84         4.08        11.44        46.55        36.36 
TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A6VO TCGA-PL-A8LV TCGA-S3-AA10 
       23.47        65.62        28.21         0.23         7.92 

$`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       136.73        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        48.46        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        32.75        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        24.39        21.30        23.21        26.96        21.14 
TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ 
       21.90        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        43.00        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 
       24.99         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        38.01        28.96        33.01        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        33.01 
TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 
       93.04        40.01        33.01        30.97        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        50.04 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q 
       49.05        45.07        29.98        33.07         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        22.19         1.12        16.57        19.79        23.24 
TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV 
       24.79         1.55         0.07         1.12         1.81         1.18 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AN-A03X 
        0.43         1.68         1.74         1.12         1.32         0.33 
TCGA-AN-A03Y TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D 
        0.33         0.33         0.62         2.96         1.78         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ 
        8.02         0.16         0.33         6.44         4.64         7.96 
TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX 
        7.00         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-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-A0J6 TCGA-AO-A0J7 
       59.05        29.13        32.78        21.40        37.48        20.32 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE 
       22.36        53.03        21.53        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        50.24        62.04        55.33        71.80 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D 
       99.25       108.72       106.78        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-A0Y5 TCGA-AQ-A1H2 
       70.39         0.53        17.79        24.79         5.65        15.62 
TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ 
       32.52         2.56        32.91         9.99       111.32        49.32 
TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX 
        5.26        74.79        86.66        29.75        98.93        64.83 
TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AI 
       55.86        76.14       101.95       114.02        85.97        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-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY 
       37.81        76.21        61.28        63.62        62.14        20.22 
TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
      109.58        73.02        96.89        78.51        84.20         0.85 
TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X 
       87.22        76.01        53.36        85.35        50.96        83.77 
TCGA-AR-A24Z TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE 
       79.00        73.18        72.76        58.92        93.83       128.65 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN 
       20.25        62.86        42.87         7.36        40.04        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP 
       39.39        40.54        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-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM 
       50.70        65.72       112.37       176.98        18.77       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-A0RO TCGA-B6-A0RQ 
      234.28        81.17        78.02       172.96       162.05       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-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-A408 TCGA-B6-A40B TCGA-B6-A40C 
      139.17       170.17        85.35        49.94       103.63        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-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 
       40.83        39.55        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-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-A0C7 
       49.94        11.67        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-A0E6 
       45.17        47.41        16.27        15.68        14.30         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-A0H5 TCGA-BH-A0H6 
       30.35        10.78        15.16        37.78        35.51        24.56 
TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       23.08        41.00        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-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-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-A1FD TCGA-BH-A1FG TCGA-BH-A1FH 
       97.48        24.66       120.62        33.17       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-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-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-A135 TCGA-C8-A137 TCGA-C8-A1HE 
        3.12         1.78         1.45         0.62         3.85        12.33 
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-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 
        3.25         0.30         0.43         8.28         9.67         0.03 
TCGA-C8-A275 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-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-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-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-A1XA 
       18.58        17.79        16.73        25.74        23.90        27.58 
TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XL TCGA-D8-A1XM 
       18.15         2.66        17.16        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-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        30.61        19.89 
TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 
       19.00         9.21        19.20        36.82        13.48        13.12 
TCGA-E9-A1NA TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 
       36.56        35.77        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-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        24.56         0.72 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A54X 
       17.75         0.76        26.07        18.41        15.72        12.33 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE 
        0.23        14.70         0.26        13.81        14.40        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-A1OZ 
       16.57        15.68        28.77        25.94        29.95        40.41 
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-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-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-A2DH TCGA-GM-A2DI TCGA-GM-A2DK 
      194.27        53.13        53.52        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-A3YX 
       43.73        66.38        72.03        13.55        18.12        11.57 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A442 
       21.24         6.67         4.60         8.75         9.53        10.95 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP 
        7.59        17.06        15.32        14.70        14.47        14.79 
TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 
       11.57         2.63         3.88         4.14         4.50         4.50 
TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
        5.59         3.22         6.21         7.36        27.91         2.79 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
        2.10        12.66        31.99        58.62        27.65        34.92 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66K 
       16.87        24.72        22.32        20.38        26.70        33.57 
TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ TCGA-PL-A8LX 
       31.07        26.04         7.23        14.07        19.73         0.16 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z 
        0.26         3.95        16.50         6.81         8.65        10.59 
TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-W8-A86G 
        5.56         8.52         7.17         6.87         3.91         5.29 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        9.60         9.14       100.01       105.04 

  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 
            24.85             21.80 
[1] "0.0 - 146.5 (24.9)" "0.0 - 234.3 (21.8)"
[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        1        0        53        30
  5P LOSS WILD-TYPE      74       73        8        5       289       204
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5P LOSS MUTATED           0         19          3         10        2
  5P LOSS WILD-TYPE         2        123         26         53       16
                   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                74
  STAGE IA                 7                73
  STAGE IB                 1                 8
  STAGE II                 0                 5
  STAGE IIA               53               289
  STAGE IIB               30               204
  STAGE III                0                 2
  STAGE IIIA              19               123
  STAGE IIIB               3                26
  STAGE IIIC              10                53
  STAGE IV                 2                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
  5P LOSS MUTATED    27  94   9   5
  5P LOSS WILD-TYPE 238 500 115  34
D49V4, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1              27               238
  T2              94               500
  T3               9               115
  T4               5                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
  5P LOSS MUTATED    66  41  16  11
  5P LOSS WILD-TYPE 415 298  97  63
D49V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0              66               415
  N1              41               298
  N2              16                97
  N3              11                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
  5P LOSS MUTATED          0 113   2  20
  5P LOSS WILD-TYPE        5 741  17 127
D49V6, multiclass
          clus
vv         5P LOSS MUTATED 5P LOSS WILD-TYPE
  CM0 (I+)               0                 5
  M0                   113               741
  M1                     2                17
  MX                    20               127
[1] 4 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   134   1
  5P LOSS WILD-TYPE 880  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED    134    1
  5P LOSS WILD-TYPE  880   10
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE             134               880
  MALE                 1                10
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  5P LOSS MUTATED                            0                           118
  5P LOSS WILD-TYPE                          1                           636
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  5P LOSS MUTATED                                2                   4
  5P LOSS WILD-TYPE                            173                   2
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  5P LOSS MUTATED                                  4                  0
  5P LOSS WILD-TYPE                               25                 15
                   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                118               636
  INFILTRATING LOBULAR CARCINOMA                 2               173
  MEDULLARY CARCINOMA                            4                 2
  MIXED HISTOLOGY (PLEASE SPECIFY)               4                25
  MUCINOUS CARCINOMA                             0                15
  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    43  92
  5P LOSS WILD-TYPE 239 651
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     43   92
  5P LOSS WILD-TYPE  239  651
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO               43               239
  YES              92               651
[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                          30    86
  5P LOSS WILD-TYPE                       128   631
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                     30               128
  WHITE                                         86               631
[1] 4 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     3 114
  5P LOSS WILD-TYPE  33 712
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      3  114
  5P LOSS WILD-TYPE   33  712
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                33
  NOT HISPANIC OR LATINO             114               712
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5Q LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED   182  29
  5Q LOSS WILD-TYPE 704  90
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              211               794 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               29                90 
$`5Q LOSS MUTATED`
TCGA-5T-A9QA TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A04P TCGA-A2-A04Q 
        0.39        31.79        28.01        19.20        18.02        41.95 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A0CM TCGA-A2-A0D0 TCGA-A2-A0D1 
       73.84        22.06        64.04        24.79        21.14        34.55 
TCGA-A2-A0EQ TCGA-A2-A0EY TCGA-A2-A0SX TCGA-A2-A0YH TCGA-A2-A0YJ TCGA-A2-A0YM 
       79.76        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-A2-A4RW 
       19.20        33.93        83.01        38.40        34.98         7.30 
TCGA-A2-A4S3 TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A26G 
       21.90        30.61        35.67        31.73        10.72        23.74 
TCGA-A7-A26I TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A6VY 
       21.73        21.17        17.92        14.73        12.10         8.75 
TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A07U 
       31.00        17.03        53.98         9.99         8.98        24.99 
TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A08X TCGA-A8-A09A TCGA-A8-A09K TCGA-AC-A2BK 
       15.06        33.01        43.00         9.99        29.98        38.53 
TCGA-AC-A62X TCGA-AC-A6IW TCGA-AC-A8OQ TCGA-AN-A041 TCGA-AN-A04C TCGA-AN-A0AK 
        1.12         0.69         1.12         0.23         1.78         7.36 
TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FT 
        6.51         0.33         0.33         7.96         7.59         6.02 
TCGA-AN-A0FV TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XN TCGA-AN-A0XU TCGA-AO-A0J4 
        0.33         0.33         0.33         0.33         0.33        52.18 
TCGA-AO-A0J5 TCGA-AO-A0JB TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A129 TCGA-AO-A12F 
       24.16        50.70        55.33       102.58        96.10        48.36 
TCGA-AO-A1KR TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A54N TCGA-AR-A0TP TCGA-AR-A0TT 
       70.39        26.93       130.09         2.56       111.32        86.66 
TCGA-AR-A0TV TCGA-AR-A0U0 TCGA-AR-A0U2 TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AQ 
       29.75        65.36        83.87        75.55        52.77        43.07 
TCGA-AR-A1AR TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24Q TCGA-AR-A24U TCGA-AR-A24Z 
       17.23        20.22        50.89       101.52        53.36        79.00 
TCGA-AR-A250 TCGA-AR-A251 TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IO 
       56.15        78.48       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-A0BP 
       54.28        38.79        39.55        25.71        24.85        48.69 
TCGA-BH-A0BT TCGA-BH-A0BW TCGA-BH-A0C0 TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0HA 
       45.57        11.67        41.75         4.41         9.63        52.96 
TCGA-BH-A0WA TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EV TCGA-BH-A1F2 TCGA-BH-A1FC 
       23.05         7.36        51.16        12.00        31.53       114.15 
TCGA-BH-A1FE TCGA-BH-A1FN TCGA-BH-A1FU TCGA-BH-A208 TCGA-BH-A209 TCGA-C8-A12L 
       74.73        72.07        72.07        57.83       130.16        11.93 
TCGA-C8-A12O TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A138 TCGA-C8-A1HF 
       12.66         3.12         1.78         0.69         3.75        10.92 
TCGA-C8-A1HJ TCGA-C8-A1HM TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A278 TCGA-C8-A27A 
        0.16         2.30         0.23         0.36         0.03        12.20 
TCGA-C8-A27B TCGA-D8-A142 TCGA-D8-A147 TCGA-D8-A1JB TCGA-D8-A1JF TCGA-D8-A1JK 
        0.99        13.97        19.20        18.71        12.03        20.12 
TCGA-D8-A1JL TCGA-D8-A1XF TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XQ TCGA-D8-A1XT 
       20.09        15.22        14.50        19.92        16.41         6.35 
TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y3 TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27M 
       12.66        15.32        14.14        16.04        13.05        13.48 
TCGA-D8-A27R TCGA-E2-A10C TCGA-E2-A14N TCGA-E2-A150 TCGA-E2-A155 TCGA-E2-A158 
       10.09        40.11        47.15        25.41        21.04        14.79 
TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B6 TCGA-E2-A1II 
       25.05        23.34        60.53        53.62        28.50        33.70 
TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A1LA TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL 
       20.98        27.42        24.59       102.61         8.75        43.04 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N8 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1RB 
       34.92        19.89        12.00        39.55        12.59        20.81 
TCGA-E9-A1RH TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A3QA TCGA-EW-A1OW TCGA-EW-A1P0 
       34.59        23.51         0.69         0.62        22.82        41.13 
TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PH TCGA-EW-A2FV TCGA-GI-A2C9 TCGA-GM-A2DD 
        7.86        18.90        19.96        25.91       109.87        43.04 
TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A3XL TCGA-JL-A3YW TCGA-LD-A7W5 TCGA-LL-A441 
       42.71        42.28        69.30        11.84         4.08        11.44 
TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YP TCGA-LL-A6FR TCGA-OL-A5D7 TCGA-OL-A5RW 
       15.32        14.70        14.79         3.88        46.55        36.36 
TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66I TCGA-OL-A66J TCGA-PL-A8LV TCGA-PL-A8LX 
       22.32        20.38        23.47        65.62         0.23         0.16 
TCGA-S3-AA10 
        7.92 

$`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       136.73        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        48.46        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        32.75        49.48        31.99 
TCGA-A2-A3Y0 TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 
       38.37        24.39        21.30        23.21        26.96        21.14 
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        53.06        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        43.00        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        38.01 
TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O 
       28.96        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        33.01        93.04        40.01        33.01 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09B 
       30.97        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        50.04        49.05        45.07        33.07         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        22.19         1.12        16.57        19.79 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV 
       23.24        24.79         1.55         0.07         1.81         1.18 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y 
        0.43         1.68         1.74         1.32         0.33         0.33 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AM 
        0.33         0.62         2.96         1.71         8.02         0.16 
TCGA-AN-A0AS 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-A0FW TCGA-AN-A0FX TCGA-AN-A0XL TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR 
        0.36         0.33         0.33        12.33         0.30         0.33 
TCGA-AN-A0XS 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-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-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 
       29.13        32.78        21.40        37.48        20.32        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-A0JM TCGA-AO-A125 TCGA-AO-A126 
       26.24        50.24        62.04        71.80        99.25       108.72 
TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G 
      106.78        90.58        77.56        64.04        57.30        41.62 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AO-A1KT 
       28.37        14.73        82.62        61.87         0.53        17.79 
TCGA-AQ-A04H TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AQ-A7U7 
       24.79         5.65        15.62        32.52        32.91         9.99 
TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
       49.32         5.26        74.79        98.93        64.83        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AK 
       76.14       101.95       114.02        85.97        61.84        51.25 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AS 
       48.82        62.56        43.73        43.56        39.98        37.81 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24H TCGA-AR-A24L 
       76.21        61.28        63.62        62.14       109.58        73.02 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24T 
       96.89        78.51        84.20         0.85        87.22        76.01 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 
       85.35        50.96        83.77        73.18        72.76        58.92 
TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL 
       93.83       128.65        20.25        62.86        42.87         7.36 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM 
       40.04        38.17        39.39        40.54        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-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK 
       12.13       220.90        50.70       112.37       176.98        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-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-A0WV TCGA-B6-A0WW 
       89.46       157.41        97.48       188.68        79.63        17.98 
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-A1KN TCGA-B6-A2IU TCGA-B6-A401 
       58.88        43.59        73.51       139.17       170.17        85.35 
TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AY 
       49.94       103.63        55.00        24.53        20.45        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 
       28.50        46.95        40.83        39.16        48.36        56.94 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BJ 
       56.98        51.68        37.22        32.02        18.21        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-A0BV TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD 
       49.94        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-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-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-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-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-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P 
       20.12        90.84        26.66        72.56        37.74        30.28 
TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO 
       55.63        37.55        66.05        51.39        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-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD 
       25.81        89.16        97.48        24.66       120.62        33.17 
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-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-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-A12W TCGA-C8-A12X 
       11.77         0.07        12.66        12.66        12.66        12.66 
TCGA-C8-A132 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HG TCGA-C8-A1HI 
        1.45         0.62         3.85        12.33        11.34        11.34 
TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26Y TCGA-C8-A26Z 
       12.03        10.42         3.25         0.30         0.43         8.28 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y 
        9.67         0.03         0.03         0.03         0.23        11.90 
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-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-A1JJ TCGA-D8-A1JM TCGA-D8-A1JN 
       12.03        14.01        18.97        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-A1XJ TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR 
       17.16        14.73        21.83        17.69         7.96        15.85 
TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       16.31        12.99        15.16        16.54        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-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-A109 
       18.51         7.33        43.00        34.42        27.52        46.59 
TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14P 
       40.41        37.51        28.44        28.87        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-A14Z TCGA-E2-A152 TCGA-E2-A153 
       32.02        31.96        28.60        17.03        27.12        23.24 
TCGA-E2-A154 TCGA-E2-A156 TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F 
       19.43        23.87        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-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-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       37.41        32.78        33.73        28.44        22.65         3.88 
TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LB 
       22.19        11.08        54.18        39.62        19.66        40.47 
TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX 
       28.90        18.87       106.75        16.93         5.52        15.72 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1N5 
        7.20        30.61        19.00         9.21        19.20        36.82 
TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG 
       13.48        13.12        36.56        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-A1RC TCGA-E9-A1RD 
        1.38         2.76        21.21        32.09        40.24         0.66 
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-A249 TCGA-E9-A24A 
       17.06         0.85        27.22         1.94         0.95        24.56 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3X8 
        0.72        17.75         0.76        26.07        18.41        15.72 
TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP 
       12.33         0.23        14.70         0.26        13.81        14.40 
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-A1OX 
       13.25        16.57        15.68        28.77        25.94        29.95 
TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 
       29.85        40.41        39.78        52.96        29.82        23.11 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE 
       18.48        30.08        19.99         6.15        13.94        10.52 
TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A3E8 
       14.43        34.55        55.00        52.73        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-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       53.13        53.52        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        43.73        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U 
       72.03        13.55        18.12        11.57        21.24         6.67 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL 
        4.60         8.75         9.53        10.95         7.59        17.06 
TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 
       14.47        11.57         2.63         4.14         4.50         4.50 
TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
        5.59         3.22         6.21         7.36        27.91         2.79 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
        2.10        12.66        31.99        58.62        27.65        34.92 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A66H TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       16.87        24.72        26.70        33.57        31.07        26.04 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PL-A8LY TCGA-PL-A8LZ 
        7.23        14.07        28.21        19.73         0.26         3.95 
TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA12 
       16.50         6.81         8.65        10.59         5.56         8.52 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-W8-A86G TCGA-XX-A899 TCGA-XX-A89A 
        7.17         6.87         3.91         5.29         9.60         9.14 
TCGA-Z7-A8R5 TCGA-Z7-A8R6 
      100.01       105.04 

  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 
            22.82             22.34 
[1] "0.0 - 211.6 (22.8)" "0.0 - 234.3 (22.3)"
[1] "hr=" "1.2"
D50V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5Q LOSS MUTATED        16       10        2        0        90        48
  5Q LOSS WILD-TYPE      67       70        7        5       252       186
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5Q LOSS MUTATED           0         25          5         12        4
  5Q LOSS WILD-TYPE         2        117         24         51       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                67
  STAGE IA                10                70
  STAGE IB                 2                 7
  STAGE II                 0                 5
  STAGE IIA               90               252
  STAGE IIB               48               186
  STAGE III                0                 2
  STAGE IIIA              25               117
  STAGE IIIB               5                24
  STAGE IIIC              12                51
  STAGE IV                 4                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    44 148  14   8
  5Q LOSS WILD-TYPE 221 446 110  31
D50V4, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1              44               221
  T2             148               446
  T3              14               110
  T4               8                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
  5Q LOSS MUTATED   113  64  23  13
  5Q LOSS WILD-TYPE 368 275  90  61
D50V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0             113               368
  N1              64               275
  N2              23                90
  N3              13                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
  5Q LOSS MUTATED          0 188   4  24
  5Q LOSS WILD-TYPE        5 666  15 123
D50V6, multiclass
          clus
vv         5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CM0 (I+)               0                 5
  M0                   188               666
  M1                     4                15
  MX                    24               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"
D50V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED   216   0
  5Q LOSS WILD-TYPE 798  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED    216    0
  5Q LOSS WILD-TYPE  798   11
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE             216               798
  MALE                 0                11
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  5Q LOSS MUTATED                            1                           195
  5Q LOSS WILD-TYPE                          0                           559
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  5Q LOSS MUTATED                                3                   4
  5Q LOSS WILD-TYPE                            172                   2
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  5Q LOSS MUTATED                                  4                  0
  5Q LOSS WILD-TYPE                               25                 15
                   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                195               559
  INFILTRATING LOBULAR CARCINOMA                 3               172
  MEDULLARY CARCINOMA                            4                 2
  MIXED HISTOLOGY (PLEASE SPECIFY)               4                25
  MUCINOUS CARCINOMA                             0                15
  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    64 152
  5Q LOSS WILD-TYPE 218 591
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     64  152
  5Q LOSS WILD-TYPE  218  591
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO               64               218
  YES             152               591
[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                          54   129
  5Q LOSS WILD-TYPE                       104   588
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                     54               104
  WHITE                                        129               588
[1] 4 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     5 180
  5Q LOSS WILD-TYPE  31 646
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      5  180
  5Q LOSS WILD-TYPE   31  646
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                31
  NOT HISPANIC OR LATINO             180               646
[1] 2 2
[1] FALSE

Clustering(51) Variable = 6P LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED   155  18
  6P LOSS WILD-TYPE 731 101
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              173               832 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               18               101 
$`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        21.30        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        33.01        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        33.07 
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-AC-A8OR TCGA-AN-A04C TCGA-AN-A0FF TCGA-AN-A0FV 
        1.81         1.74         1.32         1.78         4.64         0.33 
TCGA-AN-A0FX TCGA-AN-A0XW TCGA-AO-A03T TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 
        0.33         5.59        47.87        37.48        20.32        22.36 
TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A54N TCGA-AQ-A54O 
       26.24        62.04        70.39        17.79         2.56        32.91 
TCGA-AR-A0TQ TCGA-AR-A1AP TCGA-AR-A1AU TCGA-AR-A24K TCGA-AR-A24P TCGA-AR-A24R 
       49.32        39.98        76.21        50.89         0.85        87.22 
TCGA-AR-A24V TCGA-AR-A252 TCGA-B6-A0IA TCGA-B6-A0IJ TCGA-B6-A0RO TCGA-B6-A0WV 
       85.35        73.18       220.90       176.98       162.05        79.63 
TCGA-B6-A401 TCGA-BH-A0AU TCGA-BH-A0B0 TCGA-BH-A0B5 TCGA-BH-A0BP TCGA-BH-A0C3 
       85.35        24.53        46.95        48.36        48.69        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-A1F5 TCGA-BH-A1FE TCGA-BH-A1FJ 
      113.82        42.28        17.69        89.16        74.73        63.35 
TCGA-BH-A1FM TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12W TCGA-C8-A137 TCGA-C8-A1HG 
       45.63        12.66        11.77        12.66         3.85        11.34 
TCGA-C8-A274 TCGA-C8-A27A TCGA-D8-A145 TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JG 
        0.03        12.20        13.48        15.78        18.90        12.03 
TCGA-D8-A1JM TCGA-D8-A1XA TCGA-D8-A1XF TCGA-D8-A1XU TCGA-D8-A1Y1 TCGA-D8-A27W 
       19.40        27.58        15.22        12.99         3.81        12.26 
TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A14V TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A15E 
       34.42        46.59        34.26        27.12        23.24        20.71 
TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15R TCGA-E2-A1AZ TCGA-E2-A1BD TCGA-E2-A1IE 
       21.63        12.92        17.06        60.53        17.10        38.30 
TCGA-E2-A1L8 TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LL TCGA-E2-A9RU TCGA-E9-A1N6 
       39.62        28.90        18.87        43.04         9.21        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-E9-A5UP 
       39.09         1.94         0.95        17.75        15.72        14.40 
TCGA-EW-A1J1 TCGA-EW-A1J6 TCGA-EW-A1P5 TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD 
       18.90        28.77        23.11        53.13        53.52        43.04 
TCGA-GM-A3XL TCGA-LL-A5YM TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-MS-A51U TCGA-OL-A6VO 
       69.30        15.32         5.59         6.21         2.79        28.21 
TCGA-OL-A6VQ TCGA-PL-A8LV TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA14 
       19.73         0.23         6.81         8.65         7.17 

$`6P LOSS WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        0.39         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN 
       47.24        20.88        13.68        31.79         7.96        39.32 
TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04T 
       28.01        18.21       104.81        18.02        41.95        73.84 
TCGA-A2-A04V TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM 
       63.12        55.43        36.13       136.73        64.57        24.79 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 
      112.08        92.48        64.04        56.81        21.14        34.55 
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-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T5 TCGA-A2-A0T6 
       44.28        17.52        17.13         8.38        17.46        18.90 
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-A0YM TCGA-A2-A0YT 
       14.50        18.61        19.33        48.46        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-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-A3XS TCGA-A2-A3XT TCGA-A2-A3XU 
       91.92        10.59        20.88        33.93        83.01        29.98 
TCGA-A2-A3XV TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW 
       32.75        38.40        34.98        31.99        38.37         7.30 
TCGA-A2-A4RX TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD 
       24.39        23.21        26.96        21.14        21.90        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-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       33.11        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-A3IY 
       24.26        23.74        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-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-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U 
        8.75        13.02         1.02        17.98        53.06        29.03 
TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F 
       31.00        17.03        53.98        43.00        19.99        18.97 
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-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 TCGA-A8-A085 
       24.99         9.99        28.04        18.05        15.06        36.95 
TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08J TCGA-A8-A08L 
       13.02         0.99        38.01        28.96        37.05         9.99 
TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z 
       31.00         0.99        33.01        93.04        43.00        40.01 
TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A 
       33.01        30.97        17.95        41.98         9.99         9.99 
TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09Q TCGA-A8-A09V 
       12.00        50.04        49.05        45.07        25.02        15.02 
TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A7 TCGA-A8-A0AD 
        0.99        14.01        12.00        19.04         0.99        38.04 
TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2FB TCGA-AC-A2FF 
        0.95         2.37         2.66         1.48        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        22.19         1.12        16.57        19.79 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IV 
       23.24        24.79         1.55         0.07         1.12         1.18 
TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OQ TCGA-AN-A03X TCGA-AN-A03Y 
        0.69         0.43         1.68         1.12         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-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-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        6.44         7.96         7.00         7.59         7.17         6.28 
TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN 
        6.02         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-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P 
        5.33        80.28        47.84        66.77        81.63        84.69 
TCGA-AO-A03R TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 
       68.75        59.05        29.13        32.78        21.40        52.18 
TCGA-AO-A0J5 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD 
       24.16        53.03        21.53        50.70        50.86        72.00 
TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JI TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 
       76.77        21.37        50.24        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       108.72       106.78        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-A0TR 
        5.65        15.62        32.52         9.99       111.32         5.26 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
       74.79        86.66        29.75        98.93        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       101.95        83.87       114.02        85.97 
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-A1AV 
       43.73        43.56        43.07        17.23        37.81        61.28 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M 
       63.62        62.14        20.22       109.58        73.02        96.89 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24Q TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24W 
       78.51        84.20       101.52        76.01        53.36        50.96 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A255 
       83.77        79.00        56.15        78.48        72.76        58.92 
TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL 
       93.83       128.65        20.25        62.86        42.87         7.36 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM 
       40.04        38.17        39.39        40.54        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-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH 
       12.13       129.57        50.70        65.72       146.50       112.37 
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-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-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-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-A0AW TCGA-BH-A0AY 
       49.94       103.63        55.00        38.79        20.45        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0B7 
       28.50        40.83        39.55        39.16        56.94        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-A0BQ TCGA-BH-A0BR 
       21.70        44.05        61.68        35.67        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-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-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-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 
       10.78        15.16        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-A0HY TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       12.89        50.79         5.59        24.95        42.35        44.81 
TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M 
       23.05         8.81         2.01        20.12        90.84        72.56 
TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18T TCGA-BH-A18U 
       37.74        30.28        55.63        37.55         7.36        51.39 
TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1EV TCGA-BH-A1EW 
       51.16        69.93        91.99        82.85        12.00        55.69 
TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB 
       49.58        25.81        31.53        97.48        24.66       120.62 
TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FL TCGA-BH-A1FN 
      114.15        33.17       122.89        36.92        55.00        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-A12Q 
      109.28         8.94        11.93        11.77        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-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-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-A275 
        0.23         0.36         0.43         8.28         9.67         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-A142 TCGA-D8-A143 TCGA-D8-A146 TCGA-D8-A147 
       13.25        20.58        13.97        14.17        21.14        19.20 
TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JF 
       14.17        17.49        16.50        18.71        18.15        12.03 
TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JN 
       14.01        18.97        20.09        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-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-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-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E 
       16.54        15.32        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-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-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A10A 
       14.50        18.51         7.33        43.00        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-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-A15P TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 
        7.73        13.02        19.56        14.07        14.99        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IF 
       53.03        29.95        32.35        28.50        16.47        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-A1L9 
       22.19        20.98        11.08        54.18        27.42        19.66 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P5 
       24.59        40.47       106.75       102.61         8.75        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        30.61        34.92        19.89 
TCGA-E2-A576 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N9 TCGA-E9-A1NC TCGA-E9-A1ND 
       19.00        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        24.56 
TCGA-E9-A295 TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54X 
        0.72         0.76        26.07        18.41         0.62        12.33 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW 
        0.23        14.70         0.26        13.81        15.39        12.20 
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-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-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 
       39.78        52.96        29.82        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-GI-A2C9 
       21.27        17.49        10.16        10.59         7.40       109.87 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK 
       59.57       194.27        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 
       43.73        66.38        72.03        13.55        18.12        11.84 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF 
       11.57        21.24         6.67         4.08         4.60         8.75 
TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN 
        9.53        11.44        10.95         7.59        17.06        14.70 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y 
       14.47        14.79        11.57         2.63         3.88         4.14 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OK-A5Q2 
        4.50         4.50         3.22         7.36        27.91         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
       12.66        46.55        31.99        58.62        27.65        34.92 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H 
       36.36        16.87        24.72        22.32        20.38        26.70 
TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O 
       23.47        65.62        33.57        31.07        26.04         7.23 
TCGA-OL-A66P TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-AA0Z 
       14.07         0.16         0.26         3.95        16.50        10.59 
TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-W8-A86G 
        7.92         5.56         8.52         6.87         3.91         5.29 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        9.60         9.14       100.01       105.04 

  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 
            21.30             22.82 
[1] "0.0 - 220.9 (21.3)" "0.0 - 234.3 (22.8)"
[1] "hr=" "1"  
D51V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6P LOSS MUTATED        15       13        1        0        64        41
  6P LOSS WILD-TYPE      68       67        8        5       278       193
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6P LOSS MUTATED           0         22          6          8        3
  6P LOSS WILD-TYPE         2        120         23         55       15
                   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                 15                68
  STAGE IA                13                67
  STAGE IB                 1                 8
  STAGE II                 0                 5
  STAGE IIA               64               278
  STAGE IIB               41               193
  STAGE III                0                 2
  STAGE IIIA              22               120
  STAGE IIIB               6                23
  STAGE IIIC               8                55
  STAGE IV                 3                15
  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    49 104  15   7
  6P LOSS WILD-TYPE 216 490 109  32
D51V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1              49               216
  T2             104               490
  T3              15               109
  T4               7                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
  6P LOSS MUTATED    85  60  18  11
  6P LOSS WILD-TYPE 396 279  95  63
D51V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0              85               396
  N1              60               279
  N2              18                95
  N3              11                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
  6P LOSS MUTATED          2 152   3  18
  6P LOSS WILD-TYPE        3 702  16 129
D51V6, multiclass
          clus
vv         6P LOSS MUTATED 6P LOSS WILD-TYPE
  CM0 (I+)               2                 3
  M0                   152               702
  M1                     3                16
  MX                    18               129
[1] 4 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   174   1
  6P LOSS WILD-TYPE 840  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED    174    1
  6P LOSS WILD-TYPE  840   10
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE             174               840
  MALE                 1                10
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  6P LOSS MUTATED                            0                           137
  6P LOSS WILD-TYPE                          1                           617
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  6P LOSS MUTATED                               22                   1
  6P LOSS WILD-TYPE                            153                   5
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  6P LOSS MUTATED                                  5                  4
  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                137               617
  INFILTRATING LOBULAR CARCINOMA                22               153
  MEDULLARY CARCINOMA                            1                 5
  MIXED HISTOLOGY (PLEASE SPECIFY)               5                24
  MUCINOUS CARCINOMA                             4                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    55 120
  6P LOSS WILD-TYPE 227 623
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     55  120
  6P LOSS WILD-TYPE  227  623
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO               55               227
  YES             120               623
[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                          29   112
  6P LOSS WILD-TYPE                       129   605
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                     29               129
  WHITE                                        112               605
[1] 4 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     4 138
  6P LOSS WILD-TYPE  32 688
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      4  138
  6P LOSS WILD-TYPE   32  688
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                32
  NOT HISPANIC OR LATINO             138               688
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6Q LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED   231  26
  6Q LOSS WILD-TYPE 655  93
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              257               748 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               26                93 
$`6Q LOSS MUTATED`
TCGA-5T-A9QA TCGA-A1-A0SE TCGA-A1-A0SN TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U 
        0.39        43.43        39.32        82.16        73.84        22.06 
TCGA-A2-A04W TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU 
       64.04        88.60       107.93        75.55        75.25         5.19 
TCGA-A2-A0CV TCGA-A2-A0D4 TCGA-A2-A0EO TCGA-A2-A0ET TCGA-A2-A0SV TCGA-A2-A0T3 
       63.45        25.22        80.28        35.05        27.12        18.71 
TCGA-A2-A0T4 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A25A 
       20.52        18.90        20.75        23.77        17.36       107.70 
TCGA-A2-A25B TCGA-A2-A25E TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XV TCGA-A2-A3XW 
       16.31        91.92        39.65        33.93        32.75        49.48 
TCGA-A2-A4RY TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3J1 
       21.30        31.73        12.72        20.61        11.34        11.28 
TCGA-A7-A426 TCGA-A8-A06O TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 
       11.97        13.02        26.01         1.02        53.98         9.01 
TCGA-A8-A07J TCGA-A8-A07S TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J 
       12.00         7.99        33.01        19.96        12.00        37.05 
TCGA-A8-A08O TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I 
       31.00        12.00         9.99         1.02        49.05        45.07 
TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A0A4 
       29.98        33.07         1.02         8.98        19.04        13.02 
TCGA-A8-A0A6 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-AC-A23G TCGA-AC-A2BK TCGA-AC-A2BM 
       21.04        13.02        17.03        10.85        38.53        38.20 
TCGA-AC-A2FM TCGA-AC-A3BB TCGA-AC-A3W5 TCGA-AC-A62Y TCGA-AC-A8OP TCGA-AC-A8OR 
       26.04         0.99        16.57         1.81         1.74         1.32 
TCGA-AN-A041 TCGA-AN-A04C TCGA-AN-A0AS TCGA-AN-A0FF TCGA-AN-A0FV TCGA-AN-A0FX 
        0.23         1.78         0.33         4.64         0.33         0.33 
TCGA-AN-A0XW TCGA-AO-A03N TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A0J3 TCGA-AO-A0J6 
        5.59        66.77        68.75        47.87        21.40        37.48 
TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL 
       20.32        22.36        26.24        50.24        62.04        55.33 
TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0TQ TCGA-AR-A0TR 
       70.39        17.79         2.56        32.91        49.32         5.26 
TCGA-AR-A0TZ TCGA-AR-A0U2 TCGA-AR-A1AU TCGA-AR-A24K TCGA-AR-A24P TCGA-AR-A24R 
       76.14        83.87        76.21        50.89         0.85        87.22 
TCGA-AR-A24V TCGA-AR-A252 TCGA-AR-A255 TCGA-B6-A0IA TCGA-B6-A0IJ TCGA-B6-A0RG 
       85.35        73.18        58.92       220.90       176.98        68.45 
TCGA-B6-A0RO TCGA-B6-A0RU TCGA-B6-A0WV TCGA-B6-A0WY TCGA-B6-A1KC TCGA-B6-A1KN 
      162.05       131.21        79.63       113.79        43.59       139.17 
TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0B0 
      170.17        85.35        49.94        55.00        24.53        46.95 
TCGA-BH-A0B5 TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BW 
       48.36        21.70        61.68        48.69        27.19        11.67 
TCGA-BH-A0C3 TCGA-BH-A0DE TCGA-BH-A0DH TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0E2 
       48.13        31.17        38.01        48.23        15.65        14.30 
TCGA-BH-A0EI TCGA-BH-A0H0 TCGA-BH-A0H7 TCGA-BH-A0HA TCGA-BH-A0HW TCGA-BH-A0HX 
       24.43        15.16        23.08        52.96        51.32        27.25 
TCGA-BH-A0W3 TCGA-BH-A18F TCGA-BH-A18I TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18S 
       23.93         8.81         7.23        90.84        26.66        66.05 
TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1EU TCGA-BH-A1F5 TCGA-BH-A1FC TCGA-BH-A1FE 
       69.93       113.82        42.28        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-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1N5 
       28.90        18.87        43.04         9.21        19.20        36.82 
TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1NA TCGA-E9-A1NE TCGA-E9-A1QZ TCGA-E9-A1R0 
       13.48        12.00        36.56        35.77        11.90        14.30 
TCGA-E9-A1R4 TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RG TCGA-E9-A1RH 
        6.12         2.76        32.09        20.81        21.27        34.59 
TCGA-E9-A1RI TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A2JS 
       35.64        13.32        39.09         1.94         0.95        17.75 
TCGA-E9-A3X8 TCGA-E9-A5UO TCGA-E9-A5UP TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J5 
       15.72        13.81        14.40        18.90        13.25        15.68 
TCGA-EW-A1J6 TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P5 TCGA-EW-A3E8 TCGA-GM-A2DB 
       28.77        29.85        41.13        23.11        21.27        53.13 
TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A3XL TCGA-GM-A3XN TCGA-LD-A66U 
       53.52        43.04        42.71        69.30        66.38        21.24 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A5YM TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A8F5 
        4.60         8.75        15.32         4.50         5.59         6.21 
TCGA-MS-A51U TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PL-A8LV 
        2.79        31.07         7.23        28.21        19.73         0.23 
TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA12 TCGA-S3-AA14 
       16.50         6.81         8.65         8.52         7.17 

$`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 
      136.73        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        48.46        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        24.39        23.21        26.96        21.14        21.90 
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        53.06        29.03        31.00        17.03        43.00 
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        24.99         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        38.01        28.96 
TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X 
        9.99        31.00         0.99        33.01        93.04        43.00 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 
       40.01        33.01        30.97        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        50.04        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 
       22.19         1.12        19.79        23.24        24.79         1.55 
TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO 
        0.07         1.12         1.18         0.69         0.43         1.68 
TCGA-AC-A8OQ TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A 
        1.12         0.33         0.33         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-A0AT TCGA-AN-A0FD TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN 
        0.33         6.44         7.96         7.00         7.59         7.17 
TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL 
        6.28         6.02         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-AO-A03L TCGA-AO-A03M TCGA-AO-A03O TCGA-AO-A03P 
        0.33         5.33        80.28        47.84        81.63        84.69 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J9 
       59.05        29.13        32.78        52.18        24.16        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-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 
       71.80       102.58        99.25       108.72       106.78        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-A1KS TCGA-AQ-A04H 
       28.37        14.73        82.62        61.87         0.53        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        32.52         9.99 
TCGA-AR-A0TP TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX 
      111.32        74.79        86.66        29.75        98.93        64.83 
TCGA-AR-A0TY TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH 
       55.86        65.36       101.95       114.02        85.97        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-A1AV 
       43.56        39.98        43.07        17.23        37.81        61.28 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M 
       63.62        62.14        20.22       109.58        73.02        96.89 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24Q TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24W 
       78.51        84.20       101.52        76.01        53.36        50.96 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A256 
       83.77        79.00        56.15        78.48        72.76        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM 
      128.65        20.25        62.86        42.87         7.36        40.04 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN 
       38.17        39.39        40.54        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-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IK 
      129.57        50.70        65.72       146.50       112.37        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-A0RP 
      189.01       234.28        81.17        78.02       172.96       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-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-A1KF TCGA-B6-A1KI TCGA-B6-A402 TCGA-B6-A40B 
       68.94        58.88       101.52        73.51        54.28       103.63 
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-A0BL TCGA-BH-A0BO TCGA-BH-A0BR 
       18.21        25.71        24.85        44.05        35.67        53.69 
TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 
       53.95        45.57        49.94        49.05        41.75        44.02 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO 
       42.90        45.83        23.44        22.13        13.91        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-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-A0GY TCGA-BH-A0GZ TCGA-BH-A0H3 TCGA-BH-A0H5 
       24.49        31.00        30.35        10.78        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-A18G TCGA-BH-A18J TCGA-BH-A18M 
       42.35        44.81        23.05         2.01        20.12        72.56 
TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18T TCGA-BH-A18U 
       37.74        30.28        55.63        37.55         7.36        51.39 
TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX 
       51.16        91.99        82.85        12.00        55.69        49.58 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB 
       17.69        25.81        31.53        97.48        24.66       120.62 
TCGA-BH-A1FD TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR 
       33.17       122.89        36.92        55.00        72.07       144.59 
TCGA-BH-A1FU TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 
       72.07         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-A12N TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12X 
       11.93        11.77         0.07        12.66        12.66        12.66 
TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A138 
        3.12         1.78         1.45         0.69         0.62         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-A26Z 
        2.30         3.25         0.30         0.23         0.36         8.28 
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-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-A1JF TCGA-D8-A1JH TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JN 
       12.03        14.01        20.09        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-A1XC TCGA-D8-A1XD TCGA-D8-A1XG 
       16.73        25.74        23.90         2.66        17.16        14.73 
TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS 
       21.83        14.50         7.96        16.41        15.85        16.31 
TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y2 TCGA-D8-A1Y3 
       15.16        12.66        16.54        15.32        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-A27V TCGA-D8-A3Z5 
       16.41        13.48         4.80         0.76        12.53        14.50 
TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B 
       18.51         7.33        43.00        27.52        40.41        37.51 
TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q 
       40.11        28.44        47.15        44.68        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-A154 TCGA-E2-A155 TCGA-E2-A156 
       28.60        17.03        25.41        19.43        21.04        23.87 
TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15G 
       14.79        25.05        23.34        22.82        17.29        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-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-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ 
       28.50        37.41        32.78        33.73        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 
       22.65        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        30.61        34.92 
TCGA-E2-A574 TCGA-E2-A576 TCGA-E9-A1N9 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NF 
       19.89        19.00        13.12        39.55        12.59        20.05 
TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1R7 
       21.57         9.86         0.62         2.10         1.38        21.21 
TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A226 TCGA-E9-A227 
       40.24         0.66        34.65         6.58        34.13         0.79 
TCGA-E9-A228 TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 
       12.53        22.75        12.89        23.51        24.10        17.06 
TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JT 
        0.69         0.85        27.22        24.56         0.72         0.76 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK 
       26.07        18.41         0.62        12.33         0.23        14.70 
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-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        43.73        72.03        13.55 
TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LL-A440 
       18.12        11.84        11.57         6.67         4.08         9.53 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO 
       11.44        10.95         7.59        17.06        14.70        14.47 
TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z 
       14.79        11.57         2.63         3.88         4.14         4.50 
TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 
        3.22         7.36        27.91         2.10        12.66        46.55 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX 
       31.99        58.62        27.65        34.92        36.36        16.87 
TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J 
       24.72        22.32        20.38        26.70        23.47        65.62 
TCGA-OL-A66K TCGA-OL-A66N TCGA-OL-A66P TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ 
       33.57        26.04        14.07         0.16         0.26         3.95 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-W8-A86G 
       10.59         7.92         5.56         6.87         3.91         5.29 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        9.60         9.14       100.01       105.04 

  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 
            21.40             22.82 
[1] "0.2 - 220.9 (21.4)" "0.0 - 234.3 (22.8)"
[1] "hr=" "1.1"
D52V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6Q LOSS MUTATED        20       23        2        0        87        66
  6Q LOSS WILD-TYPE      63       57        7        5       255       168
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6Q LOSS MUTATED           0         33          9         13        4
  6Q LOSS WILD-TYPE         2        109         20         50       14
                   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                 20                63
  STAGE IA                23                57
  STAGE IB                 2                 7
  STAGE II                 0                 5
  STAGE IIA               87               255
  STAGE IIB               66               168
  STAGE III                0                 2
  STAGE IIIA              33               109
  STAGE IIIB               9                20
  STAGE IIIC              13                50
  STAGE IV                 4                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
  6Q LOSS MUTATED    76 148  25  11
  6Q LOSS WILD-TYPE 189 446  99  28
D52V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1              76               189
  T2             148               446
  T3              25                99
  T4              11                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
  6Q LOSS MUTATED   118  94  27  17
  6Q LOSS WILD-TYPE 363 245  86  57
D52V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0             118               363
  N1              94               245
  N2              27                86
  N3              17                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
  6Q LOSS MUTATED          2 219   5  34
  6Q LOSS WILD-TYPE        3 635  14 113
D52V6, multiclass
          clus
vv         6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CM0 (I+)               2                 3
  M0                   219               635
  M1                     5                14
  MX                    34               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"
D52V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED   259   1
  6Q LOSS WILD-TYPE 755  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED    259    1
  6Q LOSS WILD-TYPE  755   10
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE             259               755
  MALE                 1                10
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  6Q LOSS MUTATED                            0                           197
  6Q LOSS WILD-TYPE                          1                           557
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  6Q LOSS MUTATED                               38                   2
  6Q LOSS WILD-TYPE                            137                   4
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  6Q LOSS MUTATED                                  9                  6
  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                197               557
  INFILTRATING LOBULAR CARCINOMA                38               137
  MEDULLARY CARCINOMA                            2                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               9                20
  MUCINOUS CARCINOMA                             6                 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    85 175
  6Q LOSS WILD-TYPE 197 568
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     85  175
  6Q LOSS WILD-TYPE  197  568
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               85               197
  YES             175               568
[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                          45   173
  6Q LOSS WILD-TYPE                       113   544
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                     45               113
  WHITE                                        173               544
[1] 4 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     7 209
  6Q LOSS WILD-TYPE  29 617
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      7  209
  6Q LOSS WILD-TYPE   29  617
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   7                29
  NOT HISPANIC OR LATINO             209               617
[1] 2 2
[1] FALSE

Clustering(53) Variable = 7P LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED    96  11
  7P LOSS WILD-TYPE 790 108
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
              107               898 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               11               108 
$`7P LOSS MUTATED`
TCGA-5T-A9QA TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A2-A04T TCGA-A2-A0CT TCGA-A2-A0D4 
        0.39        31.79        28.01        73.84        75.25        25.22 
TCGA-A2-A0EQ TCGA-A2-A0ET TCGA-A2-A0SX TCGA-A2-A0T3 TCGA-A2-A0YT TCGA-A2-A1FW 
       79.76        35.05        50.43        18.71        23.77        17.36 
TCGA-A2-A1G1 TCGA-A2-A4RX TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A26I 
       19.20        24.39        21.90        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        43.00 
TCGA-A8-A07G TCGA-A8-A07R TCGA-A8-A08B TCGA-A8-A08F TCGA-A8-A08L TCGA-A8-A08S 
       18.97         8.98        38.01        33.01         9.99        33.01 
TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A09Q TCGA-A8-A0A2 TCGA-A8-A0A9 TCGA-AC-A23E 
       33.01        30.97        25.02        19.04        13.02         2.37 
TCGA-AC-A2QH TCGA-AC-A62X TCGA-AN-A04C TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FZ 
        1.02         1.12         1.78         0.16         0.33         0.33 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AO-A03L TCGA-AO-A0J7 TCGA-AO-A12F TCGA-AO-A1KS 
        0.33         0.33        80.28        20.32        48.36         0.53 
TCGA-AQ-A54N TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AQ TCGA-AR-A255 TCGA-AR-A2LK 
        2.56        85.97        61.84        43.07        58.92        42.87 
TCGA-B6-A0IJ TCGA-B6-A0IO TCGA-B6-A0RG TCGA-B6-A0RS TCGA-B6-A0WY TCGA-B6-A402 
      176.98       110.14        68.45       100.70       113.79        54.28 
TCGA-B6-A408 TCGA-BH-A0BG TCGA-BH-A0C0 TCGA-BH-A0HI TCGA-BH-A18F TCGA-BH-A18L 
       49.94        24.85        41.75        20.38         8.81        26.66 
TCGA-BH-A18Q TCGA-BH-A18U TCGA-BH-A1F8 TCGA-BH-A42T TCGA-C8-A1HF TCGA-C8-A1HM 
       55.63        51.39        24.66         0.99        10.92         2.30 
TCGA-C8-A274 TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JE TCGA-D8-A1JM TCGA-D8-A1JU 
        0.03        19.20        17.49        18.90        19.40        14.70 
TCGA-D8-A1X5 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XK TCGA-D8-A1XQ TCGA-D8-A27M 
       18.58        27.58        18.15        14.50        16.41        13.48 
TCGA-E2-A14Z TCGA-E2-A15H TCGA-E2-A15S TCGA-E2-A1L7 TCGA-E9-A1N6 TCGA-E9-A1RF 
       17.03        12.92        14.07        27.42        13.48         6.58 
TCGA-E9-A22B TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A54Y TCGA-E9-A5UP 
       22.75        23.51         0.69         1.94         0.23        14.40 
TCGA-EW-A1PC TCGA-GI-A2C9 TCGA-GM-A2DI TCGA-GM-A3XL TCGA-LL-A5YP TCGA-LL-A7T0 
        6.15       109.87        61.91        69.30        14.79         3.22 
TCGA-OL-A5RY TCGA-PL-A8LV TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA10 
       24.72         0.23         6.81        10.59         7.92 

$`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       136.73        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-A0YM TCGA-A2-A1FV 
       14.50        18.61        19.33        48.46        31.73        23.47 
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-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV 
       20.88        39.65        33.93        83.01        29.98        32.75 
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-A7-A0CE TCGA-A7-A0CG 
       21.30        23.21        26.96        21.14        35.31        34.29 
TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E 
       35.47        37.45        35.67        33.11        31.73        10.72 
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-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW 
       14.50        21.17        17.92        14.73        12.10        10.72 
TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q 
       11.05        10.29         9.37         8.75        13.02         1.02 
TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 
       17.98        53.06        31.00        26.01         1.02        53.98 
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-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 
       10.98         7.99        24.99         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        28.96        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 
       43.00        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        50.04        49.05        45.07 
TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       29.98        33.07         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        22.19         1.12        16.57        19.79        23.24 
TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW 
       24.79         1.55         0.07         1.81         1.18         0.69 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AN-A03X 
        0.43         1.68         1.74         1.12         1.32         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-A0AT TCGA-AN-A0FD 
        8.02         7.36         6.51         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-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-A0XU TCGA-AN-A0XV 
        0.33        12.33         0.30         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-A0J3 TCGA-AO-A0J4 
       47.87        59.05        29.13        32.78        21.40        52.18 
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        50.24 
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       108.72 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
      106.78        96.10        90.58        77.56        64.04        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-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-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
       32.52        32.91         9.99       111.32        49.32         5.26 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
       74.79        86.66        29.75        98.93        64.83        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AH 
       76.14        65.36       101.95        83.87       114.02        75.55 
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-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       39.98        17.23        37.81        76.21        61.28        63.62 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M 
       62.14        20.22       109.58        50.89        73.02        96.89 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24T 
       78.51        84.20         0.85       101.52        87.22        76.01 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 
       53.36        85.35        50.96        83.77        79.00        56.15 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH 
       78.48        73.18        72.76        93.83       128.65        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       62.86         7.36        40.04        38.17        39.39        40.54 
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-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
       65.72       146.50       112.37        18.77       126.12        84.59 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL 
      110.93       140.88       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-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-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
       21.47       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-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW 
       85.35       103.63        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-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-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO 
       18.21        25.71        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-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-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-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-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-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-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-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-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EN 
       30.28        37.55        66.05         7.36        51.16        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-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-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-A42U TCGA-BH-A42V TCGA-C8-A12L 
       10.65         6.44        20.12       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-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-A1HG 
        0.69         0.62         3.85         3.75        12.33        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-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A275 
        0.23         0.36         0.43         8.28         9.67         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-A1J8 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD 
       21.14        14.17        16.50        18.71        15.78        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-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1X6 
       20.09        20.38        21.01        12.20        13.32        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-A1XG TCGA-D8-A1XJ TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR 
       14.73        21.83        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-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-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-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-A15F TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       21.63        18.21        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-A1AZ 
        7.73        13.02        19.56        17.06        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-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-E2-A574 
        5.52        15.72         7.20        30.61        34.92        19.89 
TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 
       19.00         9.21        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-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-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 
        0.66        34.65        21.27        34.59        35.64        34.13 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22E TCGA-E9-A22H 
        0.79        12.53        13.32        39.09        12.89        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        24.56         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-A54X TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW 
       12.33        14.70         0.26        13.81        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        43.73        66.38        72.03 
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        21.24         6.67 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
        4.08         4.60         8.75         9.53        11.44        10.95 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP 
        7.59        17.06        15.32        14.70        14.47        11.57 
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-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
        6.21         7.36        27.91         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        31.99        58.62        27.65        34.92        36.36 
TCGA-OL-A5RX TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J 
       16.87        22.32        20.38        26.70        23.47        65.62 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO 
       33.57        31.07        26.04         7.23        14.07        28.21 
TCGA-OL-A6VQ TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZH 
       19.73         0.16         0.26         3.95        16.50         8.65 
TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-W8-A86G 
        5.56         8.52         7.17         6.87         3.91         5.29 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        9.60         9.14       100.01       105.04 

  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 
           19.200            23.065 
[1] "0.0 - 177.0 (19.2)" "0.0 - 234.3 (23.1)"
[1] "hr=" "1.1"
D53V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7P LOSS MUTATED         7        7        2        0        42        24
  7P LOSS WILD-TYPE      76       73        7        5       300       210
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7P LOSS MUTATED           1         15          5          4        0
  7P LOSS WILD-TYPE         1        127         24         59       18
                   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                76
  STAGE IA                 7                73
  STAGE IB                 2                 7
  STAGE II                 0                 5
  STAGE IIA               42               300
  STAGE IIB               24               210
  STAGE III                1                 1
  STAGE IIIA              15               127
  STAGE IIIB               5                24
  STAGE IIIC               4                59
  STAGE IV                 0                18
  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  71  11   5
  7P LOSS WILD-TYPE 244 523 113  34
D53V4, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  T1              21               244
  T2              71               523
  T3              11               113
  T4               5                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
  7P LOSS MUTATED    57  28  17   5
  7P LOSS WILD-TYPE 424 311  96  69
D53V5, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0              57               424
  N1              28               311
  N2              17                96
  N3               5                69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  7P LOSS MUTATED          0  99   0   9
  7P LOSS WILD-TYPE        5 755  19 138
D53V6, multiclass
          clus
vv         7P LOSS MUTATED 7P LOSS WILD-TYPE
  CM0 (I+)               0                 5
  M0                    99               755
  M1                     0                19
  MX                     9               138
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V7, binary
                   cls
clus                  0   1
  7P LOSS MUTATED   108   0
  7P LOSS WILD-TYPE 906  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED    108    0
  7P LOSS WILD-TYPE  906   11
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE             108               906
  MALE                 0                11
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  7P LOSS MUTATED                            0                            94
  7P LOSS WILD-TYPE                          1                           660
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  7P LOSS MUTATED                                5                   2
  7P LOSS WILD-TYPE                            170                   4
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  7P LOSS MUTATED                                  2                  0
  7P LOSS WILD-TYPE                               27                 15
                   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                 94               660
  INFILTRATING LOBULAR CARCINOMA                 5               170
  MEDULLARY CARCINOMA                            2                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               2                27
  MUCINOUS CARCINOMA                             0                15
  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    32  76
  7P LOSS WILD-TYPE 250 667
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     32   76
  7P LOSS WILD-TYPE  250  667
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO               32               250
  YES              76               667
[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                          22    64
  7P LOSS WILD-TYPE                       136   653
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                     22               136
  WHITE                                         64               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"
D53V12, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     1  86
  7P LOSS WILD-TYPE  35 740
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      1   86
  7P LOSS WILD-TYPE   35  740
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                35
  NOT HISPANIC OR LATINO              86               740
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7Q LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED   100  14
  7Q LOSS WILD-TYPE 786 105
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
              114               891 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               14               105 
$`7Q LOSS MUTATED`
TCGA-5T-A9QA TCGA-A1-A0SO TCGA-A2-A0CT TCGA-A2-A0D4 TCGA-A2-A0EQ TCGA-A2-A0ET 
        0.39        28.01        75.25        25.22        79.76        35.05 
TCGA-A2-A0SX TCGA-A2-A0T3 TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1G1 TCGA-A2-A4RX 
       50.43        18.71        23.77        17.36        19.20        24.39 
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-A07R 
       17.03        53.98         9.01        18.97        14.01         8.98 
TCGA-A8-A08B TCGA-A8-A08S TCGA-A8-A092 TCGA-A8-A099 TCGA-A8-A09I TCGA-A8-A09W 
       38.01        33.01        30.97         9.99        45.07         0.99 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A9 TCGA-AC-A23E TCGA-AC-A2QH TCGA-AC-A62V 
       12.00        19.04        13.02         2.37         1.02         0.07 
TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A0AJ TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FT 
        0.62         1.78         8.02         0.16         0.33         6.02 
TCGA-AN-A0FZ TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AO-A03L TCGA-AO-A0J7 TCGA-AO-A0JE 
        0.33         0.33         0.33        80.28        20.32        76.77 
TCGA-AO-A1KS TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A24H TCGA-AR-A24W TCGA-AR-A255 
        0.53        83.87        85.97       109.58        50.96        58.92 
TCGA-AR-A2LK TCGA-B6-A0IC TCGA-B6-A0IO TCGA-B6-A0RS TCGA-B6-A0WY TCGA-B6-A408 
       42.87        50.70       110.14       100.70       113.79        49.94 
TCGA-BH-A0AZ TCGA-BH-A0BG TCGA-BH-A0DZ TCGA-BH-A0HI TCGA-BH-A0W7 TCGA-BH-A18F 
       28.50        24.85        16.27        20.38        44.81         8.81 
TCGA-BH-A18L TCGA-BH-A18Q TCGA-BH-A18U TCGA-BH-A1EV TCGA-BH-A1FN TCGA-BH-A42T 
       26.66        55.63        51.39        12.00        72.07         0.99 
TCGA-C8-A12W TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HM TCGA-D8-A1JE TCGA-D8-A1JJ 
       12.66         3.75        10.92         2.30        18.90        20.09 
TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XK TCGA-D8-A1XQ 
       14.70        18.58        27.58        18.15        14.50        16.41 
TCGA-D8-A1XU TCGA-D8-A27M TCGA-E2-A14Z TCGA-E2-A15H TCGA-E2-A15M TCGA-E2-A1BC 
       12.99        13.48        17.03        12.92         7.73        16.47 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LB TCGA-E9-A1N6 TCGA-E9-A1R3 TCGA-E9-A1R4 
       27.42        39.62        40.47        13.48         2.10         6.12 
TCGA-E9-A1R7 TCGA-E9-A1RF TCGA-E9-A22B TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A24A 
       21.21         6.58        22.75         0.69         1.94        24.56 
TCGA-E9-A3HO TCGA-E9-A54Y TCGA-E9-A5UP TCGA-EW-A1PC TCGA-GI-A2C9 TCGA-GM-A2DI 
       26.07         0.23        14.40         6.15       109.87        61.91 
TCGA-LL-A5YP TCGA-LL-A7SZ TCGA-OL-A5RY TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA10 
       14.79         5.59        24.72         6.81        10.59         7.92 

$`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       136.73 
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        48.46 
TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 
       31.73        23.47        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        32.75        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        21.30        23.21        26.96        21.14 
TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DA 
       21.90        35.31        34.29        35.47        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-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-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-A6VY TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06X 
        8.75        13.02         1.02        17.98        53.06        31.00 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07J 
       26.01         1.02        43.00        19.99        18.97        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        24.99         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-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L 
       28.96        33.01        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        43.00        40.01 
TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09B 
       33.01        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        50.04        49.05        29.98        33.07         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        22.19         1.12        16.57 
TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62X TCGA-AC-A62Y 
       19.79        23.24        24.79         1.55         1.12         1.81 
TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OQ 
        1.18         0.69         0.43         1.68         1.74         1.12 
TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A04A 
        1.32         0.33         0.33         0.23         0.33         2.96 
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-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        4.64         7.96         7.00         7.59         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-A0XU TCGA-AN-A0XV TCGA-AN-A0XW 
       12.33         0.30         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-A0J5 
       59.05        29.13        32.78        21.40        52.18        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-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL 
       72.00        21.37        26.24        50.24        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       108.72       106.78        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        32.52 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
        2.56        32.91         9.99       111.32        49.32         5.26 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
       74.79        86.66        29.75        98.93        64.83        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AI 
       76.14        65.36       101.95       114.02        75.55        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-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
       39.98        43.07        17.23        37.81        76.21        61.28 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M 
       63.62        62.14        20.22        50.89        73.02        96.89 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24T 
       78.51        84.20         0.85       101.52        87.22        76.01 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 
       53.36        85.35        83.77        79.00        56.15        78.48 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       73.18        72.76        93.83       128.65        20.25        62.86 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
        7.36        40.04        38.17        39.39        40.54        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-A0IE TCGA-B6-A0IG 
      149.59        12.13       220.90       129.57        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-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-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-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-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
       21.47       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-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV 
       85.35        54.28       103.63        55.00        24.53        38.79 
TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 
       20.45        25.55        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-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO 
       18.21        25.71        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-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-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 
       45.17        47.41         4.41        15.68        14.30         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-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-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-A0WA TCGA-BH-A18G 
        5.59        23.93        24.95        42.35        23.05         2.01 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P 
        7.23        20.12        90.84        72.56        37.74        30.28 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO 
       37.55        66.05         7.36        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-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-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-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V 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-A135 TCGA-C8-A137 
        3.12         1.78         1.45         0.69         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-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-A1JF 
       17.49        16.50        18.71        15.78        18.15        12.03 
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-A1X6 TCGA-D8-A1X7 
       20.38        21.01        12.20        13.32        17.79        16.73 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG 
       25.74        23.90         2.66        17.16        15.22        14.73 
TCGA-D8-A1XJ TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS 
       21.83        19.92        17.69         7.96        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-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-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-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A152 
       34.26        32.02        31.96        28.60        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-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-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-A1BD TCGA-E2-A1IE TCGA-E2-A1IF 
       29.95        32.35        28.50        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-A1L9 TCGA-E2-A1LA 
       22.19        20.98        11.08        54.18        19.66        24.59 
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-A56Z TCGA-E2-A570 TCGA-E2-A573 
       16.93         5.52        15.72         7.20        30.61        34.92 
TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 
       19.89        19.00         9.21        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-A1R5 
       21.57         9.86        11.90        14.30         0.62         1.38 
TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE 
        2.76        32.09        20.81        40.24         0.66        34.65 
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-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 
       13.32        39.09        12.89        23.51        24.10        17.06 
TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT 
        0.85        27.22         0.95         0.72        17.75         0.76 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5FL 
       18.41         0.62        15.72        12.33        14.70         0.26 
TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
       13.81        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 
       43.73        69.30        66.38        72.03        13.55        18.12 
TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 
       11.84        11.57        21.24         6.67         4.08         4.60 
TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL 
        8.75         9.53        11.44        10.95         7.59        17.06 
TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR 
       15.32        14.70        14.47        11.57         2.63         3.88 
TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 
        4.14         4.50         4.50         3.22         6.21         7.36 
TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 
       27.91         2.79         2.10        12.66        46.55        31.99 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RZ 
       58.62        27.65        34.92        36.36        16.87        22.32 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L 
       20.38        26.70        23.47        65.62        33.57        31.07 
TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PL-A8LV 
       26.04         7.23        14.07        28.21        19.73         0.23 
TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZH TCGA-S3-AA11 
        0.16         0.26         3.95        16.50         8.65         5.56 
TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-W8-A86G TCGA-XX-A899 
        8.52         7.17         6.87         3.91         5.29         9.60 
TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        9.14       100.01       105.04 

  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 
           18.365            23.340 
[1] "0.1 - 113.8 (18.4)" "0.0 - 234.3 (23.3)"
[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        0        41        25
  7Q LOSS WILD-TYPE      76       71        7        5       301       209
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7Q LOSS MUTATED           1         20          4          4        1
  7Q LOSS WILD-TYPE         1        122         25         59       17
                   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                76
  STAGE IA                 9                71
  STAGE IB                 2                 7
  STAGE II                 0                 5
  STAGE IIA               41               301
  STAGE IIB               25               209
  STAGE III                1                 1
  STAGE IIIA              20               122
  STAGE IIIB               4                25
  STAGE IIIC               4                59
  STAGE IV                 1                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
  7Q LOSS MUTATED    23  77  12   4
  7Q LOSS WILD-TYPE 242 517 112  35
D54V4, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1              23               242
  T2              77               517
  T3              12               112
  T4               4                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
  7Q LOSS MUTATED    55  34  18   7
  7Q LOSS WILD-TYPE 426 305  95  67
D54V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0              55               426
  N1              34               305
  N2              18                95
  N3               7                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
  7Q LOSS MUTATED          1 103   1  11
  7Q LOSS WILD-TYPE        4 751  18 136
D54V6, multiclass
          clus
vv         7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CM0 (I+)               1                 4
  M0                   103               751
  M1                     1                18
  MX                    11               136
[1] 4 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   115   1
  7Q LOSS WILD-TYPE 899  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED    115    1
  7Q LOSS WILD-TYPE  899   10
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE             115               899
  MALE                 1                10
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  7Q LOSS MUTATED                            0                            98
  7Q LOSS WILD-TYPE                          1                           656
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  7Q LOSS MUTATED                               11                   0
  7Q LOSS WILD-TYPE                            164                   6
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  7Q LOSS MUTATED                                  2                  0
  7Q LOSS WILD-TYPE                               27                 15
                   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                 98               656
  INFILTRATING LOBULAR CARCINOMA                11               164
  MEDULLARY CARCINOMA                            0                 6
  MIXED HISTOLOGY (PLEASE SPECIFY)               2                27
  MUCINOUS CARCINOMA                             0                15
  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    35  81
  7Q LOSS WILD-TYPE 247 662
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     35   81
  7Q LOSS WILD-TYPE  247  662
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO               35               247
  YES              81               662
[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                          19    72
  7Q LOSS WILD-TYPE                       139   645
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                     19               139
  WHITE                                         72               645
[1] 4 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  92
  7Q LOSS WILD-TYPE  36 734
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0   92
  7Q LOSS WILD-TYPE   36  734
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                36
  NOT HISPANIC OR LATINO              92               734
[1] 2 2
[1] FALSE

Clustering(55) Variable = 8P LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED   315  55
  8P LOSS WILD-TYPE 571  64
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              370               635 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               55                64 
$`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-A25B TCGA-A2-A25D TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XZ 
       19.56        16.31        18.15        83.01        29.98        31.99 
TCGA-A2-A4RW TCGA-A2-A4S3 TCGA-A7-A0D9 TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A26G 
        7.30        21.90        37.45        31.73        10.72        23.74 
TCGA-A7-A26J TCGA-A7-A3IZ TCGA-A7-A3J1 TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D 
       20.61        10.59        11.28        21.17        17.92        14.73 
TCGA-A7-A5ZV TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A075 
       12.10        13.02        13.02        17.98        53.06        17.03 
TCGA-A8-A07E TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07W 
       19.99        17.03         9.99        10.98         7.99         9.99 
TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08S 
       15.06        36.95        19.96        37.05        31.00        33.01 
TCGA-A8-A08X TCGA-A8-A091 TCGA-A8-A097 TCGA-A8-A09D TCGA-A8-A09K TCGA-A8-A09N 
       43.00        33.01        12.00        50.04        29.98         1.02 
TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A0A7 TCGA-AC-A23H TCGA-AC-A2FO 
       25.02         8.98        19.04         0.99         2.66        50.70 
TCGA-AC-A2QH TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A8OP TCGA-AN-A03Y TCGA-AN-A041 
        1.02         1.12        16.57         1.74         0.33         0.23 
TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0AT 
        0.62         2.96         1.78         0.16         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0XL TCGA-AN-A0XN 
        6.44         6.28         0.33         0.33         0.33         0.33 
TCGA-AN-A0XO TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AO-A03N TCGA-AO-A03O 
       12.33         0.33         0.33         0.33        66.77        81.63 
TCGA-AO-A03P TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 
       84.69        29.13        32.78        21.40        52.18        24.16 
TCGA-AO-A0J6 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JE TCGA-AO-A0JG 
       37.48        53.03        21.53        50.70        76.77        26.24 
TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A126 TCGA-AO-A12D TCGA-AO-A12G 
       55.33        71.80       102.58       108.72        64.04        41.62 
TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AR-A0TP 
       70.39        17.79       130.09         5.65        15.62       111.32 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
       74.79        86.66        29.75        98.93        64.83        55.86 
TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AM 
      101.95        83.87       114.02        52.77        51.25        62.56 
TCGA-AR-A1AP TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24H 
       39.98        17.23        37.81        63.62        62.14       109.58 
TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24Z TCGA-AR-A250 
       50.89        73.02        53.36        85.35        79.00        56.15 
TCGA-AR-A2LE TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I9 TCGA-B6-A0IG 
      128.65        10.59        77.62       143.38        12.13       146.50 
TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RS 
      176.98        18.77       126.12       140.88        68.45       100.70 
TCGA-B6-A0RU TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WY TCGA-B6-A0X5 
      131.21        97.48       188.68        17.98       113.79        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KN TCGA-B6-A408 TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AY 
       58.88       139.17        49.94        55.00        38.79        25.55 
TCGA-BH-A0B2 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0BR 
       40.83        56.94        56.98        44.05        48.69        53.69 
TCGA-BH-A0BV TCGA-BH-A0C0 TCGA-BH-A0C7 TCGA-BH-A0DG TCGA-BH-A0DL TCGA-BH-A0E6 
       49.94        41.75        42.90        23.44        48.23         9.63 
TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0H7 TCGA-BH-A0HK TCGA-BH-A0HW 
       24.49        31.00        24.43        23.08         5.85        51.32 
TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0W3 TCGA-BH-A0W5 TCGA-BH-A0WA TCGA-BH-A18F 
       27.25        50.79        23.93        42.35        23.05         8.81 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18N TCGA-BH-A18S TCGA-BH-A18T 
        7.23        20.12        90.84        37.74        66.05         7.36 
TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EW TCGA-BH-A1EY TCGA-BH-A1F0 
       51.39        51.16        69.93        55.69        17.69        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F8 TCGA-BH-A1FD TCGA-BH-A1FH TCGA-BH-A1FN TCGA-BH-A1FU 
       31.53        24.66        33.17        36.92        72.07        72.07 
TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A42V TCGA-C8-A12M 
        6.90        38.60        57.83       130.16         8.94        11.77 
TCGA-C8-A12N TCGA-C8-A12P TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 
       11.77        11.77         1.78         1.45         0.69         3.85 
TCGA-C8-A138 TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM 
        3.75        11.34        11.34        12.03        10.42         2.30 
TCGA-C8-A1HN TCGA-C8-A26W TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M8 
        3.25         0.23         0.03        12.20         0.99         0.23 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A1J8 
       11.90        20.88        13.25        14.17        13.48        14.17 
TCGA-D8-A1J9 TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JG TCGA-D8-A1JJ TCGA-D8-A1JK 
       17.49        15.78        18.15        12.03        20.09        20.12 
TCGA-D8-A1JT TCGA-D8-A1X8 TCGA-D8-A1XD TCGA-D8-A1XJ TCGA-D8-A1XM TCGA-D8-A1XQ 
       13.32        25.74        17.16        21.83        17.69        16.41 
TCGA-D8-A1XS TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27L 
       16.31        15.52        14.24        16.04        13.05        16.41 
TCGA-D8-A27M TCGA-D8-A27R TCGA-D8-A27W TCGA-D8-A3Z6 TCGA-E2-A105 TCGA-E2-A108 
       13.48        10.09        12.26        18.51        43.00        27.52 
TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A14N TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14V 
       40.41        40.11        47.15        33.17        33.30        34.26 
TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A15A TCGA-E2-A15C 
       32.02        31.96        17.03        25.41        23.34        22.82 
TCGA-E2-A15H TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15R TCGA-E2-A1B0 TCGA-E2-A1B5 
       12.92        19.40         9.04        17.06        53.62        32.35 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IO 
       38.30        37.41        32.78        33.73        33.70        20.98 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LI 
       54.18        27.42        39.62        28.90        18.87       102.61 
TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A56Z TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N8 
        8.75        43.04         7.20        19.89         9.21        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-A22E TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A3QA TCGA-E9-A54Y TCGA-EW-A1IX 
       12.89         0.69         1.94         0.62         0.23        39.72 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P3 TCGA-EW-A1P8 
       25.94        22.82        29.85        40.41        52.96         7.86 
TCGA-EW-A1PA TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS 
       18.90        10.52        14.43        19.96        55.00        52.73 
TCGA-EW-A2FV TCGA-EW-A3U0 TCGA-EW-A424 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       25.91        17.49        10.59       109.87        59.57       194.27 
TCGA-GM-A3NW TCGA-GM-A3XL TCGA-GM-A5PV TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A7W5 
      110.50        69.30        13.55        11.84        11.57         4.08 
TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A50Y TCGA-LL-A5YM TCGA-LL-A5YN 
        4.60         9.53        11.44         7.59        15.32        14.70 
TCGA-LL-A6FR TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-OL-A5RW TCGA-OL-A5RY 
        3.88         3.22         6.21         7.36        36.36        24.72 
TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66J TCGA-OL-A66P TCGA-S3-A6ZH TCGA-S3-AA14 
       22.32        20.38        65.62        14.07         8.65         7.17 
TCGA-S3-AA17 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
        3.91         9.60         9.14       105.04 

$`8P LOSS WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        0.39         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SQ TCGA-A2-A04N 
       47.24        20.88        13.68         7.96        18.21       104.81 
TCGA-A2-A04R TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CM TCGA-A2-A0CQ 
       82.16        64.04        55.43       136.73        24.79        88.60 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D0 
      107.93        75.55        75.25        63.45        56.81        21.14 
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-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EY TCGA-A2-A0ST 
       79.76        74.40        37.05        35.05        24.16        99.19 
TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T2 TCGA-A2-A0T4 
       54.64        27.12        44.88        44.28         8.38        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-A0YI TCGA-A2-A0YJ TCGA-A2-A0YL TCGA-A2-A0YM 
       15.42        21.90        14.50        18.61        48.46        31.73 
TCGA-A2-A1FV TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G6 TCGA-A2-A259 
       23.47        22.45        20.25        19.20        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD 
      107.70        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        32.75        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 
       24.39        21.30        23.21        26.96        21.14        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-A26H 
       12.72        23.61        29.56        31.36        24.26        23.80 
TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 
       21.73        22.32        11.34        10.29        13.41        14.70 
TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A5ZW TCGA-A7-A5ZX 
       11.97        14.93        13.74        14.50        10.72        11.05 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06Q TCGA-A8-A06U 
       10.29         9.37        10.42         8.75         1.02        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        43.00 
TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07R TCGA-A8-A07U 
       18.97        18.97        14.01        12.00         8.98        24.99 
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        38.01        28.96 
TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08T 
       33.01        12.00         9.99        31.00         0.99        93.04 
TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A 
       40.01        30.97        17.95        41.98         9.99         9.99 
TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09V 
       12.00         1.02        49.05        45.07        33.07        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-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-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN 
       38.79        26.04         0.92         2.27         0.99         0.69 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS 
       14.83        22.19        19.79        23.24        24.79         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-A6NO TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A046 TCGA-AN-A04D 
        1.68         1.12         1.32         0.33         0.33         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0FF TCGA-AN-A0FJ 
        8.02         7.36         6.51         0.33         4.64         7.96 
TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FY 
        7.00         7.59         7.17         6.02         0.36         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L 
        0.33         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        50.24        62.04        99.25 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12F 
      106.78        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        32.52         2.56        32.91         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        85.97        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        76.21        61.28 
TCGA-AR-A1AY TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q 
       20.22        96.89        78.51        84.20         0.85       101.52 
TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A251 TCGA-AR-A252 
       87.22        76.01        50.96        83.77        78.48        73.18 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK 
       72.76        58.92        93.83        20.25        62.86        42.87 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
        7.36        40.04        38.17        39.39        40.54        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       103.63 
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-A0W7 TCGA-BH-A18G 
       36.85        12.89         5.59        24.95        44.81         2.01 
TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A1EO 
       26.66        72.56        30.28        55.63        37.55        91.99 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EX TCGA-BH-A1F5 
      113.82        82.85        42.28        12.00        49.58        89.16 
TCGA-BH-A1F6 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FJ 
       97.48       120.62       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-A3Z5 TCGA-D8-A4Z1 TCGA-E2-A107 
        0.76        13.08        12.53        14.50         7.33        34.42 
TCGA-E2-A109 TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14P 
       46.59        37.51        28.44        28.87        44.68        40.96 
TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14U TCGA-E2-A14Y TCGA-E2-A152 TCGA-E2-A153 
       38.24        38.60        43.33        28.60        27.12        23.24 
TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15D 
       19.43        21.04        23.87        14.79        25.05        17.29 
TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15L TCGA-E2-A15M 
       20.71        21.63        18.21        17.42        20.58         7.73 
TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B1 
       13.02        19.56        14.07        14.99        60.53        53.03 
TCGA-E2-A1B4 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IJ TCGA-E2-A1IK 
       29.95        28.50        16.47        17.10        28.44        22.65 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB 
        3.88        22.19        11.08        19.66        24.59        40.47 
TCGA-E2-A1LH TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 
      106.75        16.93         5.52        15.72        30.61        34.92 
TCGA-E2-A576 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1NA TCGA-E9-A1NC 
       19.00        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-A22B TCGA-E9-A22G 
       21.27        35.64         0.79        12.53        22.75        23.51 
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        24.56 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3X8 
        0.72        17.75         0.76        26.07        18.41        15.72 
TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE 
       12.33        14.70         0.26        13.81        14.40        15.39 
TCGA-EW-A1IW TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 
       12.20         8.48        18.21        18.90        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OX TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 
       15.68        28.77        29.95        41.13        39.78        29.82 
TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD 
       23.11        18.48        30.08        19.99         6.15        13.94 
TCGA-EW-A1PG TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A423 TCGA-GI-A2C8 TCGA-GM-A2DB 
       34.55        22.09        21.27        10.16         7.40        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-A3NY TCGA-GM-A3XG 
       90.84        76.64        77.33        53.36        38.20        43.73 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A9QF 
       66.38        72.03        18.12        21.24         6.67         8.75 
TCGA-LL-A442 TCGA-LL-A5YL TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ 
       10.95        17.06        14.47        14.79        11.57         2.63 
TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LQ-A4E4 TCGA-MS-A51U 
        4.14         4.50         4.50         5.59        27.91         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        31.99        58.62        27.65 
TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66K TCGA-OL-A66L 
       34.92        16.87        26.70        23.47        33.57        31.07 
TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PL-A8LV TCGA-PL-A8LX 
       26.04         7.23        28.21        19.73         0.23         0.16 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA10 
        0.26         3.95        16.50         6.81        10.59         7.92 
TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA15 TCGA-W8-A86G TCGA-Z7-A8R5 
        5.56         8.52         6.87         5.29       100.01 

  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 
           23.065            22.190 
[1] "0.0 - 194.3 (23.1)" "0.0 - 234.3 (22.2)"
[1] "hr=" "1.4"
D55V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8P LOSS MUTATED        31       29        3        1       130        85
  8P LOSS WILD-TYPE      52       51        6        4       212       149
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8P LOSS MUTATED           0         53          9         24        6
  8P LOSS WILD-TYPE         2         89         20         39       12
                   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                 31                52
  STAGE IA                29                51
  STAGE IB                 3                 6
  STAGE II                 1                 4
  STAGE IIA              130               212
  STAGE IIB               85               149
  STAGE III                0                 2
  STAGE IIIA              53                89
  STAGE IIIB               9                20
  STAGE IIIC              24                39
  STAGE IV                 6                12
  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    99 227  36  15
  8P LOSS WILD-TYPE 166 367  88  24
D55V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1              99               166
  T2             227               367
  T3              36                88
  T4              15                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
  8P LOSS MUTATED   178 119  47  26
  8P LOSS WILD-TYPE 303 220  66  48
D55V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0             178               303
  N1             119               220
  N2              47                66
  N3              26                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          3 322   6  46
  8P LOSS WILD-TYPE        2 532  13 101
D55V6, multiclass
          clus
vv         8P LOSS MUTATED 8P LOSS WILD-TYPE
  CM0 (I+)               3                 2
  M0                   322               532
  M1                     6                13
  MX                    46               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"
D55V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   374   3
  8P LOSS WILD-TYPE 640   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    374    3
  8P LOSS WILD-TYPE  640    8
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE             374               640
  MALE                 3                 8
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  8P LOSS MUTATED                            1                           307
  8P LOSS WILD-TYPE                          0                           447
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  8P LOSS MUTATED                               39                   2
  8P LOSS WILD-TYPE                            136                   4
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  8P LOSS MUTATED                                  7                  2
  8P LOSS WILD-TYPE                               22                 13
                   vv
clus                OTHER  SPECIFY
  8P LOSS MUTATED               18
  8P LOSS WILD-TYPE             26
D55V8, multiclass
                                  clus
vv                                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                307               447
  INFILTRATING LOBULAR CARCINOMA                39               136
  MEDULLARY CARCINOMA                            2                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               7                22
  MUCINOUS CARCINOMA                             2                13
  OTHER  SPECIFY                                18                26
[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   110 267
  8P LOSS WILD-TYPE 172 476
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    110  267
  8P LOSS WILD-TYPE  172  476
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO              110               172
  YES             267               476
[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                          63   252
  8P LOSS WILD-TYPE                        95   465
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                     63                95
  WHITE                                        252               465
[1] 4 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    11 312
  8P LOSS WILD-TYPE  25 514
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     11  312
  8P LOSS WILD-TYPE   25  514
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                  11                25
  NOT HISPANIC OR LATINO             312               514
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8Q LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    69  14
  8Q LOSS WILD-TYPE 817 105
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               83               922 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               14               105 
$`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        50.04        50.70        16.57         0.23 
TCGA-AN-A04A TCGA-AN-A0FD TCGA-AN-A0XO TCGA-AO-A03P TCGA-AO-A0J2 TCGA-AO-A0J9 
        2.96         6.44        12.33        84.69        32.78        53.03 
TCGA-AO-A0JA TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AQ-A0Y5 TCGA-AR-A0TY 
       21.53        55.33        71.80       102.58         5.65        55.86 
TCGA-AR-A0U3 TCGA-AR-A24H TCGA-AR-A24K TCGA-B6-A0IK TCGA-B6-A0IQ TCGA-B6-A0RG 
      114.02       109.58        50.89        18.77       140.88        68.45 
TCGA-B6-A0RS TCGA-B6-A0WS TCGA-B6-A0X5 TCGA-B6-A408 TCGA-BH-A0B7 TCGA-BH-A0BR 
      100.70        97.48        68.94        49.94        56.98        53.69 
TCGA-BH-A0C7 TCGA-BH-A0DG TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0W3 TCGA-BH-A18S 
       42.90        23.44        24.49        31.00        23.93        66.05 
TCGA-BH-A18T TCGA-BH-A1EN TCGA-BH-A1F8 TCGA-BH-A1FD TCGA-C8-A12P TCGA-C8-A132 
        7.36        69.93        24.66        33.17        11.77         1.45 
TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HI TCGA-C8-A1HL TCGA-C8-A26W 
        0.69         3.85         3.75        11.34        10.42         0.23 
TCGA-D8-A140 TCGA-D8-A145 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A27W TCGA-D8-A3Z6 
       13.25        13.48        14.17        17.49        12.26        18.51 
TCGA-E2-A14V TCGA-E2-A15K TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1L8 TCGA-E2-A1LG 
       34.26         9.04        32.78        33.73        39.62        18.87 
TCGA-E2-A1LL TCGA-E9-A1N8 TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A244 TCGA-EW-A1PE 
       43.04        12.00         1.38        21.21         0.69        10.52 
TCGA-EW-A3U0 TCGA-EW-A424 TCGA-LL-A440 TCGA-LL-A8F5 TCGA-OL-A5RW TCGA-OL-A5RZ 
       17.49        10.59         9.53         6.21        36.36        22.32 
TCGA-OL-A5S0 TCGA-OL-A66P TCGA-S3-A6ZH TCGA-S3-AA14 TCGA-XX-A899 
       20.38        14.07         8.65         7.17         9.60 

$`8Q LOSS WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        0.39         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN 
       47.24        20.88        13.68        31.79         7.96        39.32 
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 
      136.73        64.57        24.79       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-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        48.46 
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-A3XU TCGA-A2-A3XV TCGA-A2-A3XW 
       39.65        33.93        83.01        29.98        32.75        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        24.39        21.30 
TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE 
       23.21        26.96        21.14        21.90        38.30        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D 
       34.29        35.47        30.61        35.67        33.11        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-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-A7-A6VY TCGA-A8-A06O 
       11.05        10.29         9.37        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        53.06        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        43.00 
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        24.99         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        38.01 
TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L 
       28.96        33.01        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        33.01        93.04        43.00 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 
       40.01        33.01        30.97        17.95        41.98         9.99 
TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K 
        9.99        12.00         1.02        49.05        45.07        29.98 
TCGA-A8-A09M 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-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-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-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-A3OD TCGA-AC-A3QP TCGA-AC-A3TN 
        2.27         0.99         0.69        14.83        22.19         1.12 
TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X 
       19.79        23.24        24.79         1.55         0.07         1.12 
TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OP 
        1.81         1.18         0.69         0.43         1.68         1.74 
TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A046 TCGA-AN-A049 
        1.12         1.32         0.33         0.33         0.33         0.62 
TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM 
        1.78         1.71         8.02         7.36         6.51         0.16 
TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK 
        0.33         0.33         0.33         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-A0XP 
        0.33         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-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-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       59.05        29.13        21.40        52.18        24.16        37.48 
TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE 
       20.32        22.36        50.70        50.86        72.00        76.77 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A125 TCGA-AO-A126 
       21.37        26.24        50.24        62.04        99.25       108.72 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
      106.78        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-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP 
       15.62        32.52         2.56        32.91         9.99       111.32 
TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW 
       49.32         5.26        74.79        86.66        29.75        98.93 
TCGA-AR-A0TX TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U4 
       64.83        76.14        65.36       101.95        83.87        85.97 
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        37.81 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24L 
       76.21        61.28        63.62        62.14        20.22        73.02 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R 
       96.89        78.51        84.20         0.85       101.52        87.22 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
       76.01        53.36        85.35        50.96        83.77        79.00 
TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
       56.15        78.48        73.18        72.76        58.92        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM 
      128.65        20.25        62.86        42.87         7.36        40.04 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN 
       38.17        39.39        40.54        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-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0RE 
      176.98       126.12        84.59       110.14       110.93       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-A0WT 
      102.77       140.48        89.46       131.21       157.41       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-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI 
      186.48        28.27        58.88        43.59       101.52        73.51 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A40B TCGA-B6-A40C 
      139.17       170.17        85.35        54.28       103.63        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-A0B9 
       40.83        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-A0BP TCGA-BH-A0BQ TCGA-BH-A0BS 
       44.05        61.68        35.67        48.69        27.19        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-A0DD TCGA-BH-A0DE TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       48.13        45.83        31.17        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-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-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-A18U TCGA-BH-A18V 
       37.74        30.28        55.63        37.55        51.39        51.16 
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-A1FB TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
      120.62       114.15        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-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-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-A12Q TCGA-C8-A12U TCGA-C8-A12V 
       11.77        11.77        12.66         0.07        12.66        12.66 
TCGA-C8-A12W TCGA-C8-A12X 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-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN 
       10.92        11.34         0.16        12.03         2.30         3.25 
TCGA-C8-A26V TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 
        0.30         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-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A146 
       11.90        20.88        20.58        13.97        14.17        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-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-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-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-A4Z1 TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 
       12.53        14.50         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-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z 
       33.30        43.33        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-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-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15L 
       21.63        18.21        12.92        17.42        19.40        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-A1II TCGA-E2-A1IJ 
       16.47        17.10        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-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH 
       27.42        19.66        24.59        40.47        28.90       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-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N4 
       30.61        34.92        19.89        19.00         9.21        19.20 
TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND 
       36.82        13.48        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-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB 
        0.62         2.10         6.12         2.76        32.09        20.81 
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-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A245 
       22.75        12.89        23.51        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        24.56         0.72        17.75 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X 
        0.76        26.07        18.41         0.62        15.72        12.33 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE 
        0.23        14.70         0.26        13.81        14.40        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        43.73        69.30 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX 
       66.38        72.03        13.55        18.12        11.84        11.57 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A441 
       21.24         6.67         4.08         4.60         8.75        11.44 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO 
       10.95         7.59        17.06        15.32        14.70        14.47 
TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z 
       14.79        11.57         2.63         3.88         4.14         4.50 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
        4.50         5.59         3.22         7.36        27.91         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        31.99        58.62        27.65 
TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J 
       34.92        16.87        24.72        26.70        23.47        65.62 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A6VO TCGA-OL-A6VQ 
       33.57        31.07        26.04         7.23        28.21        19.73 
TCGA-PL-A8LV TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG 
        0.23         0.16         0.26         3.95        16.50         6.81 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA15 TCGA-S3-AA17 
       10.59         7.92         5.56         8.52         6.87         3.91 
TCGA-W8-A86G TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        5.29         9.14       100.01       105.04 

  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 
           20.380            22.785 
[1] "0.2 - 140.9 (20.4)" "0.0 - 234.3 (22.8)"
[1] "hr=" "1.7"
D56V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8Q LOSS MUTATED         5        7        0        0        28        24
  8Q LOSS WILD-TYPE      78       73        9        5       314       210
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8Q LOSS MUTATED           0         12          3          5        0
  8Q LOSS WILD-TYPE         2        130         26         58       18
                   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                  5                78
  STAGE IA                 7                73
  STAGE IB                 0                 9
  STAGE II                 0                 5
  STAGE IIA               28               314
  STAGE IIB               24               210
  STAGE III                0                 2
  STAGE IIIA              12               130
  STAGE IIIB               3                26
  STAGE IIIC               5                58
  STAGE IV                 0                18
  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    18  54  10   3
  8Q LOSS WILD-TYPE 247 540 114  36
D56V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1              18               247
  T2              54               540
  T3              10               114
  T4               3                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
  8Q LOSS MUTATED    35  34   9   5
  8Q LOSS WILD-TYPE 446 305 104  69
D56V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0              35               446
  N1              34               305
  N2               9               104
  N3               5                69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  8Q LOSS MUTATED          1  69   0  15
  8Q LOSS WILD-TYPE        4 785  19 132
D56V6, multiclass
          clus
vv         8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CM0 (I+)               1                 4
  M0                    69               785
  M1                     0                19
  MX                    15               132
[1] 4 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    85   0
  8Q LOSS WILD-TYPE 929  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     85    0
  8Q LOSS WILD-TYPE  929   11
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE              85               929
  MALE                 0                11
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  8Q LOSS MUTATED                            0                            69
  8Q LOSS WILD-TYPE                          1                           685
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  8Q LOSS MUTATED                               11                   0
  8Q LOSS WILD-TYPE                            164                   6
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  8Q LOSS MUTATED                                  1                  2
  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                 69               685
  INFILTRATING LOBULAR CARCINOMA                11               164
  MEDULLARY CARCINOMA                            0                 6
  MIXED HISTOLOGY (PLEASE SPECIFY)               1                28
  MUCINOUS CARCINOMA                             2                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    18  67
  8Q LOSS WILD-TYPE 264 676
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     18   67
  8Q LOSS WILD-TYPE  264  676
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO               18               264
  YES              67               676
[1] 2 2
[1] FALSE
D56V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q LOSS MUTATED                                  0     8
  8Q LOSS WILD-TYPE                                1    48
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED                          20    53
  8Q LOSS WILD-TYPE                       138   664
D56V11, multiclass
                                  clus
vv                                 8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          8                48
  BLACK OR AFRICAN AMERICAN                     20               138
  WHITE                                         53               664
[1] 4 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  72
  8Q LOSS WILD-TYPE  32 754
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      4   72
  8Q LOSS WILD-TYPE   32  754
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                32
  NOT HISPANIC OR LATINO              72               754
[1] 2 2
[1] FALSE

Clustering(57) Variable = 9P LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED   252  41
  9P LOSS WILD-TYPE 634  78
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              293               712 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               41                78 
$`9P LOSS MUTATED`
TCGA-A1-A0SJ TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A0CL TCGA-A2-A0CT TCGA-A2-A0D0 
       13.68        28.01        18.02        64.57        75.25        21.14 
TCGA-A2-A0EO TCGA-A2-A0EQ TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0SV TCGA-A2-A0SW 
       80.28        79.76        35.05        34.29        27.12        44.88 
TCGA-A2-A0T0 TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YT TCGA-A2-A1FW 
       17.52        18.21        21.90        21.67        23.77        17.36 
TCGA-A2-A1FX TCGA-A2-A1G1 TCGA-A2-A25B TCGA-A2-A25E TCGA-A2-A3XS TCGA-A2-A3XV 
       36.79        19.20        16.31        91.92        33.93        32.75 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A4S1 TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA 
       38.40        34.98        26.96        30.61        37.45        35.67 
TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A26G TCGA-A7-A2KD TCGA-A7-A4SA TCGA-A7-A4SB 
       31.73        12.72        23.74        22.32        14.93        13.74 
TCGA-A7-A4SF TCGA-A7-A6VV TCGA-A8-A06O TCGA-A8-A06R TCGA-A8-A06U TCGA-A8-A06Z 
       17.92        10.29        13.02        17.98        29.03         1.02 
TCGA-A8-A075 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07G TCGA-A8-A07W TCGA-A8-A08G 
       17.03         9.01        43.00        18.97         9.99        19.96 
TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A097 
       12.00        37.05        31.00        31.00         0.99        12.00 
TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09M 
        9.99        12.00         1.02        49.05        45.07        33.07 
TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09W TCGA-A8-A0A2 
        1.02        25.02         8.98        19.04         0.99        19.04 
TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-AC-A2BM TCGA-AC-A2FF 
       21.04         0.99        13.02        17.03        38.20        55.43 
TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A62V TCGA-AC-A6IW TCGA-AC-A8OP 
        1.02         0.92         2.27         0.07         0.69         1.74 
TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C 
        0.33         0.33         0.23         0.62         2.96         1.78 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0FJ TCGA-AN-A0FW 
        8.02         7.36         6.51         0.16         7.96         0.36 
TCGA-AN-A0FZ TCGA-AN-A0XS TCGA-AN-A0XU TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03N 
        0.33         0.33         0.33         5.59        80.28        66.77 
TCGA-AO-A03O TCGA-AO-A03V TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0JA TCGA-AO-A0JD 
       81.63        29.13        52.18        24.16        21.53        72.00 
TCGA-AO-A0JE TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04L 
       76.77        48.36        61.87         0.53        17.79       130.09 
TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A54O TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS 
        5.65        15.62        32.91        49.32         5.26        74.79 
TCGA-AR-A0TV TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 
       29.75        55.86        76.14       101.95        83.87       114.02 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AW 
       85.97        75.55        61.84        39.98        43.07        63.62 
TCGA-AR-A24K TCGA-AR-A24N TCGA-AR-A24R TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24Z 
       50.89        78.51        87.22        85.35        50.96        79.00 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A2LK TCGA-AR-A2LL TCGA-B6-A0I9 
       78.48        73.18        58.92        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-A1JJ TCGA-D8-A1JK TCGA-D8-A1JM TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1XA 
       20.09        20.12        19.40        18.58        17.79        27.58 
TCGA-D8-A1XD TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XY TCGA-D8-A1Y3 
       17.16        16.41        16.31         6.35        16.54        14.14 
TCGA-D8-A27F TCGA-D8-A27N TCGA-D8-A27R TCGA-D8-A27W TCGA-E2-A109 TCGA-E2-A14O 
       16.04         4.80        10.09        12.26        46.59        44.68 
TCGA-E2-A14R TCGA-E2-A14T TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A152 
       38.60        33.30        32.02        31.96        17.03        27.12 
TCGA-E2-A15A TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15S TCGA-E2-A1LA 
       23.34        20.71        21.63        12.92        14.07        24.59 
TCGA-E2-A1LB TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A573 TCGA-E9-A1N9 
       40.47       106.75       102.61         8.75        34.92        13.12 
TCGA-E9-A1NA TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R2 TCGA-E9-A1R4 
       36.56        20.05         9.86        11.90         0.62         6.12 
TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RG 
        2.76        21.21        20.81        40.24        34.65        21.27 
TCGA-E9-A1RH TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A5UO TCGA-E9-A5UP 
       34.59        39.09        22.75        12.89        13.81        14.40 
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-LD-A7W5 TCGA-LL-A441 TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A7SZ TCGA-LL-A7T0 
        4.08        11.44        14.79         2.63         5.59         3.22 
TCGA-OL-A5D6 TCGA-OL-A5RZ TCGA-OL-A66N TCGA-OL-A66P TCGA-S3-A6ZH 
       12.66        22.32        26.04        14.07         8.65 

$`9P LOSS WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        0.39         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP 
       47.24        20.88        31.79         7.96        39.32        19.20 
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-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CM 
       63.12        64.04        55.43        36.13       136.73        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        48.46        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        24.39 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE 
       21.30        23.21        21.14        21.90        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        53.06 
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 
       24.99        28.04        18.05        15.06        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08L TCGA-A8-A08S 
        0.99        38.01        28.96        33.01         9.99        33.01 
TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 
       93.04        43.00        40.01        33.01        30.97        17.95 
TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09D TCGA-A8-A09K TCGA-A8-A09V TCGA-A8-A09X 
       41.98         9.99        50.04        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        22.19 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS 
        1.12        16.57        19.79        23.24        24.79         1.55 
TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OQ 
        1.12         1.81         1.18         0.43         1.68         1.12 
TCGA-AC-A8OR TCGA-AN-A046 TCGA-AN-A04D TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT 
        1.32         0.33         1.71         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-A0FX TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN 
        6.02         0.33         0.33         0.33         0.33         0.33 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AO-A03M 
       12.33         0.30         0.33         0.33         5.33        47.84 
TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A0J2 TCGA-AO-A0J3 
       84.69        68.75        47.87        59.05        32.78        21.40 
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-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM 
       21.37        26.24        50.24        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       108.72       106.78        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-A1KR TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A1H3 TCGA-AQ-A54N 
       82.62        70.39        24.79        26.93        32.52         2.56 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0U0 
        9.99       111.32        86.66        98.93        64.83        65.36 
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-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A1AY 
       17.23        37.81        76.21        61.28        62.14        20.22 
TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q 
      109.58        73.02        96.89        84.20         0.85       101.52 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A254 TCGA-AR-A256 
       76.01        53.36        83.77        56.15        72.76        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
      128.65        20.25        62.86        40.04        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       40.54        20.38        54.74        16.04        20.45        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IE 
       77.62       143.38       149.59       220.90        50.70        65.72 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP 
      146.50       112.37       176.98       126.12        84.59       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-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU 
       78.02       172.96       140.48       100.70        89.46       131.21 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ 
      157.41        97.48       188.68        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-A402 TCGA-B6-A40B 
      101.52        73.51       139.17       170.17        54.28       103.63 
TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 
       55.00        38.79        25.55        46.95        40.83        39.16 
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-A0BQ TCGA-BH-A0BS TCGA-BH-A0BT 
       21.70        61.68        35.67        27.19        53.95        45.57 
TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG 
       49.05        41.75        44.02        45.83        31.17        23.44 
TCGA-BH-A0DH TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT 
       38.01        48.23        17.26        15.65         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-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-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-A18M TCGA-BH-A18N TCGA-BH-A18P 
        2.01         7.23        20.12        72.56        37.74        30.28 
TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ET 
       55.63        37.55        66.05        51.16        91.99        82.85 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1F5 
       42.28        12.00        55.69        49.58        25.81        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-A1FR TCGA-BH-A201 TCGA-BH-A202 
       36.92        63.35        55.00       144.59         6.90         0.72 
TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42U 
       38.60        83.31        10.65         6.44        20.12       109.28 
TCGA-BH-A42V TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12Q TCGA-C8-A12V TCGA-C8-A132 
        8.94        11.77        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-A1HN TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Z 
        0.16        12.03         3.25         0.23         0.36         8.28 
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-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-A1JH TCGA-D8-A1JI TCGA-D8-A1JL TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS 
       14.01        18.97        20.09        20.38        21.01        12.20 
TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XB 
       13.32        14.70        16.73        25.74        23.90        18.15 
TCGA-D8-A1XC TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL 
        2.66        15.22        14.73        21.83        14.50        19.92 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW 
       17.69         7.96        15.85        12.99        15.16        12.66 
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-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27P 
       13.05        14.43         9.44        16.41        13.48         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-A14P TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14U 
       28.87        47.15        40.96        38.24        33.17        43.33 
TCGA-E2-A14V TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 
       34.26        28.60        25.41        23.24        19.43        21.04 
TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15G 
       23.87        14.79        25.05        22.82        17.29        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-A1B0 TCGA-E2-A1B1 
       19.56        17.06        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-A1LE TCGA-E2-A1LG TCGA-E2-A1LL TCGA-E2-A2P5 
       39.62        19.66        28.90        18.87        43.04        16.93 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A574 TCGA-E2-A576 
        5.52        15.72         7.20        30.61        19.89        19.00 
TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1NC 
        9.21        19.20        36.82        13.48        12.00        39.55 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1R0 TCGA-E9-A1R3 TCGA-E9-A1R5 
       12.59        35.77        21.57        14.30         2.10         1.38 
TCGA-E9-A1RA TCGA-E9-A1RD TCGA-E9-A1RF TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
       32.09         0.66         6.58        35.64        34.13         0.79 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 
       12.53        13.32        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        24.56         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-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A6HE TCGA-EW-A1IW 
       12.33         0.23        14.70         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-A1P6 
       15.68        29.95        40.41        41.13        39.78        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-A2FW TCGA-EW-A3U0 TCGA-GI-A2C8 TCGA-GM-A2D9 
       34.55        19.96        22.09        17.49         7.40        59.57 
TCGA-GM-A2DA TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI 
      194.27        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        43.73        69.30        66.38        72.03        13.55 
TCGA-GM-A5PX TCGA-JL-A3YW TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LD-A9QF 
       18.12        11.84        21.24         6.67         4.60         8.75 
TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN 
        9.53        10.95         7.59        17.06        15.32        14.70 
TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 
       14.47        11.57         3.88         4.14         4.50         4.50 
TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D7 
        6.21         7.36        27.91         2.79         2.10        46.55 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX 
       31.99        58.62        27.65        34.92        36.36        16.87 
TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K 
       24.72        20.38        26.70        23.47        65.62        33.57 
TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PL-A8LV TCGA-PL-A8LX 
       31.07         7.23        28.21        19.73         0.23         0.16 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA10 
        0.26         3.95        16.50         6.81        10.59         7.92 
TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-W8-A86G 
        5.56         8.52         7.17         6.87         3.91         5.29 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        9.60         9.14       100.01       105.04 

  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 
            21.53             23.24 
[1] "0.1 - 162.1 (21.5)" "0.0 - 234.3 (23.2)"
[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        1       103        59
  9P LOSS WILD-TYPE      62       66        9        4       239       175
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9P LOSS MUTATED           1         49         16         19       10
  9P LOSS WILD-TYPE         1         93         13         44        8
                   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                62
  STAGE IA                14                66
  STAGE IB                 0                 9
  STAGE II                 1                 4
  STAGE IIA              103               239
  STAGE IIB               59               175
  STAGE III                1                 1
  STAGE IIIA              49                93
  STAGE IIIB              16                13
  STAGE IIIC              19                44
  STAGE IV                10                 8
  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    54 195  31  18
  9P LOSS WILD-TYPE 211 399  93  21
D57V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1              54               211
  T2             195               399
  T3              31                93
  T4              18                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
  9P LOSS MUTATED   136  87  47  24
  9P LOSS WILD-TYPE 345 252  66  50
D57V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0             136               345
  N1              87               252
  N2              47                66
  N3              24                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
  9P LOSS MUTATED          1 249  11  37
  9P LOSS WILD-TYPE        4 605   8 110
D57V6, multiclass
          clus
vv         9P LOSS MUTATED 9P LOSS WILD-TYPE
  CM0 (I+)               1                 4
  M0                   249               605
  M1                    11                 8
  MX                    37               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"
D57V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED   292   6
  9P LOSS WILD-TYPE 722   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    292    6
  9P LOSS WILD-TYPE  722    5
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE             292               722
  MALE                 6                 5
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  9P LOSS MUTATED                            0                           254
  9P LOSS WILD-TYPE                          1                           500
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  9P LOSS MUTATED                               20                   3
  9P LOSS WILD-TYPE                            155                   3
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  9P LOSS MUTATED                                  9                  3
  9P LOSS WILD-TYPE                               20                 12
                   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                254               500
  INFILTRATING LOBULAR CARCINOMA                20               155
  MEDULLARY CARCINOMA                            3                 3
  MIXED HISTOLOGY (PLEASE SPECIFY)               9                20
  MUCINOUS CARCINOMA                             3                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"
D57V9, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    95 203
  9P LOSS WILD-TYPE 187 540
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     95  203
  9P LOSS WILD-TYPE  187  540
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               95               187
  YES             203               540
[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                          49   191
  9P LOSS WILD-TYPE                       109   526
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                     49               109
  WHITE                                        191               526
[1] 4 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    12 232
  9P LOSS WILD-TYPE  24 594
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     12  232
  9P LOSS WILD-TYPE   24  594
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                  12                24
  NOT HISPANIC OR LATINO             232               594
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9Q LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED   234  34
  9Q LOSS WILD-TYPE 652  85
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              268               737 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               34                85 
$`9Q LOSS MUTATED`
TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A04W TCGA-A2-A0CL 
       13.68         7.96        28.01        18.02        64.04        64.57 
TCGA-A2-A0CT TCGA-A2-A0D0 TCGA-A2-A0EO TCGA-A2-A0EQ TCGA-A2-A0ET TCGA-A2-A0EU 
       75.25        21.14        80.28        79.76        35.05        34.29 
TCGA-A2-A0SX TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YT TCGA-A2-A1FW 
       50.43        18.21        21.90        21.67        23.77        17.36 
TCGA-A2-A1FX TCGA-A2-A1G1 TCGA-A2-A3XS TCGA-A2-A3XV TCGA-A2-A3XX TCGA-A2-A3XY 
       36.79        19.20        33.93        32.75        38.40        34.98 
TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A13D 
       26.96        21.90        35.31        37.45        35.67        31.73 
TCGA-A7-A13F TCGA-A7-A26G TCGA-A7-A2KD TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SF 
       12.72        23.74        22.32        13.74        14.50        17.92 
TCGA-A7-A6VV TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06X 
       10.29        13.02         1.02        17.98        53.06        31.00 
TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07G TCGA-A8-A07R TCGA-A8-A08F 
        1.02         9.01        43.00        18.97         8.98        33.01 
TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08X 
       12.00        37.05        31.00        31.00         0.99        43.00 
TCGA-A8-A097 TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09Q 
       12.00        12.00         1.02        45.07        33.07        25.02 
TCGA-A8-A09T TCGA-A8-A0A2 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB 
       19.04        19.04        21.04         0.99        13.02        17.03 
TCGA-AC-A2BM TCGA-AC-A2FF TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A62V 
       38.20        55.43         1.02         0.92         2.27         0.07 
TCGA-AC-A6IW TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A04C 
        0.69         1.74         0.33         0.33         0.23         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        52.18        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        32.91        49.32        74.79        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH 
       76.14        65.36       101.95       114.02        85.97        75.55 
TCGA-AR-A1AI TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AW TCGA-AR-A1AY TCGA-AR-A24K 
       61.84        39.98        43.07        63.62        20.22        50.89 
TCGA-AR-A24N TCGA-AR-A24R TCGA-AR-A24V TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 
       78.51        87.22        85.35        79.00        78.48        73.18 
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        34.92        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-E9-A5UP TCGA-EW-A1J6 
       21.27        34.59        22.75        13.81        14.40        28.77 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A2FR 
       25.94        22.82        29.85        52.96        23.11        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-A2C9 TCGA-GM-A2DB TCGA-JL-A3YX TCGA-LL-A441 TCGA-LL-A5YM TCGA-LL-A5YP 
      109.87        53.13        11.57        11.44        15.32        14.79 
TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-OL-A5RZ TCGA-OL-A5S0 
        2.63         3.88         5.59         3.22        22.32        20.38 
TCGA-OL-A66N TCGA-OL-A66P TCGA-S3-A6ZF TCGA-S3-A6ZH 
       26.04        14.07        16.50         8.65 

$`9Q LOSS WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        0.39         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A1-A0SQ 
       47.24        20.88        31.79        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-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
       55.43        36.13       136.73        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        48.46        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        24.39        21.30        23.21        21.14        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        24.99 
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        38.01        28.96        19.96         9.99        33.01 
TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 
       93.04        40.01        33.01        30.97        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        50.04        49.05        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        22.19         1.12        16.57 
TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62X TCGA-AC-A62Y 
       19.79        23.24        24.79         1.55         1.12         1.81 
TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AN-A046 
        1.18         0.43         1.68         1.12         1.32         0.33 
TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AL TCGA-AN-A0AR 
        0.62         2.96         1.71         8.02         6.51         0.33 
TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FL 
        0.33         0.33         6.44         4.64         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-A0XT 
        0.33         0.33        12.33         0.30         0.33         0.33 
TCGA-AN-A0XV TCGA-AO-A03M TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U 
        5.33        47.84        84.69        68.75        47.87        59.05 
TCGA-AO-A0J2 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA 
       32.78        37.48        20.32        22.36        53.03        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        50.24 
TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 
       62.04        71.80       102.58        99.25       108.72       106.78 
TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G 
       96.10        90.58        77.56        64.04        57.30        41.62 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A1H3 
       28.37        14.73        82.62        24.79        26.93        32.52 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW 
        9.99       111.32         5.26        86.66        29.75        98.93 
TCGA-AR-A0TX TCGA-AR-A0U2 TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM 
       64.83        83.87        52.77        51.25        48.82        62.56 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
       43.73        43.56        17.23        37.81        76.21        61.28 
TCGA-AR-A1AX TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24O TCGA-AR-A24P 
       62.14       109.58        73.02        96.89        84.20         0.85 
TCGA-AR-A24Q TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A250 
      101.52        76.01        53.36        50.96        83.77        56.15 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       72.76        58.92        93.83       128.65        20.25        62.86 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM 
       40.04        38.17        39.39        40.54        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-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ 
      220.90        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-A0RM TCGA-B6-A0RN TCGA-B6-A0RQ TCGA-B6-A0RS 
      189.01       234.28        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-A0WY 
       89.46       131.21       157.41        97.48       188.68       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-A40B TCGA-B6-A40C 
      101.52        73.51       139.17       170.17       103.63        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-A0B4 TCGA-BH-A0B6 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BG 
       39.16        56.94        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-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C7 
       53.95        11.67        49.05        41.75        44.02        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-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       48.23        17.26        15.65         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-A0EE TCGA-BH-A0EI TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       32.65        31.00        24.43        15.16        37.78        35.51 
TCGA-BH-A0H6 TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       24.56        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-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-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P 
        7.23        20.12        26.66        72.56        37.74        30.28 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ET 
       37.55        66.05        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-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FG 
       31.53        89.16        97.48       120.62       114.15       122.89 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A202 
       36.92        63.35        55.00       144.59         6.90         0.72 
TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42U 
       38.60        83.31        10.65         6.44        20.12       109.28 
TCGA-BH-A42V TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12Q TCGA-C8-A12V TCGA-C8-A132 
        8.94        11.77        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-A1HG 
        0.69         0.62         3.75        12.33        10.92        11.34 
TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V 
       11.34        12.03        10.42         2.30         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-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-A142 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA 
       13.97        21.14        19.20        14.17        17.49        16.50 
TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH 
       18.71        18.15        18.90        12.03        12.03        14.01 
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-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XB TCGA-D8-A1XC 
       14.70        16.73        25.74        23.90        18.15         2.66 
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-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW 
        7.96        15.85         6.35        12.99        15.16        12.66 
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-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-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-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14Y TCGA-E2-A153 TCGA-E2-A154 
       33.30        43.33        34.26        28.60        23.24        19.43 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15G 
       21.04        23.87        14.79        22.82        17.29        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-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-A1LE TCGA-E2-A1LG 
       27.42        39.62        19.66        24.59        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        30.61 
TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 
       19.89        19.00         9.21        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        24.56 
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-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A6HE 
       15.72        12.33         0.23        14.70         0.26        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-A1OX TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 
       16.57        15.68        29.95        40.41        41.13        39.78 
TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB 
       29.82        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-A2FW TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DC TCGA-GM-A2DD 
       22.09         7.40        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        43.73        69.30 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-LD-A66U 
       66.38        72.03        13.55        18.12        11.84        21.24 
TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A442 
        6.67         4.08         4.60         8.75         9.53        10.95 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A73Y 
        7.59        17.06        14.70        14.47        11.57         4.14 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
        4.50         4.50         6.21         7.36        27.91         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        31.99        58.62        27.65 
TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A66H TCGA-OL-A66I 
       34.92        36.36        16.87        24.72        26.70        23.47 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A6VO TCGA-OL-A6VQ 
       65.62        33.57        31.07         7.23        28.21        19.73 
TCGA-PL-A8LV TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZG TCGA-S3-AA0Z 
        0.23         0.16         0.26         3.95         6.81        10.59 
TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 
        7.92         5.56         8.52         7.17         6.87         3.91 
TCGA-W8-A86G TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        5.29         9.60         9.14       100.01       105.04 

  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 
            23.54             22.06 
[1] "0.1 - 211.6 (23.5)" "0.0 - 234.3 (22.1)"
[1] "hr=" "1.2"
D58V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9Q LOSS MUTATED        19       15        0        1        97        54
  9Q LOSS WILD-TYPE      64       65        9        4       245       180
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9Q LOSS MUTATED           1         42         12         19        7
  9Q LOSS WILD-TYPE         1        100         17         44       11
                   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                64
  STAGE IA                15                65
  STAGE IB                 0                 9
  STAGE II                 1                 4
  STAGE IIA               97               245
  STAGE IIB               54               180
  STAGE III                1                 1
  STAGE IIIA              42               100
  STAGE IIIB              12                17
  STAGE IIIC              19                44
  STAGE IV                 7                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
  9Q LOSS MUTATED    51 172  32  16
  9Q LOSS WILD-TYPE 214 422  92  23
D58V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1              51               214
  T2             172               422
  T3              32                92
  T4              16                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
  9Q LOSS MUTATED   130  78  38  23
  9Q LOSS WILD-TYPE 351 261  75  51
D58V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0             130               351
  N1              78               261
  N2              38                75
  N3              23                51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CM0 (I+)  M0  M1  MX
  9Q LOSS MUTATED          0 226   8  38
  9Q LOSS WILD-TYPE        5 628  11 109
D58V6, multiclass
          clus
vv         9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CM0 (I+)               0                 5
  M0                   226               628
  M1                     8                11
  MX                    38               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"
D58V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED   266   6
  9Q LOSS WILD-TYPE 748   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED    266    6
  9Q LOSS WILD-TYPE  748    5
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE             266               748
  MALE                 6                 5
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  9Q LOSS MUTATED                            0                           229
  9Q LOSS WILD-TYPE                          1                           525
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  9Q LOSS MUTATED                               18                   2
  9Q LOSS WILD-TYPE                            157                   4
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  9Q LOSS MUTATED                                  9                  3
  9Q LOSS WILD-TYPE                               20                 12
                   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                229               525
  INFILTRATING LOBULAR CARCINOMA                18               157
  MEDULLARY CARCINOMA                            2                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               9                20
  MUCINOUS CARCINOMA                             3                12
  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    89 183
  9Q LOSS WILD-TYPE 193 560
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     89  183
  9Q LOSS WILD-TYPE  193  560
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO               89               193
  YES             183               560
[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                          54   169
  9Q LOSS WILD-TYPE                       104   548
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                     54               104
  WHITE                                        169               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"
D58V12, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    11 211
  9Q LOSS WILD-TYPE  25 615
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     11  211
  9Q LOSS WILD-TYPE   25  615
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                  11                25
  NOT HISPANIC OR LATINO             211               615
[1] 2 2
[1] FALSE

Clustering(59) Variable = 10P LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED   136  24
  10P LOSS WILD-TYPE 750  95
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               160                845 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                24                 95 
$`10P LOSS MUTATED`
TCGA-5T-A9QA TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A2-A04T 
        0.39        13.68        31.79        39.32        19.20        73.84 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D4 
       75.55        75.25         5.19        64.04        21.14        25.22 
TCGA-A2-A0YE TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4S1 
       18.21        17.36        36.79         7.30        24.39        26.96 
TCGA-A2-A4S3 TCGA-A7-A0CJ TCGA-A7-A13F TCGA-A7-A26E TCGA-A7-A2KD TCGA-A7-A4SB 
       21.90        30.61        12.72        31.36        22.32        13.74 
TCGA-A7-A4SE TCGA-A8-A06R TCGA-A8-A076 TCGA-A8-A07I TCGA-A8-A084 TCGA-A8-A08F 
       21.17        17.98        53.98        14.01        15.06        33.01 
TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A097 TCGA-A8-A09B TCGA-A8-A09R TCGA-A8-A0A6 
       12.00         9.99        12.00        12.00         8.98        21.04 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23H TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ 
       17.03        38.04         2.66         1.02         0.92         2.27 
TCGA-AC-A62Y TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AN-A049 TCGA-AN-A0AK TCGA-AN-A0AT 
        1.81         0.69         0.43         0.62         7.36         0.33 
TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0XN TCGA-AN-A0XP TCGA-AN-A0XS TCGA-AN-A0XU 
        0.33         0.36         0.33         0.30         0.33         0.33 
TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03U TCGA-AO-A0JD TCGA-AO-A12F TCGA-AQ-A04J 
       47.84        66.77        59.05        72.00        48.36        26.93 
TCGA-AR-A0TR TCGA-AR-A0TV TCGA-AR-A0U2 TCGA-AR-A1AN TCGA-AR-A24L TCGA-AR-A24Q 
        5.26        29.75        83.87        43.73        73.02       101.52 
TCGA-AR-A24R TCGA-AR-A24W TCGA-AR-A250 TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LK 
       87.22        50.96        56.15        72.76        93.83        42.87 
TCGA-AR-A2LO TCGA-AR-A2LR TCGA-AR-A5QQ TCGA-B6-A0IK TCGA-B6-A0RL TCGA-B6-A0RS 
       39.39        20.38        10.59        18.77        81.17       100.70 
TCGA-B6-A0RU TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A408 TCGA-BH-A0AU TCGA-BH-A0B3 
      131.21        73.51       139.17        49.94        24.53        39.55 
TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BJ TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BZ 
       56.98        37.22        21.70        45.57        49.94        49.05 
TCGA-BH-A0C1 TCGA-BH-A0C7 TCGA-BH-A0EB TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HW 
       44.02        42.90        24.49        41.00        52.96        51.32 
TCGA-BH-A0WA TCGA-BH-A18I TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1EU TCGA-BH-A1F8 
       23.05         7.23        51.16        91.99        42.28        24.66 
TCGA-BH-A1FH TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A202 TCGA-BH-A208 TCGA-C8-A12L 
       36.92        45.63        72.07         0.72        57.83        11.93 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A138 TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HN 
        1.45         0.69         3.75        11.34        12.03         3.25 
TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Y TCGA-D8-A1J8 TCGA-D8-A1JE TCGA-D8-A1JG 
        0.30         0.23         0.43        14.17        18.90        12.03 
TCGA-D8-A1JK TCGA-D8-A1XB TCGA-D8-A1XQ TCGA-D8-A1XV TCGA-D8-A27F TCGA-D8-A27I 
       20.12        18.15        16.41        15.16        16.04        14.43 
TCGA-D8-A27T TCGA-E2-A10C TCGA-E2-A14T TCGA-E2-A14Z TCGA-E2-A15F TCGA-E2-A15R 
       13.08        40.11        33.30        17.03        21.63        17.06 
TCGA-E2-A15S TCGA-E2-A1IN TCGA-E2-A1L7 TCGA-E2-A1LG TCGA-E2-A56Z TCGA-E9-A1ND 
       14.07        22.19        27.42        18.87         7.20        12.59 
TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1R3 TCGA-E9-A1RC TCGA-E9-A1RF TCGA-E9-A1RG 
       20.05         9.86         2.10        40.24         6.58        21.27 
TCGA-E9-A226 TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A248 TCGA-E9-A54Y TCGA-E9-A5FK 
       34.13        22.75        12.89         1.94         0.23        14.70 
TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-GM-A3XL TCGA-LL-A6FP TCGA-LL-A7T0 
       23.11         7.86        18.90        69.30        11.57         3.22 
TCGA-OL-A5RW TCGA-OL-A66I TCGA-PL-A8LX TCGA-S3-A6ZG 
       36.36        23.47         0.16         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       136.73        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 
       48.46        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        32.75        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        21.30        23.21        21.14 
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        53.06        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        43.00        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 
       24.99         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        38.01        28.96        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        33.01        93.04        43.00        40.01 
TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A 
       33.01        30.97        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        50.04        49.05        45.07        29.98        33.07 
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        22.19         1.12        16.57        19.79 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IV 
       23.24        24.79         1.55         0.07         1.12         1.18 
TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y 
        1.68         1.74         1.12         1.32         0.33         0.33 
TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ 
        0.23         0.33         2.96         1.78         1.71         8.02 
TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0FD TCGA-AN-A0FF 
        6.51         0.16         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-A0FT 
        7.96         7.00         7.59         7.17         6.28         6.02 
TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XO TCGA-AN-A0XR 
        0.33         0.33         0.33         0.33        12.33         0.33 
TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03O TCGA-AO-A03P 
        0.33         5.33         5.59        80.28        81.63        84.69 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 
       68.75        47.87        29.13        32.78        21.40        52.18 
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-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI 
       50.70        50.86        76.77        21.37        26.24        50.24 
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       108.72 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
      106.78        96.10        90.58        77.56        64.04        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-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 
        0.53        17.79        24.79       130.09         5.65        15.62 
TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ 
       32.52         2.56        32.91         9.99       111.32        49.32 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
       74.79        86.66        98.93        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       101.95       114.02        85.97        75.55        61.84 
TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AO TCGA-AR-A1AP 
       52.77        51.25        48.82        62.56        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        37.81        76.21        61.28        63.62 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24M TCGA-AR-A24N 
       62.14        20.22       109.58        50.89        96.89        78.51 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24X 
       84.20         0.85        76.01        53.36        85.35        83.77 
TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LH 
       79.00        78.48        73.18        58.92       128.65        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ TCGA-AR-A5QM 
       62.86         7.36        40.04        38.17        40.54        54.74 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 
       16.04        20.45        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-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ 
      176.98       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-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-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-A2IU TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A40B TCGA-B6-A40C 
      101.52       170.17        85.35        54.28       103.63        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-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-A0BW TCGA-BH-A0C0 TCGA-BH-A0C3 
       27.19        53.69        53.95        11.67        41.75        48.13 
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-A0EE TCGA-BH-A0EI 
        9.63        44.81        46.19        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-A0H7 TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       23.08        26.50        20.38         5.85         2.50        13.61 
TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 
       36.85        12.89        27.25        50.79         5.59        23.93 
TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18J 
       24.95        42.35        44.81         8.81         2.01        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-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1ES 
       37.55        66.05         7.36        51.39        69.93       113.82 
TCGA-BH-A1ET TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 
       82.85        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-A1FJ TCGA-BH-A1FL TCGA-BH-A1FR TCGA-BH-A1FU 
       74.73       122.89        63.35        55.00       144.59        72.07 
TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q 
        6.90        38.60        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-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-A135 TCGA-C8-A137 TCGA-C8-A1HE 
       12.66         3.12         1.78         0.62         3.85        12.33 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A26X 
       10.92        11.34         0.16        10.42         2.30         0.36 
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-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JF 
       17.49        16.50        18.71        15.78        18.15        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-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-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-A1XT TCGA-D8-A1XU TCGA-D8-A1XW 
        7.96        15.85        16.31         6.35        12.99        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-A27K TCGA-D8-A27L TCGA-D8-A27M 
       17.42        13.45        13.05         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-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O 
       40.41        37.51        28.44        28.87        47.15        44.68 
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-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-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-A15M TCGA-E2-A15O TCGA-E2-A15P 
       19.40         9.04        20.58         7.73        13.02        19.56 
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-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-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-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 
        5.52        15.72        30.61        34.92        19.89        19.00 
TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 
        9.21        19.20        36.82        13.48        12.00        13.12 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1QZ TCGA-E9-A1R0 
       36.56        39.55        35.77        21.57        11.90        14.30 
TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA 
        0.62         6.12         1.38         2.76        21.21        32.09 
TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A227 
       20.81         0.66        34.65        34.59        35.64         0.79 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 
       12.53        13.32        39.09        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        24.56         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-A54X TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW 
       12.33         0.26        13.81        14.40        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-A1P6 
       40.41        41.13        39.78        52.96        29.82        18.48 
TCGA-EW-A1P7 TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
       30.08        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-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-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        43.73        66.38        72.03 
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        21.24         6.67 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
        4.08         4.60         8.75         9.53        11.44        10.95 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP 
        7.59        17.06        15.32        14.70        14.47        14.79 
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-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
        6.21         7.36        27.91         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        31.99        58.62        27.65        34.92        16.87 
TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K 
       24.72        22.32        20.38        26.70        65.62        33.57 
TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ 
       31.07        26.04         7.23        14.07        28.21        19.73 
TCGA-PL-A8LV TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZH TCGA-S3-AA0Z 
        0.23         0.26         3.95        16.50         8.65        10.59 
TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 
        7.92         5.56         8.52         7.17         6.87         3.91 
TCGA-W8-A86G TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        5.29         9.60         9.14       100.01       105.04 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.16               0.03 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            139.17             234.28 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             20.71              23.34 
[1] "0.2 - 139.2 (20.7)" "0.0 - 234.3 (23.3)"
[1] "hr=" "1.8"
D59V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10P LOSS MUTATED         9        6        1        1        56        36
  10P LOSS WILD-TYPE      74       74        8        4       286       198
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10P LOSS MUTATED           1         32          6         11        3
  10P LOSS WILD-TYPE         1        110         23         52       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                 74
  STAGE IA                  6                 74
  STAGE IB                  1                  8
  STAGE II                  1                  4
  STAGE IIA                56                286
  STAGE IIB                36                198
  STAGE III                 1                  1
  STAGE IIIA               32                110
  STAGE IIIB                6                 23
  STAGE IIIC               11                 52
  STAGE IV                  3                 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    26 110  17   9
  10P LOSS WILD-TYPE 239 484 107  30
D59V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1               26                239
  T2              110                484
  T3               17                107
  T4                9                 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
  10P LOSS MUTATED    66  55  26  12
  10P LOSS WILD-TYPE 415 284  87  62
D59V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0               66                415
  N1               55                284
  N2               26                 87
  N3               12                 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
  10P LOSS MUTATED          1 146   3  12
  10P LOSS WILD-TYPE        4 708  16 135
D59V6, multiclass
          clus
vv         10P LOSS MUTATED 10P LOSS WILD-TYPE
  CM0 (I+)                1                  4
  M0                    146                708
  M1                      3                 16
  MX                     12                135
[1] 4 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   162   0
  10P LOSS WILD-TYPE 852  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED    162    0
  10P LOSS WILD-TYPE  852   11
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE              162                852
  MALE                  0                 11
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  10P LOSS MUTATED                            0                           126
  10P LOSS WILD-TYPE                          1                           628
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  10P LOSS MUTATED                               17                   0
  10P LOSS WILD-TYPE                            158                   6
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  10P LOSS MUTATED                                  7                  1
  10P LOSS WILD-TYPE                               22                 14
                    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                 126                628
  INFILTRATING LOBULAR CARCINOMA                 17                158
  MEDULLARY CARCINOMA                             0                  6
  MIXED HISTOLOGY (PLEASE SPECIFY)                7                 22
  MUCINOUS CARCINOMA                              1                 14
  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    44 118
  10P LOSS WILD-TYPE 238 625
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     44  118
  10P LOSS WILD-TYPE  238  625
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                44                238
  YES              118                625
[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                          19   113
  10P LOSS WILD-TYPE                       139   604
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                      19                139
  WHITE                                         113                604
[1] 4 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     3 131
  10P LOSS WILD-TYPE  33 695
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      3  131
  10P LOSS WILD-TYPE   33  695
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 33
  NOT HISPANIC OR LATINO              131                695
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED   187  31
  10Q LOSS WILD-TYPE 699  88
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               218                787 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                31                 88 
$`10Q LOSS MUTATED`
TCGA-5T-A9QA TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A2-A04T 
        0.39        13.68        31.79        39.32        19.20        73.84 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D4 
       75.55        75.25         5.19        64.04        21.14        25.22 
TCGA-A2-A0SV TCGA-A2-A0T0 TCGA-A2-A0T3 TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YJ 
       27.12        17.52        18.71        18.21        21.90        18.61 
TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1G1 TCGA-A2-A25B TCGA-A2-A3XT TCGA-A2-A4RW 
       17.36        36.79        19.20        16.31        83.01         7.30 
TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A13D 
       24.39        26.96        21.90        30.61        35.67        31.73 
TCGA-A7-A13F TCGA-A7-A26E TCGA-A7-A2KD TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE 
       12.72        31.36        22.32        13.74        14.50        21.17 
TCGA-A7-A56D TCGA-A7-A6VV TCGA-A8-A06R TCGA-A8-A06U TCGA-A8-A076 TCGA-A8-A07I 
       14.73        10.29        17.98        29.03        53.98        14.01 
TCGA-A8-A07R TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08X 
        8.98        15.06        33.01        12.00         9.99        43.00 
TCGA-A8-A097 TCGA-A8-A09B TCGA-A8-A09E TCGA-A8-A09R TCGA-A8-A0A6 TCGA-A8-A0AB 
       12.00        12.00        49.05         8.98        21.04        17.03 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ 
       38.04         0.95         2.66         1.02         0.92         2.27 
TCGA-AC-A62Y TCGA-AC-A6IW TCGA-AC-A8OQ TCGA-AN-A0AK TCGA-AN-A0AT TCGA-AN-A0FV 
        1.81         0.69         1.12         7.36         0.33         0.33 
TCGA-AN-A0FW TCGA-AN-A0XN TCGA-AN-A0XP TCGA-AN-A0XS TCGA-AN-A0XU TCGA-AN-A0XW 
        0.36         0.33         0.30         0.33         0.33         5.59 
TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0JA TCGA-AO-A0JD 
       47.84        66.77        59.05        29.13        21.53        72.00 
TCGA-AO-A124 TCGA-AO-A12F TCGA-AQ-A04J TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TR 
      102.58        48.36        26.93        32.91         9.99         5.26 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0U2 TCGA-AR-A1AY TCGA-AR-A24L TCGA-AR-A24Q 
       29.75        98.93        83.87        20.22        73.02       101.52 
TCGA-AR-A24R TCGA-AR-A24W TCGA-AR-A250 TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LK 
       87.22        50.96        56.15        72.76        93.83        42.87 
TCGA-AR-A2LL TCGA-AR-A2LO TCGA-AR-A2LR TCGA-AR-A5QQ TCGA-B6-A0IK TCGA-B6-A0RE 
        7.36        39.39        20.38        10.59        18.77       211.56 
TCGA-B6-A0RL TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A402 
       81.17       100.70       131.21        73.51       139.17        54.28 
TCGA-B6-A408 TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0B3 TCGA-BH-A0B7 TCGA-BH-A0BA 
       49.94        24.53        38.79        39.55        56.98        37.22 
TCGA-BH-A0BJ TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 
       21.70        45.57        49.94        11.67        49.05        44.02 
TCGA-BH-A0EB TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HW TCGA-BH-A0WA 
       24.49        23.08        41.00        52.96        51.32        23.05 
TCGA-BH-A18I TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1EU TCGA-BH-A1F6 
        7.23         7.36        51.16        91.99        42.28        97.48 
TCGA-BH-A1F8 TCGA-BH-A1FC TCGA-BH-A1FH TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A202 
       24.66       114.15        36.92        45.63        72.07         0.72 
TCGA-BH-A208 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12U TCGA-C8-A132 TCGA-C8-A134 
       57.83        11.93        11.77        12.66         1.45         0.69 
TCGA-C8-A138 TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W 
        3.75        11.34        12.03         3.25         0.30         0.23 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A27A TCGA-D8-A13Y TCGA-D8-A142 TCGA-D8-A1J8 
        0.36         0.43        12.20        11.90        13.97        14.17 
TCGA-D8-A1J9 TCGA-D8-A1JG TCGA-D8-A1JK TCGA-D8-A1X5 TCGA-D8-A1XB TCGA-D8-A1XF 
       17.49        12.03        20.12        18.58        18.15        15.22 
TCGA-D8-A1XJ TCGA-D8-A1XQ TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A27F TCGA-D8-A27I 
       21.83        16.41        12.99        15.16        16.04        14.43 
TCGA-D8-A27T TCGA-E2-A10C TCGA-E2-A14N TCGA-E2-A14T TCGA-E2-A14Z TCGA-E2-A159 
       13.08        40.11        47.15        33.30        17.03        25.05 
TCGA-E2-A15F TCGA-E2-A15P TCGA-E2-A1IE TCGA-E2-A1IN TCGA-E2-A1L7 TCGA-E2-A1LG 
       21.63        19.56        38.30        22.19        27.42        18.87 
TCGA-E2-A1LH TCGA-E2-A1LK TCGA-E2-A56Z TCGA-E2-A574 TCGA-E9-A1ND TCGA-E9-A1NF 
      106.75         8.75         7.20        19.89        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-A2JS TCGA-E9-A54Y TCGA-E9-A5FK 
       22.75        12.89         1.94        17.75         0.23        14.70 
TCGA-EW-A1OW TCGA-EW-A1OZ TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A2FV 
       22.82        40.41        23.11         7.86        18.90        25.91 
TCGA-GM-A2DC TCGA-GM-A3XL TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A7W5 TCGA-LL-A6FP 
       53.52        69.30        11.84        11.57         4.08        11.57 
TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-OL-A5RW TCGA-OL-A66I TCGA-OL-A6VO TCGA-PL-A8LX 
        3.22         6.21        36.36        23.47        28.21         0.16 
TCGA-S3-A6ZG TCGA-S3-A6ZH 
        6.81         8.65 

$`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       136.73        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        48.46        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        32.75        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        21.30        23.21        21.14        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 
       53.06        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 
       43.00        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        24.99         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        38.01        28.96 
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        33.01 
TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 
       93.04        40.01        33.01        30.97        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        50.04        45.07        29.98 
TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
       33.07         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        22.19         1.12        16.57        19.79 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IV 
       23.24        24.79         1.55         0.07         1.12         1.18 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y 
        0.43         1.68         1.74         1.32         0.33         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-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0FD 
        8.02         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-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XO 
        6.02         0.33         0.33         0.33         0.33        12.33 
TCGA-AN-A0XR TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AO-A03L TCGA-AO-A03O TCGA-AO-A03P 
        0.33         0.33         5.33        80.28        81.63        84.69 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 
       68.75        47.87        32.78        21.40        52.18        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-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL 
       76.77        21.37        26.24        50.24        62.04        55.33 
TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A 
       71.80        99.25       108.72       106.78        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-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AR-A0TP 
      130.09         5.65        15.62        32.52         2.56       111.32 
TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
       49.32        74.79        86.66        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       101.95       114.02        85.97        75.55        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-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
       39.98        43.07        17.23        37.81        76.21        61.28 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24M TCGA-AR-A24N 
       63.62        62.14       109.58        50.89        96.89        78.51 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24X 
       84.20         0.85        76.01        53.36        85.35        83.77 
TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LH 
       79.00        78.48        73.18        58.92       128.65        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN 
       62.86        40.04        38.17        40.54        54.74        16.04 
TCGA-AR-A5QP TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA 
       20.45        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-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG 
      126.12        84.59       110.14       110.93       140.88        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-A40B TCGA-B6-A40C TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ 
       85.35       103.63        55.00        20.45        25.55        28.50 
TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B9 
       46.95        40.83        39.16        48.36        56.94        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-A0C0 
       35.67        48.69        27.19        53.69        53.95        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-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-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       35.51        24.56        26.50        20.38         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX 
       13.61        36.85        12.89        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-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-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1ES 
       55.63        37.55        66.05        51.39        69.93       113.82 
TCGA-BH-A1ET TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 
       82.85        12.00        55.69        49.58        17.69        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG 
       31.53        89.16       120.62        33.17        74.73       122.89 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A203 
       63.35        55.00       144.59        72.07         6.90        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-A135 
       12.66        12.66        12.66         3.12         1.78         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-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 
        2.30         8.28         9.67         0.03         0.03         0.03 
TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 
        0.99         0.03         0.23        20.88        13.25        20.58 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1JA TCGA-D8-A1JB 
       14.17        13.48        21.14        19.20        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-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-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XL 
       27.58         2.66        17.16        14.73        14.50        19.92 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XW 
       17.69         7.96        15.85        16.31         6.35        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-A27K TCGA-D8-A27L TCGA-D8-A27M 
       17.42        13.45        13.05         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-A10E TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14P 
       40.41        37.51        28.44        28.87        44.68        40.96 
TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W 
       38.24        38.60        33.17        43.33        34.26        32.02 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 
       31.96        28.60        25.41        27.12        23.24        19.43 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D 
       21.04        23.87        14.79        23.34        22.82        17.29 
TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       20.71        18.21        12.92        17.42        19.40         9.04 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
       20.58         7.73        13.02        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-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-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       28.44        22.65         3.88        20.98        11.08        54.18 
TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LI 
       39.62        19.66        24.59        40.47        28.90       102.61 
TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 
       43.04        16.93         5.52        15.72        30.61        34.92 
TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 
       19.00         9.21        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        24.56 
TCGA-E9-A295 TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
        0.72         0.76        26.07        18.41         0.62        15.72 
TCGA-E9-A54X TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW 
       12.33         0.26        13.81        14.40        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-A1OX TCGA-EW-A1OY TCGA-EW-A1P0 
       15.68        28.77        25.94        29.95        29.85        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PB 
       39.78        52.96        29.82        18.48        30.08        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-A2FS TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 
       55.00        52.73        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-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        43.73 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-LD-A66U TCGA-LD-A74U 
       66.38        72.03        13.55        18.12        21.24         6.67 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y 
        4.60         8.75         9.53        11.44        10.95         7.59 
TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FQ 
       17.06        15.32        14.70        14.47        14.79         2.63 
TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A9Q3 
        3.88         4.14         4.50         4.50         5.59         7.36 
TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 
       27.91         2.79         2.10        12.66        46.55        31.99 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       58.62        27.65        34.92        16.87        24.72        22.32 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       20.38        26.70        65.62        33.57        31.07        26.04 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ TCGA-PL-A8LV TCGA-PL-A8LY TCGA-PL-A8LZ 
        7.23        14.07        19.73         0.23         0.26         3.95 
TCGA-S3-A6ZF TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 
       16.50        10.59         7.92         5.56         8.52         7.17 
TCGA-S3-AA15 TCGA-S3-AA17 TCGA-W8-A86G TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
        6.87         3.91         5.29         9.60         9.14       100.01 
TCGA-Z7-A8R6 
      105.04 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.16               0.03 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            211.56             234.28 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             20.17              23.80 
[1] "0.2 - 211.6 (20.2)" "0.0 - 234.3 (23.8)"
[1] "hr=" "1.7"
D60V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10Q LOSS MUTATED        15       11        2        2        70        48
  10Q LOSS WILD-TYPE      68       69        7        3       272       186
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10Q LOSS MUTATED           1         38          7         19        4
  10Q LOSS WILD-TYPE         1        104         22         44       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                 68
  STAGE IA                 11                 69
  STAGE IB                  2                  7
  STAGE II                  2                  3
  STAGE IIA                70                272
  STAGE IIB                48                186
  STAGE III                 1                  1
  STAGE IIIA               38                104
  STAGE IIIB                7                 22
  STAGE IIIC               19                 44
  STAGE IV                  4                 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    40 141  24  13
  10Q LOSS WILD-TYPE 225 453 100  26
D60V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1               40                225
  T2              141                453
  T3               24                100
  T4               13                 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
  10Q LOSS MUTATED    93  71  32  20
  10Q LOSS WILD-TYPE 388 268  81  54
D60V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0               93                388
  N1               71                268
  N2               32                 81
  N3               20                 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
  10Q LOSS MUTATED          1 193   4  21
  10Q LOSS WILD-TYPE        4 661  15 126
D60V6, multiclass
          clus
vv         10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CM0 (I+)                1                  4
  M0                    193                661
  M1                      4                 15
  MX                     21                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"
D60V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED   218   1
  10Q LOSS WILD-TYPE 796  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED    218    1
  10Q LOSS WILD-TYPE  796   10
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE              218                796
  MALE                  1                 10
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  10Q LOSS MUTATED                            0                           175
  10Q LOSS WILD-TYPE                          1                           579
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  10Q LOSS MUTATED                               21                   1
  10Q LOSS WILD-TYPE                            154                   5
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  10Q LOSS MUTATED                                  7                  1
  10Q LOSS WILD-TYPE                               22                 14
                    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                 175                579
  INFILTRATING LOBULAR CARCINOMA                 21                154
  MEDULLARY CARCINOMA                             1                  5
  MIXED HISTOLOGY (PLEASE SPECIFY)                7                 22
  MUCINOUS CARCINOMA                              1                 14
  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    60 159
  10Q LOSS WILD-TYPE 222 584
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     60  159
  10Q LOSS WILD-TYPE  222  584
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                60                222
  YES              159                584
[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                          41   139
  10Q LOSS WILD-TYPE                       117   578
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                      41                117
  WHITE                                         139                578
[1] 4 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     3 182
  10Q LOSS WILD-TYPE  33 644
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      3  182
  10Q LOSS WILD-TYPE   33  644
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 33
  NOT HISPANIC OR LATINO              182                644
[1] 2 2
[1] FALSE

Clustering(61) Variable = 11P LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED   225  36
  11P LOSS WILD-TYPE 661  83
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               261                744 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                36                 83 
$`11P LOSS MUTATED`
TCGA-5T-A9QA TCGA-A1-A0SJ TCGA-A1-A0SN TCGA-A2-A04P TCGA-A2-A04T TCGA-A2-A0CO 
        0.39        13.68        39.32        18.02        73.84       112.08 
TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ET TCGA-A2-A0SX 
       56.81        34.55        79.76        74.40        35.05        50.43 
TCGA-A2-A0T1 TCGA-A2-A0YG TCGA-A2-A0YJ TCGA-A2-A0YT TCGA-A2-A1FX TCGA-A2-A25B 
       17.13        21.90        18.61        23.77        36.79        16.31 
TCGA-A2-A25E TCGA-A2-A3XS TCGA-A2-A3XX TCGA-A2-A3Y0 TCGA-A7-A0CE TCGA-A7-A0DA 
       91.92        33.93        38.40        38.37        35.31        35.67 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A26E TCGA-A7-A4SA TCGA-A7-A4SE 
       31.73        10.72        12.72        31.36        14.93        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        53.06         1.02         9.01 
TCGA-A8-A07B TCGA-A8-A07I TCGA-A8-A07W TCGA-A8-A082 TCGA-A8-A08F TCGA-A8-A08G 
       43.00        14.01         9.99        18.05        33.01        19.96 
TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08X 
       37.05         9.99        31.00         0.99        33.01        43.00 
TCGA-A8-A093 TCGA-A8-A097 TCGA-A8-A09B TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09T 
       17.95        12.00        12.00        49.05        45.07        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        16.57         0.69         0.43 
TCGA-AC-A8OQ TCGA-AN-A041 TCGA-AN-A04A TCGA-AN-A0AL TCGA-AN-A0FS TCGA-AN-A0FT 
        1.12         0.23         2.96         6.51         6.28         6.02 
TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AO-A03M 
        0.33         0.36         0.33         0.33         0.33        47.84 
TCGA-AO-A03P TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JL 
       84.69        20.32        53.03        21.53        50.70        55.33 
TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A54N 
       57.30        48.36        41.62         0.53        17.79         2.56 
TCGA-AQ-A54O TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U2 
       32.91        86.66        29.75        76.14        65.36        83.87 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AK TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A24H 
      114.02        85.97        51.25        76.21        63.62       109.58 
TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24Z TCGA-AR-A2LL TCGA-AR-A2LO TCGA-B6-A0I9 
       87.22        76.01        79.00         7.36        39.39        12.13 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IO TCGA-B6-A0RU TCGA-B6-A0WV 
       65.72       146.50        18.77       110.14       131.21        79.63 
TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0X1 TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A402 
       17.98        21.47       186.48       101.52       139.17        54.28 
TCGA-B6-A40B TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0BA 
      103.63        38.79        25.55        48.36        56.94        37.22 
TCGA-BH-A0BD TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0BV TCGA-BH-A0C0 TCGA-BH-A0C1 
       18.21        44.05        48.69        49.94        41.75        44.02 
TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0EE 
       48.13        42.90        22.13        13.91        48.23        31.00 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H7 TCGA-BH-A0HA TCGA-BH-A0HX TCGA-BH-A0HY 
       10.78        15.16        23.08        52.96        27.25        50.79 
TCGA-BH-A18L TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A1EN TCGA-BH-A1ES 
       26.66        30.28        55.63         7.36        69.93       113.82 
TCGA-BH-A1F2 TCGA-BH-A1F8 TCGA-BH-A1FC TCGA-BH-A203 TCGA-BH-A28Q TCGA-BH-A42T 
       31.53        24.66       114.15        38.60         6.44         0.99 
TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12W 
       11.93        11.77        11.77         0.07        12.66        12.66 
TCGA-C8-A132 TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI 
        1.45         0.62         3.75        10.92        11.34        11.34 
TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A278 
       12.03        10.42         3.25         0.36         0.43         0.03 
TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A145 TCGA-D8-A1J8 TCGA-D8-A1JC TCGA-D8-A1JD 
       20.88        13.97        13.48        14.17        15.78        18.15 
TCGA-D8-A1JE TCGA-D8-A1JI TCGA-D8-A1JK TCGA-D8-A1X6 TCGA-D8-A1XJ TCGA-D8-A1XS 
       18.90        18.97        20.12        17.79        21.83        16.31 
TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A27G TCGA-D8-A27R TCGA-D8-A27W 
       12.99        12.66        15.32        13.45        10.09        12.26 
TCGA-E2-A105 TCGA-E2-A109 TCGA-E2-A10C TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Z 
       43.00        46.59        40.11        38.60        31.96        17.03 
TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A1BD TCGA-E2-A1IG 
       14.79        25.05        20.71        18.21        17.10        32.78 
TCGA-E2-A1IH TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LA TCGA-E2-A1LH TCGA-E2-A1LI 
       33.73        27.42        39.62        24.59       106.75       102.61 
TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A573 TCGA-E2-A9RU TCGA-E9-A1N9 TCGA-E9-A1NA 
        8.75        43.04        34.92         9.21        13.12        36.56 
TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI 
       12.59        20.05         6.58        21.27        34.59        35.64 
TCGA-E9-A228 TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A3HO TCGA-E9-A3QA 
       12.53        22.75        12.89        23.51        26.07         0.62 
TCGA-E9-A5UO TCGA-E9-A5UP TCGA-EW-A1OZ TCGA-EW-A1P4 TCGA-EW-A1P8 TCGA-EW-A1PC 
       13.81        14.40        40.41        29.82         7.86         6.15 
TCGA-EW-A1PF TCGA-EW-A2FR TCGA-GM-A2DI TCGA-GM-A2DO TCGA-GM-A3XL TCGA-LD-A7W5 
       14.43        55.00        61.91        53.36        69.30         4.08 
TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A7T0 TCGA-LL-A8F5 
       15.32        14.47        14.79        11.57         3.22         6.21 
TCGA-LQ-A4E4 TCGA-OL-A5D6 TCGA-OL-A5RW TCGA-OL-A5RZ TCGA-OL-A66J TCGA-OL-A66K 
       27.91        12.66        36.36        22.32        65.62        33.57 
TCGA-OL-A66O TCGA-PL-A8LV TCGA-PL-A8LX TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH 
        7.23         0.23         0.16        16.50         6.81         8.65 
TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        9.14       100.01       105.04 

$`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       136.73        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        48.46        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        32.75        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        24.39        21.30        23.21 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH 
       26.96        21.14        21.90        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        24.99        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        38.01        28.96        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        33.01        30.97        41.98         9.99 
TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N 
        9.99         1.02        50.04        29.98        33.07         1.02 
TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A4 
       25.02         8.98        15.02         0.99        14.01        13.02 
TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G 
       21.04         0.99        13.02        38.04         0.95        10.85 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FK TCGA-AC-A2FO 
        2.66         1.48        40.57        55.43        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        22.19 
TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V 
        1.12        19.79        23.24        24.79         1.55         0.07 
TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OR 
        1.12         1.81         1.18         1.68         1.74         1.32 
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-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT 
        8.02         7.36         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-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-A03L TCGA-AO-A03N 
        0.33         0.33         5.33         5.59        80.28        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-A0J8 TCGA-AO-A0JC 
       21.40        52.18        24.16        37.48        22.36        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        50.24        62.04 
TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 
       71.80       102.58        99.25       108.72       106.78        96.10 
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-AO-A1KQ TCGA-AO-A1KR TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 
       61.87        70.39        24.79        26.93       130.09         5.65 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
       15.62        32.52         9.99       111.32        49.32         5.26 
TCGA-AR-A0TS TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0U1 TCGA-AR-A1AH 
       74.79        98.93        64.83        55.86       101.95        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-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AV TCGA-AR-A1AX 
       39.98        43.07        17.23        37.81        61.28        62.14 
TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       20.22        50.89        73.02        96.89        78.51        84.20 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X 
        0.85       101.52        53.36        85.35        50.96        83.77 
TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
       56.15        78.48        73.18        72.76        58.92        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN 
      128.65        20.25        62.86        42.87        40.04        38.17 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       40.54        20.38        54.74        16.04        20.45        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC 
       77.62       143.38       149.59       220.90       129.57        50.70 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ 
      112.37       176.98       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-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-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 
      157.41        97.48       188.68       113.79       129.57       129.70 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A2IU 
       28.27        68.94        58.88        43.59        73.51       170.17 
TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AZ 
       85.35        49.94        55.00        24.53        20.45        28.50 
TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B7 TCGA-BH-A0B9 
       46.95        40.83        39.55        39.16        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-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DO TCGA-BH-A0DP 
       45.83        31.17        23.44        38.01        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-A0EI TCGA-BH-A0GY TCGA-BH-A0H3 TCGA-BH-A0H5 
       32.65        24.49        24.43        30.35        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-A0HW TCGA-BH-A0RX TCGA-BH-A0W3 
       13.61        36.85        12.89        51.32         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-A18M TCGA-BH-A18N TCGA-BH-A18R 
        7.23        20.12        90.84        72.56        37.74        37.55 
TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1EU 
       66.05        51.39        51.16        91.99        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-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH 
       97.48       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-A202 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O 
        6.90         0.72        83.31        57.83       130.16        10.65 
TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12V 
       20.12       109.28         8.94        11.77        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A1HE 
       12.66         3.12         1.78         0.69         3.85        12.33 
TCGA-C8-A1HJ TCGA-C8-A1HM TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Z TCGA-C8-A273 
        0.16         2.30         0.30         0.23         8.28         9.67 
TCGA-C8-A274 TCGA-C8-A275 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-A140 TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A146 TCGA-D8-A147 
       11.90        13.25        20.58        14.17        21.14        19.20 
TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH 
       17.49        16.50        18.71        12.03        12.03        14.01 
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-A1X5 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 
       13.32        14.70        18.58        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-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-A1XT TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 
        6.35        15.16        16.54        15.52         3.81        14.24 
TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K 
       14.14        17.42        16.04        13.05        14.43         9.44 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V 
       16.41        13.48         4.80         0.76        13.08        12.53 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10A 
       14.50        18.51         7.33        34.42        27.52        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-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-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-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-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-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN 
       37.41        33.70        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-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
       18.87        16.93         5.52        15.72         7.20        30.61 
TCGA-E2-A574 TCGA-E2-A576 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 
       19.89        19.00        19.20        36.82        13.48        12.00 
TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 
       39.55        35.77        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-A226 
       32.09        20.81        40.24         0.66        34.65        34.13 
TCGA-E9-A227 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 
        0.79        13.32        39.09        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        24.56         0.72 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y 
       17.75         0.76        18.41        15.72        12.33         0.23 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
       14.70         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-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-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-A1PD TCGA-EW-A1PE TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FS TCGA-EW-A2FV 
       13.94        10.52        34.55        19.96        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-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       42.71        42.28        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-A5PV 
      110.50        38.20        43.73        66.38        72.03        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        21.24         6.67         4.60 
TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL 
        8.75         9.53        11.44        10.95         7.59        17.06 
TCGA-LL-A5YN TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 
       14.70         2.63         3.88         4.14         4.50         4.50 
TCGA-LL-A7SZ TCGA-LL-A9Q3 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D7 TCGA-OL-A5D8 
        5.59         7.36         2.79         2.10        46.55        31.99 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5S0 
       58.62        27.65        34.92        16.87        24.72        20.38 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66P TCGA-OL-A6VO 
       26.70        23.47        31.07        26.04        14.07        28.21 
TCGA-OL-A6VQ TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 
       19.73         0.26         3.95        10.59         7.92         5.56 
TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-W8-A86G TCGA-XX-A899 
        8.52         7.17         6.87         3.91         5.29         9.60 

  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 
            21.530             22.935 
[1] "0.0 - 186.5 (21.5)" "0.0 - 234.3 (22.9)"
[1] "hr=" "1.4"
D61V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11P LOSS MUTATED        19       11        3        1        89        54
  11P LOSS WILD-TYPE      64       69        6        4       253       180
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11P LOSS MUTATED           0         48         14         18        5
  11P LOSS WILD-TYPE         2         94         15         45       13
                    vv
clus                 STAGE TIS STAGE X
  11P LOSS MUTATED           1       3
  11P LOSS WILD-TYPE         0      13
D61V3, multiclass
            clus
vv           11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  19                 64
  STAGE IA                 11                 69
  STAGE IB                  3                  6
  STAGE II                  1                  4
  STAGE IIA                89                253
  STAGE IIB                54                180
  STAGE III                 0                  2
  STAGE IIIA               48                 94
  STAGE IIIB               14                 15
  STAGE IIIC               18                 45
  STAGE IV                  5                 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
  11P LOSS MUTATED    56 160  31  18
  11P LOSS WILD-TYPE 209 434  93  21
D61V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1               56                209
  T2              160                434
  T3               31                 93
  T4               18                 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   115  84  41  20
  11P LOSS WILD-TYPE 366 255  72  54
D61V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0              115                366
  N1               84                255
  N2               41                 72
  N3               20                 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          0 224   6  36
  11P LOSS WILD-TYPE        5 630  13 111
D61V6, multiclass
          clus
vv         11P LOSS MUTATED 11P LOSS WILD-TYPE
  CM0 (I+)                0                  5
  M0                    224                630
  M1                      6                 13
  MX                     36                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"
D61V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED   264   2
  11P LOSS WILD-TYPE 750   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED    264    2
  11P LOSS WILD-TYPE  750    9
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE              264                750
  MALE                  2                  9
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  11P LOSS MUTATED                            0                           205
  11P LOSS WILD-TYPE                          1                           549
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  11P LOSS MUTATED                               36                   4
  11P LOSS WILD-TYPE                            139                   2
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  11P LOSS MUTATED                                  9                  2
  11P LOSS WILD-TYPE                               20                 13
                    vv
clus                 OTHER  SPECIFY
  11P LOSS MUTATED               10
  11P LOSS WILD-TYPE             34
D61V8, multiclass
                                  clus
vv                                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 205                549
  INFILTRATING LOBULAR CARCINOMA                 36                139
  MEDULLARY CARCINOMA                             4                  2
  MIXED HISTOLOGY (PLEASE SPECIFY)                9                 20
  MUCINOUS CARCINOMA                              2                 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"
D61V9, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    76 190
  11P LOSS WILD-TYPE 206 553
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     76  190
  11P LOSS WILD-TYPE  206  553
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                76                206
  YES              190                553
[1] 2 2
[1] FALSE
D61V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P LOSS MUTATED                                  1    18
  11P LOSS WILD-TYPE                                0    38
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED                          56   162
  11P LOSS WILD-TYPE                       102   555
D61V11, multiclass
                                  clus
vv                                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                          18                 38
  BLACK OR AFRICAN AMERICAN                      56                102
  WHITE                                         162                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"
D61V12, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     4 209
  11P LOSS WILD-TYPE  32 617
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      4  209
  11P LOSS WILD-TYPE   32  617
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 32
  NOT HISPANIC OR LATINO              209                617
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED   311  35
  11Q LOSS WILD-TYPE 575  84
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               346                659 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                35                 84 
$`11Q LOSS MUTATED`
TCGA-5T-A9QA TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN 
        0.39        14.37        43.43        13.68         7.96        39.32 
TCGA-A1-A0SQ TCGA-A2-A04P TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04V TCGA-A2-A0CK 
       18.21        18.02        82.16        73.84        63.12       136.73 
TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CT TCGA-A2-A0CX TCGA-A2-A0D4 TCGA-A2-A0EQ 
       24.79       112.08        75.25        56.81        25.22        79.76 
TCGA-A2-A0ER TCGA-A2-A0ET TCGA-A2-A0EW TCGA-A2-A0SU TCGA-A2-A0SX TCGA-A2-A0T1 
       74.40        35.05        29.75        54.64        50.43        17.13 
TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YF TCGA-A2-A0YI 
       18.71        20.52        20.75        32.55        15.42        14.50 
TCGA-A2-A0YK TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A25B TCGA-A2-A25E 
       19.33        23.77        17.36        36.79        16.31        91.92 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XX TCGA-A2-A3Y0 TCGA-A2-A4RW 
       20.88        39.65        33.93        38.40        38.37         7.30 
TCGA-A7-A0CE TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F 
       35.31        30.61        35.67        31.73        10.72        12.72 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A3J1 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD 
       29.56        31.36        11.28        14.93        13.74        14.50 
TCGA-A7-A4SE TCGA-A7-A6VV TCGA-A8-A06O TCGA-A8-A06T TCGA-A8-A06Z TCGA-A8-A079 
       21.17        10.29        13.02        53.06         1.02         9.01 
TCGA-A8-A07B TCGA-A8-A07I TCGA-A8-A07W TCGA-A8-A082 TCGA-A8-A08F TCGA-A8-A08G 
       43.00        14.01         9.99        18.05        33.01        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        33.01        43.00 
TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A097 TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09E 
       33.01        17.95        12.00        12.00        50.04        49.05 
TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A0A1 
       45.07        29.98        33.07         8.98        19.04        12.00 
TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-AC-A23C 
       19.04        13.02        21.04        13.02        17.03         0.95 
TCGA-AC-A23E TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FG TCGA-AC-A2FM TCGA-AC-A2QH 
        2.37        38.53        38.20        36.99        26.04         1.02 
TCGA-AC-A3HN TCGA-AC-A3W5 TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A8OQ 
        0.69        16.57         1.18         0.69         0.43         1.12 
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-A0FV TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XS TCGA-AN-A0XT 
        0.33         0.36         0.33         0.33         0.33         0.33 
TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03P TCGA-AO-A03T TCGA-AO-A0J3 
        5.59        80.28        47.84        84.69        47.87        21.40 
TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JG TCGA-AO-A0JL TCGA-AO-A12E 
       20.32        53.03        21.53        26.24        55.33        57.30 
TCGA-AO-A12F TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A1H2 TCGA-AQ-A54N TCGA-AQ-A54O 
       48.36         0.53        17.79        15.62         2.56        32.91 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 
       86.66        29.75        76.14        65.36       101.95        83.87 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AM TCGA-AR-A1AU 
      114.02        85.97        61.84        51.25        62.56        76.21 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24R TCGA-AR-A24Z 
       61.28        63.62       109.58        73.02        87.22        79.00 
TCGA-AR-A250 TCGA-AR-A255 TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LO TCGA-B6-A0I9 
       56.15        58.92        42.87         7.36        39.39        12.13 
TCGA-B6-A0IB TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0RG TCGA-B6-A0RL 
      129.57       146.50        18.77       126.12        68.45        81.17 
TCGA-B6-A0RU TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0X1 TCGA-B6-A0X7 
      131.21        79.63        17.98        21.47       186.48        58.88 
TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A402 TCGA-B6-A40B TCGA-BH-A0AU TCGA-BH-A0AY 
      101.52       139.17        54.28       103.63        24.53        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B5 TCGA-BH-A0BA TCGA-BH-A0BD TCGA-BH-A0BL TCGA-BH-A0BP 
       28.50        48.36        37.22        18.21        44.05        48.69 
TCGA-BH-A0BV TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD 
       49.94        41.75        44.02        48.13        42.90        45.83 
TCGA-BH-A0DE TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0E2 TCGA-BH-A0EE TCGA-BH-A0EI 
       31.17        13.91        48.23        14.30        31.00        24.43 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H7 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HP 
       10.78        15.16        23.08        52.96        26.50        13.61 
TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0WA TCGA-BH-A18L TCGA-BH-A18P 
       12.89        27.25        50.79        23.05        26.66        30.28 
TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1F2 TCGA-BH-A1F8 TCGA-BH-A28Q TCGA-BH-A42T 
       69.93       113.82        31.53        24.66         6.44         0.99 
TCGA-C8-A12M TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12W TCGA-C8-A132 
       11.77        11.77         0.07        12.66        12.66         1.45 
TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK 
        0.62         3.75        10.92        11.34        11.34        12.03 
TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z 
       10.42         3.25         0.23         0.36         0.43         8.28 
TCGA-C8-A278 TCGA-C8-A27A TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A145 TCGA-D8-A1J8 
        0.03        12.20        20.88        13.97        13.48        14.17 
TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JI TCGA-D8-A1JK TCGA-D8-A1X6 
       15.78        18.15        18.90        18.97        20.12        17.79 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XF TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XZ 
       25.74        23.90        15.22        16.31        12.99        15.32 
TCGA-D8-A1Y0 TCGA-D8-A27G TCGA-D8-A27I TCGA-D8-A27R TCGA-D8-A27V TCGA-D8-A27W 
       15.52        13.45        14.43        10.09        12.53        12.26 
TCGA-E2-A105 TCGA-E2-A109 TCGA-E2-A14O TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14V 
       43.00        46.59        44.68        38.60        33.17        34.26 
TCGA-E2-A14X TCGA-E2-A155 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15E TCGA-E2-A15G 
       31.96        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-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N5 TCGA-E9-A1N9 TCGA-E9-A1NA 
       34.92        19.00         9.21        36.82        13.12        36.56 
TCGA-E9-A1QZ TCGA-E9-A1R2 TCGA-E9-A1R7 TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI 
       11.90         0.62        21.21         6.58        21.27        35.64 
TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A247 TCGA-E9-A295 TCGA-E9-A3HO 
       22.75        12.89        23.51        27.22         0.72        26.07 
TCGA-E9-A3QA TCGA-E9-A5UO TCGA-E9-A5UP TCGA-EW-A1IW TCGA-EW-A1J1 TCGA-EW-A1J2 
        0.62        13.81        14.40        12.20        18.90        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P4 TCGA-EW-A1PC 
       16.57        15.68        29.85        40.41        29.82         6.15 
TCGA-EW-A1PD TCGA-EW-A1PF TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A423 TCGA-EW-A424 
       13.94        14.43        55.00        52.73        10.16        10.59 
TCGA-GM-A2D9 TCGA-GM-A2DO TCGA-GM-A3XL TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LL-A5YM 
       59.57        53.36        69.30         4.08         4.60        15.32 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FR TCGA-LL-A7SZ TCGA-LL-A7T0 
       14.47        14.79        11.57         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        27.91         2.10        58.62        36.36        24.72 
TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66O TCGA-OL-A66P 
       22.32        20.38        65.62        33.57         7.23        14.07 
TCGA-OL-A6VO TCGA-PL-A8LV TCGA-PL-A8LX TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH 
       28.21         0.23         0.16        16.50         6.81         8.65 
TCGA-S3-AA17 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        3.91         9.14       100.01       105.04 

$`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 
       48.46        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        32.75        49.48        34.98 
TCGA-A2-A3XZ TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 
       31.99        24.39        21.30        23.21        26.96        21.14 
TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB 
       21.90        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-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX 
       11.97        17.92        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-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        24.99        28.04        15.06        36.95 
TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08I TCGA-A8-A08R 
       13.02         0.99        38.01        28.96        12.00         0.99 
TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A 
       93.04        40.01        30.97        41.98         9.99         9.99 
TCGA-A8-A09C TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X 
        1.02         1.02        25.02        15.02         0.99        14.01 
TCGA-A8-A0A7 TCGA-A8-A0AD TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2FB 
        0.99        38.04        10.85         2.66         1.48        40.57 
TCGA-AC-A2FF TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB 
       55.43        38.79        50.70         0.92         2.27         0.99 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ 
       14.83        22.19         1.12        19.79        23.24        24.79 
TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6NO TCGA-AC-A8OP 
        1.55         0.07         1.12         1.81         1.68         1.74 
TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D 
        1.32         0.33         0.33         0.62         1.78         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT 
        8.02         7.36         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-A0FX TCGA-AN-A0FY 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-AO-A03N TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03U 
        0.33         5.33        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-A0J8 
       29.13        32.78        52.18        24.16        37.48        22.36 
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        50.24 
TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 
       62.04        71.80       102.58        99.25       108.72       106.78 
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-A1KQ TCGA-AO-A1KR TCGA-AQ-A04H TCGA-AQ-A04J 
       14.73        82.62        61.87        70.39        24.79        26.93 
TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H3 TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ 
      130.09         5.65        32.52         9.99       111.32        49.32 
TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A1AH 
        5.26        74.79        98.93        64.83        55.86        75.55 
TCGA-AR-A1AJ TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ 
       52.77        48.82        43.73        43.56        39.98        43.07 
TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24M 
       17.23        37.81        62.14        20.22        50.89        96.89 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24T TCGA-AR-A24U 
       78.51        84.20         0.85       101.52        76.01        53.36 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 
       85.35        50.96        83.77        78.48        73.18        72.76 
TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN 
       93.83       128.65        20.25        62.86        40.04        38.17 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       40.54        20.38        54.74        16.04        20.45        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IE 
       77.62       143.38       149.59       220.90        50.70        65.72 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ 
      112.37       176.98        84.59       110.14       110.93       140.88 
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-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-A1KC TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40C 
       43.59        73.51       170.17        85.35        49.94        55.00 
TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 
       38.79        20.45        46.95        40.83        39.55        39.16 
TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BF TCGA-BH-A0BG 
       56.94        56.98        51.68        32.02        25.71        24.85 
TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       21.70        61.68        35.67        27.19        53.69        53.95 
TCGA-BH-A0BT TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI 
       45.57        11.67        49.05        23.44        38.01        22.13 
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-A0E1 TCGA-BH-A0E6 TCGA-BH-A0E7 
       47.41        16.27         4.41        15.68         9.63        44.81 
TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0GY TCGA-BH-A0H3 TCGA-BH-A0H5 
       46.19        32.65        24.49        30.35        37.78        35.51 
TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HQ 
       24.56        41.00        20.38         5.85         2.50        36.85 
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-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-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U 
       37.74        55.63        37.55        66.05         7.36        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-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-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-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-A2L8 TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12L TCGA-C8-A12N TCGA-C8-A12O 
       20.12       109.28         8.94        11.93        11.77        12.66 
TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A137 
       12.66        12.66         3.12         1.78         0.69         3.85 
TCGA-C8-A1HE TCGA-C8-A1HJ TCGA-C8-A1HM TCGA-C8-A26V TCGA-C8-A273 TCGA-C8-A274 
       12.33         0.16         2.30         0.30         9.67         0.03 
TCGA-C8-A275 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A140 
        0.03         0.99         0.03         0.23        11.90        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-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD 
       18.58        16.73        27.58        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-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY 
       16.41        15.85         6.35        15.16        12.66        16.54 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27H 
        3.81        14.24        14.14        17.42        16.04        13.05 
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-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10A 
       14.50        18.51         7.33        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-A14T TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A14Z 
       38.24        33.30        43.33        32.02        28.60        17.03 
TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A156 TCGA-E2-A15A 
       25.41        27.12        23.24        19.43        23.87        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-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-A1BC TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK 
       16.47        38.30        37.41        33.70        28.44        22.65 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LB 
        3.88        22.19        20.98        54.18        19.66        40.47 
TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A2P5 TCGA-E2-A2P6 
       28.90        18.87       106.75       102.61        16.93         5.52 
TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A574 TCGA-E9-A1N4 TCGA-E9-A1N6 TCGA-E9-A1N8 
       15.72        30.61        19.89        19.20        13.48        12.00 
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-A1R0 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1RA 
       14.30         2.10         6.12         1.38         2.76        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-A22H TCGA-E9-A243 
        0.79        12.53        13.32        39.09        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        24.56        17.75 
TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK 
        0.76        18.41        15.72        12.33         0.23        14.70 
TCGA-E9-A5FL TCGA-E9-A6HE TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J6 
        0.26        15.39        39.72         8.48        18.21        28.77 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 
       25.94        22.82        29.95        41.13        39.78        52.96 
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-A1PG TCGA-EW-A1PH TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 
       10.52        34.55        19.96        25.91        22.09        21.27 
TCGA-EW-A3U0 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC 
       17.49         7.40       109.87       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-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN 
       76.64        77.33       110.50        38.20        43.73        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U 
       72.03        13.55        18.12        11.84        11.57        21.24 
TCGA-LD-A74U TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y 
        6.67         8.75         9.53        11.44        10.95         7.59 
TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 
       17.06        14.70         2.63         4.14         4.50         4.50 
TCGA-LL-A9Q3 TCGA-MS-A51U TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5RU 
        7.36         2.79        12.66        46.55        31.99        27.65 
TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66L TCGA-OL-A66N 
       34.92        16.87        26.70        23.47        31.07        26.04 
TCGA-OL-A6VQ TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 
       19.73         0.26         3.95        10.59         7.92         5.56 
TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-W8-A86G TCGA-XX-A899 
        8.52         7.17         6.87         5.29         9.60 

  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 
             20.96              23.34 
[1] "0.0 - 186.5 (21.0)" "0.0 - 234.3 (23.3)"
[1] "hr=" "1"  
D62V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11Q LOSS MUTATED        19       22        4        3       117        82
  11Q LOSS WILD-TYPE      64       58        5        2       225       152
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11Q LOSS MUTATED           1         60         14         20        7
  11Q LOSS WILD-TYPE         1         82         15         43       11
                    vv
clus                 STAGE TIS STAGE X
  11Q LOSS MUTATED           0       4
  11Q LOSS WILD-TYPE         1      12
D62V3, multiclass
            clus
vv           11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  19                 64
  STAGE IA                 22                 58
  STAGE IB                  4                  5
  STAGE II                  3                  2
  STAGE IIA               117                225
  STAGE IIB                82                152
  STAGE III                 1                  1
  STAGE IIIA               60                 82
  STAGE IIIB               14                 15
  STAGE IIIC               20                 43
  STAGE IV                  7                 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
  11Q LOSS MUTATED    78 216  41  18
  11Q LOSS WILD-TYPE 187 378  83  21
D62V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1               78                187
  T2              216                378
  T3               41                 83
  T4               18                 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   153 117  52  24
  11Q LOSS WILD-TYPE 328 222  61  50
D62V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0              153                328
  N1              117                222
  N2               52                 61
  N3               24                 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
  11Q LOSS MUTATED          2 284   8  59
  11Q LOSS WILD-TYPE        3 570  11  88
D62V6, multiclass
          clus
vv         11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CM0 (I+)                2                  3
  M0                    284                570
  M1                      8                 11
  MX                     59                 88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED   347   6
  11Q LOSS WILD-TYPE 667   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED    347    6
  11Q LOSS WILD-TYPE  667    5
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE              347                667
  MALE                  6                  5
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  11Q LOSS MUTATED                            0                           258
  11Q LOSS WILD-TYPE                          1                           496
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  11Q LOSS MUTATED                               65                   4
  11Q LOSS WILD-TYPE                            110                   2
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  11Q LOSS MUTATED                                 11                  3
  11Q LOSS WILD-TYPE                               18                 12
                    vv
clus                 OTHER  SPECIFY
  11Q LOSS MUTATED               11
  11Q LOSS WILD-TYPE             33
D62V8, multiclass
                                  clus
vv                                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 258                496
  INFILTRATING LOBULAR CARCINOMA                 65                110
  MEDULLARY CARCINOMA                             4                  2
  MIXED HISTOLOGY (PLEASE SPECIFY)               11                 18
  MUCINOUS CARCINOMA                              3                 12
  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"
D62V9, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED   101 252
  11Q LOSS WILD-TYPE 181 491
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED    101  252
  11Q LOSS WILD-TYPE  181  491
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO               101                181
  YES              252                491
[1] 2 2
[1] FALSE
D62V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q LOSS MUTATED                                  1    22
  11Q LOSS WILD-TYPE                                0    34
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED                          71   220
  11Q LOSS WILD-TYPE                        87   497
D62V11, multiclass
                                  clus
vv                                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                          22                 34
  BLACK OR AFRICAN AMERICAN                      71                 87
  WHITE                                         220                497
[1] 4 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    12 271
  11Q LOSS WILD-TYPE  24 555
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     12  271
  11Q LOSS WILD-TYPE   24  555
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   12                 24
  NOT HISPANIC OR LATINO              271                555
[1] 2 2
[1] FALSE

Clustering(63) Variable = 12P LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED   121  19
  12P LOSS WILD-TYPE 765 100
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
               140                865 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                19                100 
$`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 
       24.39        26.96        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        53.06        18.97 
TCGA-A8-A08F TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A09I TCGA-A8-A09Q 
       33.01         0.99        43.00        40.01        45.07        25.02 
TCGA-AC-A23H TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A6IV TCGA-AC-A8OQ TCGA-AN-A0AM 
        2.66         0.92         2.27         1.18         1.12         0.16 
TCGA-AN-A0FD TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FV TCGA-AN-A0XN TCGA-AN-A0XO 
        6.44         7.00         7.59         0.33         0.33        12.33 
TCGA-AO-A03O TCGA-AO-A03T TCGA-AO-A0J4 TCGA-AO-A0JL TCGA-AO-A129 TCGA-AO-A12D 
       81.63        47.87        52.18        55.33        96.10        64.04 
TCGA-AR-A0TR TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AR 
        5.26        76.14        65.36        61.84        52.77        17.23 
TCGA-AR-A24K TCGA-AR-A24M TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A256 
       50.89        96.89        78.48        73.18        72.76        93.83 
TCGA-AR-A2LL TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0RE 
        7.36       146.50       112.37       176.98        18.77       211.56 
TCGA-B6-A0RI TCGA-B6-A0RP TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A1KF TCGA-B6-A1KN 
      234.28       102.77       131.21       157.41       101.52       139.17 
TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B7 TCGA-BH-A0BP TCGA-BH-A0BW TCGA-BH-A0C0 
       40.83        39.55        56.98        48.69        11.67        41.75 
TCGA-BH-A0C7 TCGA-BH-A0DG TCGA-BH-A0DQ TCGA-BH-A0E6 TCGA-BH-A0EE TCGA-BH-A0H7 
       42.90        23.44         3.22         9.63        31.00        23.08 
TCGA-BH-A1EN TCGA-BH-A1F6 TCGA-BH-A1FN TCGA-BH-A1FU TCGA-BH-A208 TCGA-C8-A12U 
       69.93        97.48        72.07        72.07        57.83        12.66 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A1HI TCGA-C8-A26Y TCGA-C8-A27A 
        1.78         1.45         0.69        11.34         0.43        12.20 
TCGA-D8-A142 TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1X5 TCGA-D8-A1XK TCGA-D8-A1XM 
       13.97        18.90        12.03        18.58        14.50        17.69 
TCGA-D8-A1XQ TCGA-D8-A1XT TCGA-D8-A27F TCGA-E2-A10A TCGA-E2-A14Q TCGA-E2-A14Z 
       16.41         6.35        16.04        40.41        38.24        17.03 
TCGA-E2-A150 TCGA-E2-A155 TCGA-E2-A159 TCGA-E2-A15E TCGA-E2-A1B5 TCGA-E2-A1BD 
       25.41        21.04        25.05        20.71        32.35        17.10 
TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A1LA TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK 
       20.98        27.42        24.59       106.75       102.61         8.75 
TCGA-E2-A573 TCGA-E2-A9RU TCGA-E9-A1R4 TCGA-E9-A22G TCGA-E9-A3X8 TCGA-E9-A5UO 
       34.92         9.21         6.12        23.51        15.72        13.81 
TCGA-E9-A5UP TCGA-EW-A1OY TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A3U0 TCGA-GM-A2DK 
       14.40        29.85         6.15        13.94        17.49        62.33 
TCGA-LL-A5YM TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Z TCGA-OL-A5D7 TCGA-OL-A5RW 
       15.32        14.79         3.88         4.50        46.55        36.36 
TCGA-OL-A66K TCGA-PL-A8LV 
       33.57         0.23 

$`12P LOSS WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        0.39         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP 
       47.24        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       136.73 
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-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN 
       21.14        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-A0T1 
       54.64        27.12        44.88        50.43        44.28        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-A0YD TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ 
       25.28        18.21        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        48.46        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-A25A TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD 
      107.70        18.15        91.92        10.59        20.88        39.65 
TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XY TCGA-A2-A3XZ 
       33.93        29.98        32.75        49.48        34.98        31.99 
TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD 
        7.30        21.30        23.21        21.14        21.90        38.30 
TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13E 
       35.31        34.29        35.47        37.45        33.11        10.72 
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-A4SB TCGA-A7-A4SD 
       11.28        13.41        14.70        11.97        13.74        14.50 
TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VW 
       21.17        14.73        12.10        10.72        11.05         9.37 
TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06U 
       10.42         8.75        13.02        13.02         1.02        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 
       43.00        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        24.99         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-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L 
       38.01        28.96        19.96        12.00        37.05         9.99 
TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A091 TCGA-A8-A092 
       31.00        31.00        33.01        93.04        33.01        30.97 
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-A09K TCGA-A8-A09M TCGA-A8-A09N 
        1.02        50.04        49.05        29.98        33.07         1.02 
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-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-A2FM 
       38.20        40.57        55.43        36.99        38.79        26.04 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
       50.70         1.02         0.99         0.69        14.83        22.19 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS 
        1.12        16.57        19.79        23.24        24.79         1.55 
TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO 
        0.07         1.12         1.81         0.69         0.43         1.68 
TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 
        1.74         1.32         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-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FF TCGA-AN-A0FJ 
        6.51         0.33         0.33         0.33         4.64         7.96 
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-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-A03P TCGA-AO-A03R TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 
       84.69        68.75        59.05        29.13        32.78        21.40 
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-A0JI TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 
       50.24        62.04        71.80       102.58        99.25       108.72 
TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G 
      106.78        90.58        77.56        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-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 
       32.52         2.56        32.91         9.99       111.32        49.32 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
       74.79        86.66        29.75        98.93        64.83        55.86 
TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AK 
      101.95        83.87       114.02        85.97        75.55        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-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY 
       37.81        76.21        61.28        63.62        62.14        20.22 
TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q 
      109.58        73.02        78.51        84.20         0.85       101.52 
TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X 
       87.22        76.01        53.36        85.35        50.96        83.77 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       79.00        56.15        58.92       128.65        20.25        62.86 
TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
       42.87        40.04        38.17        39.39        40.54        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-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG 
      126.12        84.59       110.14       110.93       140.88        68.45 
TCGA-B6-A0RH TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ 
      189.01        81.17        78.02       172.96       162.05       140.48 
TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW 
      100.70        89.46        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-A1KI TCGA-B6-A2IU TCGA-B6-A401 
       68.94        58.88        43.59        73.51       170.17        85.35 
TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV 
       54.28        49.94       103.63        55.00        24.53        38.79 
TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B4 TCGA-BH-A0B5 
       20.45        25.55        28.50        46.95        39.16        48.36 
TCGA-BH-A0B6 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       56.94        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-A0BQ 
       24.85        21.70        44.05        61.68        35.67        27.19 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BZ TCGA-BH-A0C1 
       53.69        53.95        45.57        49.94        49.05        44.02 
TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       48.13        45.83        31.17        38.01        22.13        13.91 
TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       48.23        17.26        15.65         2.56        38.47        45.17 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 
       47.41        16.27         4.41        15.68        14.30        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-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-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-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-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-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-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-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-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE 
       12.66         3.12         0.62         3.85         3.75        12.33 
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-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 
        3.25         0.30         0.23         0.36         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-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-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-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-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-A1XL TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XU 
       21.83        19.92         7.96        15.85        16.31        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-A27G TCGA-D8-A27H TCGA-D8-A27I 
       14.24        14.14        17.42        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-A10B TCGA-E2-A10C 
       43.00        34.42        27.52        46.59        37.51        40.11 
TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14R 
       28.44        28.87        47.15        44.68        40.96        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-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A156 TCGA-E2-A158 
       28.60        27.12        23.24        19.43        23.87        14.79 
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-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-A1LB 
       22.19        11.08        54.18        39.62        19.66        40.47 
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-E2-A576 TCGA-E9-A1N4 TCGA-E9-A1N5 
        7.20        30.61        19.89        19.00        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-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-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-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        24.56         0.72 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54X 
       17.75         0.76        26.07        18.41         0.62        12.33 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
        0.23        14.70         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-A1OZ TCGA-EW-A1P0 
       28.77        25.94        22.82        29.95        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-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
        7.86        18.90        19.99        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-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-A2DH TCGA-GM-A2DI 
       53.13        53.52        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-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX 
       43.73        69.30        66.38        72.03        13.55        18.12 
TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 
       11.84        11.57        21.24         6.67         4.08         4.60 
TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL 
        8.75         9.53        11.44        10.95         7.59        17.06 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A740 
       14.70        14.47        11.57         2.63         4.14         4.50 
TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
        5.59         3.22         6.21         7.36        27.91         2.79 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
        2.10        12.66        31.99        58.62        27.65        34.92 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I 
       16.87        24.72        22.32        20.38        26.70        23.47 
TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO 
       65.62        31.07        26.04         7.23        14.07        28.21 
TCGA-OL-A6VQ TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG 
       19.73         0.16         0.26         3.95        16.50         6.81 
TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 
        8.65        10.59         7.92         5.56         8.52         7.17 
TCGA-S3-AA15 TCGA-S3-AA17 TCGA-W8-A86G TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
        6.87         3.91         5.29         9.60         9.14       100.01 
TCGA-Z7-A8R6 
      105.04 

  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 
            23.475             22.320 
[1] "0.2 - 234.3 (23.5)" "0.0 - 220.9 (22.3)"
[1] "hr=" "1.1"
D63V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12P LOSS MUTATED         9       10        0        1        50        37
  12P LOSS WILD-TYPE      74       70        9        4       292       197
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12P LOSS MUTATED           0         18         10          6        1
  12P LOSS WILD-TYPE         2        124         19         57       17
                    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                 74
  STAGE IA                 10                 70
  STAGE IB                  0                  9
  STAGE II                  1                  4
  STAGE IIA                50                292
  STAGE IIB                37                197
  STAGE III                 0                  2
  STAGE IIIA               18                124
  STAGE IIIB               10                 19
  STAGE IIIC                6                 57
  STAGE IV                  1                 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
  12P LOSS MUTATED    31  87  13  12
  12P LOSS WILD-TYPE 234 507 111  27
D63V4, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1               31                234
  T2               87                507
  T3               13                111
  T4               12                 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 LOSS MUTATED    67  51  15   7
  12P LOSS WILD-TYPE 414 288  98  67
D63V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0               67                414
  N1               51                288
  N2               15                 98
  N3                7                 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
  12P LOSS MUTATED          0 129   2  13
  12P LOSS WILD-TYPE        5 725  17 134
D63V6, multiclass
          clus
vv         12P LOSS MUTATED 12P LOSS WILD-TYPE
  CM0 (I+)                0                  5
  M0                    129                725
  M1                      2                 17
  MX                     13                134
[1] 4 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   143   1
  12P LOSS WILD-TYPE 871  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED    143    1
  12P LOSS WILD-TYPE  871   10
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE              143                871
  MALE                  1                 10
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  12P LOSS MUTATED                            0                           125
  12P LOSS WILD-TYPE                          1                           629
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  12P LOSS MUTATED                                8                   2
  12P LOSS WILD-TYPE                            167                   4
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  12P LOSS MUTATED                                  3                  1
  12P LOSS WILD-TYPE                               26                 14
                    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                 125                629
  INFILTRATING LOBULAR CARCINOMA                  8                167
  MEDULLARY CARCINOMA                             2                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                3                 26
  MUCINOUS CARCINOMA                              1                 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"
D63V9, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    44 100
  12P LOSS WILD-TYPE 238 643
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     44  100
  12P LOSS WILD-TYPE  238  643
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                44                238
  YES              100                643
[1] 2 2
[1] FALSE
D63V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P LOSS MUTATED                                  0     8
  12P LOSS WILD-TYPE                                1    48
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED                          30    94
  12P LOSS WILD-TYPE                       128   623
D63V11, multiclass
                                  clus
vv                                 12P LOSS MUTATED 12P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           8                 48
  BLACK OR AFRICAN AMERICAN                      30                128
  WHITE                                          94                623
[1] 4 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     3 121
  12P LOSS WILD-TYPE  33 705
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      3  121
  12P LOSS WILD-TYPE   33  705
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 33
  NOT HISPANIC OR LATINO              121                705
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED   102  18
  12Q LOSS WILD-TYPE 784 101
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
               120                885 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                18                101 
$`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        24.39        26.96        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        33.01 
TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A09Q TCGA-AC-A2QJ TCGA-AC-A8OQ TCGA-AN-A04C 
        0.99        43.00        25.02         2.27         1.12         1.78 
TCGA-AN-A0AM TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0XO TCGA-AO-A0J4 TCGA-AO-A0JL 
        0.16         7.00         7.59        12.33        52.18        55.33 
TCGA-AO-A124 TCGA-AO-A129 TCGA-AO-A12F TCGA-AR-A0U0 TCGA-AR-A1AI TCGA-AR-A1AJ 
      102.58        96.10        48.36        65.36        61.84        52.77 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A24K TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A256 
       43.07        17.23        50.89        78.48        73.18        93.83 
TCGA-AR-A2LL TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0RE TCGA-B6-A0RI 
        7.36       146.50       112.37       176.98       211.56       234.28 
TCGA-B6-A0RP TCGA-B6-A0RU TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A402 TCGA-BH-A0AV 
      102.77       131.21       101.52       139.17        54.28        38.79 
TCGA-BH-A0B2 TCGA-BH-A0B7 TCGA-BH-A0BP TCGA-BH-A0C0 TCGA-BH-A0C7 TCGA-BH-A0DG 
       40.83        56.98        48.69        41.75        42.90        23.44 
TCGA-BH-A0DQ TCGA-BH-A0E0 TCGA-BH-A0EE TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO 
        3.22         4.41        31.00        51.16        69.93        91.99 
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-A26Y TCGA-C8-A27A TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A1JG 
        1.45         0.43        12.20        13.97        14.17        12.03 
TCGA-D8-A1XK TCGA-D8-A1XQ TCGA-D8-A27F TCGA-E2-A10A TCGA-E2-A150 TCGA-E2-A159 
       14.50        16.41        16.04        40.41        25.41        25.05 
TCGA-E2-A15E TCGA-E2-A1AZ TCGA-E2-A1B5 TCGA-E2-A1BD TCGA-E2-A1IO TCGA-E2-A1L7 
       20.71        60.53        32.35        17.10        20.98        27.42 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A573 TCGA-E2-A9RU 
      106.75       102.61         8.75        16.93        34.92         9.21 
TCGA-E9-A1RG TCGA-E9-A22G TCGA-E9-A3X8 TCGA-E9-A5UP TCGA-EW-A1P4 TCGA-EW-A1P8 
       21.27        23.51        15.72        14.40        29.82         7.86 
TCGA-EW-A1PC TCGA-EW-A3U0 TCGA-GI-A2C8 TCGA-GM-A2DK TCGA-LL-A5YP TCGA-LL-A73Z 
        6.15        17.49         7.40        62.33        14.79         4.50 
TCGA-OL-A5D7 TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-OL-A66K TCGA-OL-A6VO TCGA-PL-A8LV 
       46.55        36.36        20.38        33.57        28.21         0.23 

$`12Q LOSS WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SH 
        0.39         8.52        14.37        43.43        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       136.73 
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-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN 
       21.14        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-A0T1 
       54.64        27.12        44.88        50.43        44.28        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-A0YH TCGA-A2-A0YI 
       32.55        25.28        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        48.46        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-A3XU TCGA-A2-A3XV 
       91.92        10.59        20.88        39.65        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 
       49.48        34.98        31.99         7.30        21.30        23.21 
TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH 
       21.14        21.90        38.30        35.31        34.29        35.47 
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-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-A4SB TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX 
       13.74        21.17        14.73        12.10        10.72        11.05 
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        53.06 
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-A07I TCGA-A8-A07J 
        9.01        43.00        19.99        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        24.99 
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-A08I TCGA-A8-A08J 
        0.99        38.01        28.96        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        33.01        93.04        40.01 
TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 
       33.01        30.97        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        50.04        49.05        45.07 
TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       29.98        33.07         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-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-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-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN 
        0.92         0.99         0.69        14.83        22.19         1.12 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V 
       16.57        19.79        23.24        24.79         1.55         0.07 
TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO 
        1.12         1.81         1.18         0.69         0.43         1.68 
TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 
        1.74         1.32         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-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-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-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-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J6 
       59.05        29.13        32.78        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        50.24        62.04 
TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B 
       71.80        99.25       108.72       106.78        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-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        32.52         2.56        32.91 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT 
        9.99       111.32        49.32         5.26        74.79        86.66 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 
       29.75        98.93        64.83        55.86        76.14       101.95 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AK TCGA-AR-A1AL 
       83.87       114.02        85.97        75.55        51.25        48.82 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AU 
       62.56        43.73        43.56        39.98        37.81        76.21 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L 
       61.28        63.62        62.14        20.22       109.58        73.02 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R 
       96.89        78.51        84.20         0.85       101.52        87.22 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
       76.01        53.36        85.35        50.96        83.77        79.00 
TCGA-AR-A250 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       56.15        72.76        58.92       128.65        20.25        62.86 
TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
       42.87        40.04        38.17        39.39        40.54        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-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-A0RG TCGA-B6-A0RH TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
       68.45       189.01        81.17        78.02       172.96       162.05 
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-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-A1KI 
      186.48        28.27        68.94        58.88        43.59        73.51 
TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
      170.17        85.35        49.94       103.63        55.00        24.53 
TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 
       20.45        25.55        28.50        46.95        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-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-A0C1 TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DH 
       49.05        44.02        48.13        45.83        31.17        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-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EI 
        9.63        44.81        46.19        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-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-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-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-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-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR 
      122.89        36.92        63.35        55.00        45.63       144.59 
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-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-A12V 
       11.77        11.77        12.66        11.77         0.07        12.66 
TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 
       12.66        12.66         3.12         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-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 
        0.36         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-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-A1JF 
       16.50        18.71        15.78        18.15        18.90        12.03 
TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM 
       14.01        18.97        20.09        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-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-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-A27G TCGA-D8-A27H TCGA-D8-A27I 
       14.24        14.14        17.42        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-A10B TCGA-E2-A10C 
       43.00        34.42        27.52        46.59        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-A14W 
       38.60        33.17        33.30        43.33        34.26        32.02 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 
       31.96        28.60        17.03        27.12        23.24        19.43 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D 
       21.04        23.87        14.79        23.34        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-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B6 TCGA-E2-A1BC 
       14.99        53.62        53.03        29.95        28.50        16.47 
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-A1IU TCGA-E2-A1L6 TCGA-E2-A1L8 
       22.65         3.88        22.19        11.08        54.18        39.62 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LL 
       19.66        24.59        40.47        28.90        18.87        43.04 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A574 TCGA-E2-A576 
        5.52        15.72         7.20        30.61        19.89        19.00 
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-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-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-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 
       24.56         0.72        17.75         0.76        26.07        18.41 
TCGA-E9-A3QA TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO 
        0.62        12.33         0.23        14.70         0.26        13.81 
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-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-A423 TCGA-EW-A424 TCGA-GI-A2C9 
       25.91        22.09        21.27        10.16        10.59       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-A2DI TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO 
       42.28        61.91        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        43.73        69.30        66.38        72.03 
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        21.24         6.67 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
        4.08         4.60         8.75         9.53        11.44        10.95 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP 
        7.59        17.06        15.32        14.70        14.47        11.57 
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-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
        6.21         7.36        27.91         2.79         2.10        12.66 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY 
       31.99        58.62        27.65        34.92        16.87        24.72 
TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66N 
       22.32        26.70        23.47        65.62        31.07        26.04 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ 
        7.23        14.07        19.73         0.16         0.26         3.95 
TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 
       16.50         6.81         8.65        10.59         7.92         5.56 
TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-W8-A86G TCGA-XX-A899 
        8.52         7.17         6.87         3.91         5.29         9.60 
TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        9.14       100.01       105.04 

  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 
            27.815             21.900 
[1] "0.2 - 234.3 (27.8)" "0.0 - 220.9 (21.9)"
[1] "hr=" "1"  
D64V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12Q LOSS MUTATED         9        6        0        1        44        34
  12Q LOSS WILD-TYPE      74       74        9        4       298       200
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12Q LOSS MUTATED           0         11          8          7        1
  12Q LOSS WILD-TYPE         2        131         21         56       17
                    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                 74
  STAGE IA                  6                 74
  STAGE IB                  0                  9
  STAGE II                  1                  4
  STAGE IIA                44                298
  STAGE IIB                34                200
  STAGE III                 0                  2
  STAGE IIIA               11                131
  STAGE IIIB                8                 21
  STAGE IIIC                7                 56
  STAGE IV                  1                 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
  12Q LOSS MUTATED    24  78  10  10
  12Q LOSS WILD-TYPE 241 516 114  29
D64V4, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1               24                241
  T2               78                516
  T3               10                114
  T4               10                 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
  12Q LOSS MUTATED    64  40  10   7
  12Q LOSS WILD-TYPE 417 299 103  67
D64V5, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0               64                417
  N1               40                299
  N2               10                103
  N3                7                 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
  12Q LOSS MUTATED          0 110   1  12
  12Q LOSS WILD-TYPE        5 744  18 135
D64V6, multiclass
          clus
vv         12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CM0 (I+)                0                  5
  M0                    110                744
  M1                      1                 18
  MX                     12                135
[1] 4 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   123   0
  12Q LOSS WILD-TYPE 891  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED    123    0
  12Q LOSS WILD-TYPE  891   11
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE              123                891
  MALE                  0                 11
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  12Q LOSS MUTATED                            0                           105
  12Q LOSS WILD-TYPE                          1                           649
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  12Q LOSS MUTATED                                7                   3
  12Q LOSS WILD-TYPE                            168                   3
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  12Q LOSS MUTATED                                  1                  0
  12Q LOSS WILD-TYPE                               28                 15
                    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                 105                649
  INFILTRATING LOBULAR CARCINOMA                  7                168
  MEDULLARY CARCINOMA                             3                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)                1                 28
  MUCINOUS CARCINOMA                              0                 15
  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    38  85
  12Q LOSS WILD-TYPE 244 658
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     38   85
  12Q LOSS WILD-TYPE  244  658
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                38                244
  YES               85                658
[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                          32    79
  12Q LOSS WILD-TYPE                       126   638
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                      32                126
  WHITE                                          79                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"
D64V12, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     3 105
  12Q LOSS WILD-TYPE  33 721
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      3  105
  12Q LOSS WILD-TYPE   33  721
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 33
  NOT HISPANIC OR LATINO              105                721
[1] 2 2
[1] FALSE

Clustering(65) Variable = 13Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED   350  55
  13Q LOSS WILD-TYPE 536  64
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               405                600 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                55                 64 
$`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        48.46        31.73        23.77        23.47 
TCGA-A2-A3XT TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX 
       83.01        49.48        38.40        38.37         7.30        24.39 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A13D TCGA-A7-A13F 
       26.96        21.14        38.30        30.61        31.73        12.72 
TCGA-A7-A26E TCGA-A7-A26G TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3IZ TCGA-A7-A4SA 
       31.36        23.74        21.73        22.32        10.59        14.93 
TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY 
       14.50        17.92        10.29         9.37        10.42         8.75 
TCGA-A8-A06O TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A06Z 
       13.02        17.98        53.06        29.03        26.01         1.02 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07L TCGA-A8-A07O 
       53.98         9.01        43.00        18.97        17.03         9.99 
TCGA-A8-A07P TCGA-A8-A07W TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08B TCGA-A8-A08F 
       10.98         9.99        36.95        13.02        38.01        33.01 
TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08X 
       12.00         9.99        31.00        31.00        33.01        43.00 
TCGA-A8-A092 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M 
       30.97         9.99        12.00        45.07        29.98        33.07 
TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09X TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A9 
        1.02        25.02        14.01        19.04        13.02        13.02 
TCGA-A8-A0AD TCGA-AC-A23E TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2QH TCGA-AC-A2QJ 
       38.04         2.37        38.53        38.20         1.02         2.27 
TCGA-AC-A3BB TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IW 
        0.99        16.57        19.79         1.12         1.81         0.69 
TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A046 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D 
        1.74         0.33         0.33         2.96         1.78         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FS TCGA-AN-A0FX TCGA-AN-A0FY 
        8.02         0.33         0.33         6.28         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XN 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-A03N TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J6 
       66.77        81.63        68.75        21.40        52.18        37.48 
TCGA-AO-A0JE TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 
       76.77        50.24        62.04        55.33        71.80       102.58 
TCGA-AO-A129 TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A1KQ TCGA-AO-A1KR 
       96.10        57.30        48.36        41.62        61.87        70.39 
TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A54N 
        0.53        17.79        24.79       130.09        15.62         2.56 
TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TV TCGA-AR-A0TX 
       32.91         9.99       111.32         5.26        29.75        64.83 
TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
       76.14        65.36        83.87        85.97        75.55        61.84 
TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AR TCGA-AR-A1AW TCGA-AR-A1AY TCGA-AR-A24K 
       52.77        51.25        17.23        63.62        20.22        50.89 
TCGA-AR-A24L TCGA-AR-A24N TCGA-AR-A24Q TCGA-AR-A24T TCGA-AR-A24V TCGA-AR-A24W 
       73.02        78.51       101.52        76.01        85.35        50.96 
TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LK 
       79.00        78.48        73.18        58.92        93.83        42.87 
TCGA-AR-A2LL TCGA-AR-A5QM TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0IB TCGA-B6-A0IE 
        7.36        54.74        10.59        77.62       129.57        65.72 
TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RL TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RU 
      140.88        68.45        81.17       102.77       140.48       131.21 
TCGA-B6-A0WS TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0X5 TCGA-B6-A1KC 
       97.48        79.63        17.98        21.47        68.94        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-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B3 TCGA-BH-A0B6 TCGA-BH-A0B7 
       38.79        25.55        28.50        39.55        56.94        56.98 
TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BJ TCGA-BH-A0BP TCGA-BH-A0BR TCGA-BH-A0BV 
       37.22        32.02        21.70        48.69        53.69        49.94 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C7 TCGA-BH-A0DD 
       11.67        49.05        41.75        44.02        42.90        45.83 
TCGA-BH-A0DH TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0E0 TCGA-BH-A0E9 
       38.01        13.91        48.23        15.65         4.41        46.19 
TCGA-BH-A0EE TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H7 TCGA-BH-A0HB TCGA-BH-A0HU 
       31.00        10.78        15.16        23.08        26.50        12.89 
TCGA-BH-A0HX TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0WA TCGA-BH-A18K TCGA-BH-A18L 
       27.25         5.59        23.93        23.05        90.84        26.66 
TCGA-BH-A18Q TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EU 
       55.63        66.05         7.36        51.39        69.93        42.28 
TCGA-BH-A1EV TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F6 TCGA-BH-A1FC TCGA-BH-A1FD 
       12.00        17.69        25.81        97.48       114.15        33.17 
TCGA-BH-A1FE TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FU TCGA-BH-A202 TCGA-BH-A209 
       74.73        36.92        63.35        72.07         0.72       130.16 
TCGA-BH-A28Q TCGA-C8-A12M TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12U TCGA-C8-A130 
        6.44        11.77        12.66        11.77        12.66         3.12 
TCGA-C8-A135 TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HM 
        0.62        10.92        11.34        11.34        12.03         2.30 
TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A274 TCGA-C8-A278 
        3.25         0.30         0.36         0.43         0.03         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-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JC 
       13.48        21.14        14.17        17.49        16.50        15.78 
TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JI TCGA-D8-A1JK TCGA-D8-A1JL 
       18.15        18.90        12.03        18.97        20.12        20.09 
TCGA-D8-A1JM TCGA-D8-A1JT TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X9 TCGA-D8-A1XA 
       19.40        13.32        18.58        17.79        23.90        27.58 
TCGA-D8-A1XD TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1Y0 
       17.16        14.50        19.92        12.99        16.54        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27I TCGA-D8-A27N TCGA-D8-A27T 
        3.81        14.24        14.14        14.43         4.80        13.08 
TCGA-E2-A107 TCGA-E2-A10C TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14W TCGA-E2-A150 
       34.42        40.11        47.15        44.68        32.02        25.41 
TCGA-E2-A152 TCGA-E2-A155 TCGA-E2-A159 TCGA-E2-A15G TCGA-E2-A15M TCGA-E2-A15O 
       27.12        21.04        25.05        18.21         7.73        13.02 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A1AZ TCGA-E2-A1II TCGA-E2-A1IN 
       19.56        17.06        14.07        60.53        33.70        22.19 
TCGA-E2-A1IO TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 
       20.98        39.62        18.87         8.75        43.04        16.93 
TCGA-E2-A56Z TCGA-E2-A576 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NE 
        7.20        19.00        13.48        13.12        36.56        35.77 
TCGA-E9-A1NI TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RG 
        9.86         2.76        32.09        20.81         0.66        21.27 
TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A295 
       12.89        23.51        24.10        27.22         0.95         0.72 
TCGA-E9-A3QA TCGA-E9-A54Y TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW 
        0.62         0.23        13.81        14.40        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        21.24         6.67        15.32 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FR TCGA-LL-A7SZ TCGA-LL-A7T0 
       14.47        14.79        11.57         3.88         5.59         3.22 
TCGA-OL-A5D7 TCGA-OL-A5DA TCGA-OL-A5RW TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66I 
       46.55        58.62        36.36        22.32        20.38        23.47 
TCGA-OL-A66K TCGA-OL-A66N TCGA-OL-A66O TCGA-PL-A8LV TCGA-S3-A6ZH TCGA-S3-AA10 
       33.57        26.04         7.23         0.23         8.65         7.92 
TCGA-S3-AA14 TCGA-XX-A89A TCGA-Z7-A8R5 
        7.17         9.14       100.01 

$`13Q LOSS WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SK 
        0.39         8.52        48.10        14.27        47.24        31.79 
TCGA-A1-A0SM TCGA-A2-A04N TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04V TCGA-A2-A04W 
        7.96       104.81        82.16        73.84        63.12        64.04 
TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
       36.13       136.73        64.57        92.48        88.60       107.93 
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-A0ES TCGA-A2-A0ET TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST 
       37.05        35.05        29.75        24.72        24.16        99.19 
TCGA-A2-A0SU TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 
       54.64        50.43        44.28        17.52        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-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A1FW 
       15.42        21.90        21.67        18.61        19.33        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-A3XS TCGA-A2-A3XU TCGA-A2-A3XV 
       10.59        20.88        39.65        33.93        29.98        32.75 
TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S3 TCGA-A7-A0CE 
       34.98        31.99        21.30        23.21        21.90        35.31 
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-A13G TCGA-A7-A13H TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A3IY 
       23.61        29.56        24.26        23.80        20.61        11.34 
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-A8-A06P 
       21.17        14.73        12.10        10.72        11.05        13.02 
TCGA-A8-A06Q TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07I 
        1.02        31.00        17.03        19.99        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07Z TCGA-A8-A082 
       12.00         8.98         7.99        24.99        28.04        18.05 
TCGA-A8-A084 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08R 
       15.06         0.99        28.96        19.96        37.05         0.99 
TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 
       93.04        40.01        33.01        17.95        41.98        12.00 
TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09R TCGA-A8-A09T 
        9.99         1.02        50.04        49.05         8.98        19.04 
TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0AB 
       15.02         0.99        12.00        21.04         0.99        17.03 
TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2FB TCGA-AC-A2FF 
        0.95        10.85         2.66         1.48        40.57        55.43 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3HN 
       36.99        38.79        26.04        50.70         0.92         0.69 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS 
       14.83        22.19         1.12        23.24        24.79         1.55 
TCGA-AC-A62V TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OQ TCGA-AC-A8OR 
        0.07         1.18         0.43         1.68         1.12         1.32 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM 
        0.33         0.23         0.62         7.36         6.51         0.16 
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-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XO 
        7.17         6.02         0.33         0.36         0.33        12.33 
TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AO-A03M TCGA-AO-A03P 
        0.30         0.33         0.33         0.33        47.84        84.69 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J5 TCGA-AO-A0J7 
       47.87        59.05        29.13        32.78        24.16        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-A0JF TCGA-AO-A0JG TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A 
       21.37        26.24        99.25       108.72       106.78        90.58 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AQ-A04J 
       77.56        64.04        28.37        14.73        82.62        26.93 
TCGA-AQ-A0Y5 TCGA-AQ-A1H3 TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TW 
        5.65        32.52        49.32        74.79        86.66        98.93 
TCGA-AR-A0TY TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
       55.86       101.95       114.02        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        37.81        76.21        61.28 
TCGA-AR-A1AX TCGA-AR-A24H TCGA-AR-A24M TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R 
       62.14       109.58        96.89        84.20         0.85        87.22 
TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A254 TCGA-AR-A2LE TCGA-AR-A2LH 
       53.36        83.77        56.15        72.76       128.65        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
       62.86        40.04        38.17        39.39        40.54        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       103.63        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-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1N5 
       30.61        34.92        19.89         9.21        19.20        36.82 
TCGA-E9-A1N8 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1QZ 
       12.00        39.55        12.59        20.05        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-A1RC TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 
       40.24        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-A243 
        0.79        12.53        13.32        39.09        22.75        17.06 
TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A2JS TCGA-E9-A2JT 
        0.69         0.85         1.94        24.56        17.75         0.76 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5FL 
       26.07        18.41        15.72        12.33        14.70         0.26 
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-A1OX TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 
       15.68        28.77        29.95        41.13        39.78        29.82 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PG 
       18.48        30.08        19.99        13.94        10.52        34.55 
TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A423 TCGA-EW-A424 
       55.00        25.91        22.09        21.27        10.16        10.59 
TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DI TCGA-GM-A2DK 
        7.40       109.87        59.57       194.27        61.91        62.33 
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        43.73        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A7W5 
       72.03        13.55        18.12        11.84        11.57         4.08 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y 
        4.60         8.75         9.53        11.44        10.95         7.59 
TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 
       17.06        14.70         2.63         4.14         4.50         4.50 
TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
        6.21         7.36        27.91         2.79         2.10        12.66 
TCGA-OL-A5D8 TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A66H 
       31.99        27.65        34.92        16.87        24.72        26.70 
TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PL-A8LX 
       65.62        31.07        14.07        28.21        19.73         0.16 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA11 
        0.26         3.95        16.50         6.81        10.59         5.56 
TCGA-S3-AA12 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-W8-A86G TCGA-XX-A899 TCGA-Z7-A8R6 
        8.52         6.87         3.91         5.29         9.60       105.04 

  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 
             23.05              22.16 
[1] "0.0 - 170.2 (23.1)" "0.0 - 234.3 (22.2)"
[1] "hr=" "1.4"
D65V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  13Q LOSS MUTATED        32       25        3        2       150        96
  13Q LOSS WILD-TYPE      51       55        6        3       192       138
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  13Q LOSS MUTATED           1         59         11         22        7
  13Q LOSS WILD-TYPE         1         83         18         41       11
                    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                  32                 51
  STAGE IA                 25                 55
  STAGE IB                  3                  6
  STAGE II                  2                  3
  STAGE IIA               150                192
  STAGE IIB                96                138
  STAGE III                 1                  1
  STAGE IIIA               59                 83
  STAGE IIIB               11                 18
  STAGE IIIC               22                 41
  STAGE IV                  7                 11
  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    90 254  54  16
  13Q LOSS WILD-TYPE 175 340  70  23
D65V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1               90                175
  T2              254                340
  T3               54                 70
  T4               16                 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
  13Q LOSS MUTATED   200 133  48  27
  13Q LOSS WILD-TYPE 281 206  65  47
D65V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0              200                281
  N1              133                206
  N2               48                 65
  N3               27                 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
  13Q LOSS MUTATED          2 345   8  60
  13Q LOSS WILD-TYPE        3 509  11  87
D65V6, multiclass
          clus
vv         13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CM0 (I+)                2                  3
  M0                    345                509
  M1                      8                 11
  MX                     60                 87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED   410   5
  13Q LOSS WILD-TYPE 604   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED    410    5
  13Q LOSS WILD-TYPE  604    6
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE              410                604
  MALE                  5                  6
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  13Q LOSS MUTATED                            0                           331
  13Q LOSS WILD-TYPE                          1                           423
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  13Q LOSS MUTATED                               52                   5
  13Q LOSS WILD-TYPE                            123                   1
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  13Q LOSS MUTATED                                 10                  2
  13Q LOSS WILD-TYPE                               19                 13
                    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                 331                423
  INFILTRATING LOBULAR CARCINOMA                 52                123
  MEDULLARY CARCINOMA                             5                  1
  MIXED HISTOLOGY (PLEASE SPECIFY)               10                 19
  MUCINOUS CARCINOMA                              2                 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"
D65V9, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED   120 295
  13Q LOSS WILD-TYPE 162 448
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED    120  295
  13Q LOSS WILD-TYPE  162  448
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO               120                162
  YES              295                448
[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                          75   271
  13Q LOSS WILD-TYPE                        83   446
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                      75                 83
  WHITE                                         271                446
[1] 4 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    11 323
  13Q LOSS WILD-TYPE  25 503
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     11  323
  13Q LOSS WILD-TYPE   25  503
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   11                 25
  NOT HISPANIC OR LATINO              323                503
[1] 2 2
[1] FALSE

Clustering(66) Variable = 14Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED   210  36
  14Q LOSS WILD-TYPE 676  83
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               246                759 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                36                 83 
$`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        26.96 
TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A26G 
       21.90        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 
       33.01        19.96         9.99        12.00        45.07        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-AC-A8OQ TCGA-AN-A04C 
        1.02         2.27         1.12         0.69         1.12         1.78 
TCGA-AN-A0AK TCGA-AN-A0FJ TCGA-AN-A0FX TCGA-AN-A0XN TCGA-AO-A0J4 TCGA-AO-A0J6 
        7.36         7.96         0.33         0.33        52.18        37.48 
TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A129 TCGA-AO-A12F TCGA-AO-A1KR TCGA-AQ-A04L 
       55.33       102.58        96.10        48.36        70.39       130.09 
TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TV 
        5.65         2.56        32.91         5.26        86.66        29.75 
TCGA-AR-A0U0 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AM TCGA-AR-A1AP 
       65.36        75.55        61.84        52.77        62.56        39.98 
TCGA-AR-A1AQ TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24Q TCGA-AR-A24V 
       43.07        62.14        20.22       109.58       101.52        85.35 
TCGA-AR-A251 TCGA-AR-A255 TCGA-AR-A256 TCGA-B6-A0I9 TCGA-B6-A0IH TCGA-B6-A0IJ 
       78.48        58.92        93.83        12.13       112.37       176.98 
TCGA-B6-A0IO TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RL TCGA-B6-A0WS TCGA-B6-A0WW 
      110.14       140.88       211.56        81.17        97.48        17.98 
TCGA-B6-A0WX TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-BH-A0AU TCGA-BH-A0AV 
       21.47        43.59       101.52        73.51        24.53        38.79 
TCGA-BH-A0AW TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BF 
       20.45        39.55        48.36        56.98        51.68        25.71 
TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C7 
       24.85        21.70        11.67        49.05        44.02        42.90 
TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0H7 TCGA-BH-A0RX TCGA-BH-A0WA TCGA-BH-A18F 
        4.41         9.63        23.08         5.59        23.05         8.81 
TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EW TCGA-BH-A1EY TCGA-BH-A1F6 
       55.63         7.36        51.39        55.69        17.69        97.48 
TCGA-BH-A1F8 TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A202 TCGA-BH-A42T TCGA-C8-A12L 
       24.66       114.15        74.73         0.72         0.99        11.93 
TCGA-C8-A12M TCGA-C8-A12X TCGA-C8-A134 TCGA-C8-A1HF TCGA-C8-A1HK TCGA-C8-A1HM 
       11.77        12.66         0.69        10.92        12.03         2.30 
TCGA-C8-A1HN TCGA-C8-A26Y TCGA-C8-A27B TCGA-D8-A142 TCGA-D8-A1JC TCGA-D8-A1JG 
        3.25         0.43         0.99        13.97        15.78        12.03 
TCGA-D8-A1JJ TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JP TCGA-D8-A1XA TCGA-D8-A1XB 
       20.09        20.09        19.40        21.01        27.58        18.15 
TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XO TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XY 
       14.73        14.50         7.96         6.35        12.99        16.54 
TCGA-D8-A1Y0 TCGA-D8-A1Y3 TCGA-D8-A27I TCGA-D8-A27M TCGA-D8-A27R TCGA-D8-A27T 
       15.52        14.14        14.43        13.48        10.09        13.08 
TCGA-E2-A108 TCGA-E2-A14R TCGA-E2-A14T TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A155 
       27.52        38.60        33.30        17.03        25.41        21.04 
TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15F TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A1AZ 
       25.05        23.34        21.63         7.73        19.56        60.53 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A56Z 
       33.73        33.70        28.90       106.75       102.61         7.20 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1QZ 
       34.92        19.89        13.48        12.00        13.12        11.90 
TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1RB TCGA-E9-A22A TCGA-E9-A22B 
        6.12         1.38         2.76        20.81        39.09        22.75 
TCGA-E9-A22G TCGA-E9-A2JS TCGA-E9-A3HO TCGA-E9-A3QA TCGA-EW-A1IZ TCGA-EW-A1J6 
       23.51        17.75        26.07         0.62        18.21        28.77 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P8 TCGA-EW-A1PF TCGA-EW-A1PH 
       25.94        22.82        29.82         7.86        14.43        19.96 
TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C9 
       55.00        25.91        17.49        10.16        10.59       109.87 
TCGA-GM-A2DH TCGA-GM-A2DK TCGA-GM-A3XL TCGA-GM-A5PX TCGA-JL-A3YX TCGA-LD-A7W5 
       42.28        62.33        69.30        18.12        11.57         4.08 
TCGA-LL-A441 TCGA-LL-A5YP TCGA-LL-A7T0 TCGA-OL-A5D7 TCGA-OL-A5RZ TCGA-OL-A5S0 
       11.44        14.79         3.22        46.55        22.32        20.38 
TCGA-OL-A66I TCGA-OL-A66K TCGA-OL-A66N TCGA-OL-A6VO TCGA-PL-A8LV TCGA-PL-A8LX 
       23.47        33.57        26.04        28.21         0.23         0.16 
TCGA-S3-A6ZF TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA17 TCGA-XX-A899 TCGA-XX-A89A 
       16.50        10.59         7.92         3.91         9.60         9.14 

$`14Q LOSS WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        0.39         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
       47.24        20.88        13.68         7.96        39.32        28.01 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04X 
       18.21       104.81        41.95        82.16        63.12        55.43 
TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
       36.13       136.73        64.57        24.79       112.08        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CX 
       88.60       107.93        75.55        75.25        63.45        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-A0ER TCGA-A2-A0ES TCGA-A2-A0EV TCGA-A2-A0EW 
       80.28       107.61        74.40        37.05        31.82        29.75 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SY 
       24.72        24.16        99.19        54.64        44.88        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-A0YF TCGA-A2-A0YG 
       18.90        20.75        32.55        25.28        15.42        21.90 
TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV 
       21.67        14.50        19.33        48.46        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-A3XV TCGA-A2-A3XW TCGA-A2-A3XY 
       10.59        20.88        39.65        32.75        49.48        34.98 
TCGA-A2-A3XZ TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 
       31.99         7.30        24.39        21.30        23.21        21.14 
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-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H 
       33.11        23.61        29.56        31.36        24.26        23.80 
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-A4SA TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW 
       11.97        14.93        17.92        14.73        12.10        10.72 
TCGA-A7-A5ZX TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U 
       11.05        13.02         1.02        17.98        53.06        29.03 
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        43.00        19.99 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U 
       18.97        14.01        12.00        10.98         7.99        24.99 
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-A08I TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08P 
       38.01        28.96        12.00        37.05        31.00        31.00 
TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 
        0.99        33.01        93.04        43.00        40.01        33.01 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B 
       30.97        17.95        41.98         9.99         9.99        12.00 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R 
        1.02        50.04        49.05        33.07        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-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AD TCGA-AC-A23E TCGA-AC-A23G 
       13.02         0.99        13.02        38.04         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-A2QI TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD 
       26.04        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 
       22.19         1.12        16.57        19.79        23.24        24.79 
TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO 
        1.55         0.07         1.81         1.18         0.43         1.68 
TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 
        1.74         1.32         0.33         0.33         0.23         0.33 
TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AL TCGA-AN-A0AM 
        0.62         2.96         1.71         8.02         6.51         0.16 
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-A0FW 
        7.59         7.17         6.28         6.02         0.33         0.36 
TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL 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-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-A0J5 TCGA-AO-A0J7 
       59.05        29.13        32.78        21.40        24.16        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        50.24        62.04        71.80 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D 
       99.25       108.72       106.78        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-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A1H2 TCGA-AQ-A1H3 
        0.53        17.79        24.79        26.93        15.62        32.52 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TW TCGA-AR-A0TX 
        9.99       111.32        49.32        74.79        98.93        64.83 
TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 
       55.86        76.14       101.95        83.87       114.02        85.97 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AR TCGA-AR-A1AS 
       51.25        48.82        43.73        43.56        17.23        37.81 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M 
       76.21        61.28        63.62        50.89        73.02        96.89 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24U 
       78.51        84.20         0.85        87.22        76.01        53.36 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A254 
       50.96        83.77        79.00        56.15        73.18        72.76 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM 
      128.65        20.25        62.86        42.87         7.36        40.04 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN 
       38.17        39.39        40.54        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-A0IK TCGA-B6-A0IM 
      129.57        50.70        65.72       146.50        18.77       126.12 
TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RM 
       84.59       110.93        68.45       189.01       234.28        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-A0WY TCGA-B6-A0WZ 
      131.21       157.41       188.68        79.63       113.79       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-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C 
      170.17        85.35        54.28        49.94       103.63        55.00 
TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B6 
       25.55        28.50        46.95        40.83        39.16        56.94 
TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO 
       37.22        32.02        18.21        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-A0C0 TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH 
       41.75        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-A0E2 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE 
       14.30        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-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-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18G 
       50.79        23.93        24.95        42.35        44.81         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-A18R TCGA-BH-A18S TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO 
       30.28        37.55        66.05        51.16        69.93        91.99 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EX TCGA-BH-A1F0 
      113.82        82.85        42.28        12.00        49.58        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FG TCGA-BH-A1FH 
       31.53        89.16       120.62        33.17       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-A42U TCGA-BH-A42V TCGA-C8-A12N TCGA-C8-A12O 
        6.44        20.12       109.28         8.94        11.77        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-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE 
        1.78         1.45         0.62         3.85         3.75        12.33 
TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A26V TCGA-C8-A26W 
       11.34        11.34         0.16        10.42         0.30         0.23 
TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 
        0.36         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-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 
       20.58        14.17        13.48        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-A1JH TCGA-D8-A1JI TCGA-D8-A1JK TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1JT 
       14.01        18.97        20.12        20.38        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-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XJ TCGA-D8-A1XL TCGA-D8-A1XM 
        2.66        17.16        15.22        21.83        19.92        17.69 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XZ 
       16.41        15.85        16.31        15.16        12.66        15.32 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H 
        3.81        14.24        17.42        16.04        13.45        13.05 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27V TCGA-D8-A27W 
        9.44        16.41         4.80         0.76        12.53        12.26 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A109 
       14.50        18.51         7.33        43.00        34.42        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-A14S TCGA-E2-A14U TCGA-E2-A14V 
       44.68        40.96        38.24        33.17        43.33        34.26 
TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 
       32.02        31.96        28.60        27.12        23.24        19.43 
TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15G 
       23.87        14.79        22.82        17.29        20.71        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-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-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-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-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 
       40.47        18.87         8.75        43.04        16.93         5.52 
TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1N5 
       15.72        30.61        19.00         9.21        19.20        36.82 
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-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R7 TCGA-E9-A1RA 
        9.86        14.30         0.62         2.10        21.21        32.09 
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-A22E 
       35.64        34.13         0.79        12.53        13.32        12.89 
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-A2JT TCGA-E9-A3Q9 TCGA-E9-A3X8 
        0.95        24.56         0.72         0.76        18.41        15.72 
TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP 
       12.33         0.23        14.70         0.26        13.81        14.40 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1J1 TCGA-EW-A1J2 
       15.39        12.20        39.72         8.48        18.90        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 
       16.57        15.68        29.95        29.85        40.41        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA 
       39.78        52.96        23.11        18.48        30.08        18.90 
TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PG TCGA-EW-A2FS 
       19.99         6.15        13.94        10.52        34.55        52.73 
TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       22.09        21.27         7.40        59.57       194.27        53.13 
TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DL TCGA-GM-A2DM 
       53.52        43.04        42.71        61.91        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        43.73        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-JL-A3YW TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 
       72.03        13.55        11.84        21.24         6.67         4.60 
TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM 
        8.75         9.53        10.95         7.59        17.06        15.32 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y 
       14.70        14.47        11.57         2.63         3.88         4.14 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
        4.50         4.50         5.59         6.21         7.36        27.91 
TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.79         2.10        12.66        31.99        58.62        27.65 
TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A66H TCGA-OL-A66J 
       34.92        36.36        16.87        24.72        26.70        65.62 
TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ TCGA-PL-A8LY TCGA-PL-A8LZ 
       31.07         7.23        14.07        19.73         0.26         3.95 
TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 
        6.81         8.65         5.56         8.52         7.17         6.87 
TCGA-W8-A86G TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        5.29       100.01       105.04 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.16               0.03 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            211.56             234.28 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             21.09              23.61 
[1] "0.2 - 211.6 (21.1)" "0.0 - 234.3 (23.6)"
[1] "hr=" "1.5"
D66V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  14Q LOSS MUTATED        19       20        0        2        91        59
  14Q LOSS WILD-TYPE      64       60        9        3       251       175
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  14Q LOSS MUTATED           0         30          5         15        5
  14Q LOSS WILD-TYPE         2        112         24         48       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                 64
  STAGE IA                 20                 60
  STAGE IB                  0                  9
  STAGE II                  2                  3
  STAGE IIA                91                251
  STAGE IIB                59                175
  STAGE III                 0                  2
  STAGE IIIA               30                112
  STAGE IIIB                5                 24
  STAGE IIIC               15                 48
  STAGE IV                  5                 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    53 164  25   7
  14Q LOSS WILD-TYPE 212 430  99  32
D66V4, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1               53                212
  T2              164                430
  T3               25                 99
  T4                7                 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
  14Q LOSS MUTATED   135  70  27  15
  14Q LOSS WILD-TYPE 346 269  86  59
D66V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0              135                346
  N1               70                269
  N2               27                 86
  N3               15                 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
  14Q LOSS MUTATED          1 207   5  37
  14Q LOSS WILD-TYPE        4 647  14 110
D66V6, multiclass
          clus
vv         14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CM0 (I+)                1                  4
  M0                    207                647
  M1                      5                 14
  MX                     37                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"
D66V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED   249   1
  14Q LOSS WILD-TYPE 765  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED    249    1
  14Q LOSS WILD-TYPE  765   10
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE              249                765
  MALE                  1                 10
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  14Q LOSS MUTATED                            0                           207
  14Q LOSS WILD-TYPE                          1                           547
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  14Q LOSS MUTATED                               24                   5
  14Q LOSS WILD-TYPE                            151                   1
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  14Q LOSS MUTATED                                  3                  1
  14Q LOSS WILD-TYPE                               26                 14
                    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                 207                547
  INFILTRATING LOBULAR CARCINOMA                 24                151
  MEDULLARY CARCINOMA                             5                  1
  MIXED HISTOLOGY (PLEASE SPECIFY)                3                 26
  MUCINOUS CARCINOMA                              1                 14
  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    75 175
  14Q LOSS WILD-TYPE 207 568
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     75  175
  14Q LOSS WILD-TYPE  207  568
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                75                207
  YES              175                568
[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                          60   155
  14Q LOSS WILD-TYPE                        98   562
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                      60                 98
  WHITE                                         155                562
[1] 4 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    11 199
  14Q LOSS WILD-TYPE  25 627
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     11  199
  14Q LOSS WILD-TYPE   25  627
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   11                 25
  NOT HISPANIC OR LATINO              199                627
[1] 2 2
[1] FALSE

Clustering(67) Variable = 15Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED   257  41
  15Q LOSS WILD-TYPE 629  78
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               298                707 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                41                 78 
$`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        26.96 
TCGA-A2-A4S3 TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A26E 
       21.90        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        43.00        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        43.00        30.97 
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-A04A TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AR 
        0.69         1.74         2.96         8.02         7.36         0.33 
TCGA-AN-A0FD TCGA-AN-A0FK TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX 
        6.44         7.00         6.02         0.33         0.36         0.33 
TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XS TCGA-AO-A03L 
        0.33         0.33         0.33        12.33         0.33        80.28 
TCGA-AO-A03M TCGA-AO-A03V TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A0JD 
       47.84        29.13        37.48        20.32        53.03        72.00 
TCGA-AO-A0JL TCGA-AO-A129 TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AO-A1KT 
       55.33        96.10        48.36        61.87         0.53        17.79 
TCGA-AQ-A04H TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TV 
       24.79         2.56        32.91         5.26        86.66        29.75 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A1AH TCGA-AR-A1AI 
       64.83        55.86        65.36       101.95        75.55        61.84 
TCGA-AR-A1AJ TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AW TCGA-AR-A1AY TCGA-AR-A24Q 
       52.77        43.07        17.23        63.62        20.22       101.52 
TCGA-AR-A24R TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A256 
       87.22        85.35        50.96        79.00        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-E2-A576 TCGA-E9-A1N6 
        8.75        16.93        34.92        19.89        19.00        13.48 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1R4 TCGA-E9-A1RC 
       13.12        36.56        39.55        12.59         6.12        40.24 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A22E 
       34.65         6.58        21.27        34.59        34.13        12.89 
TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A295 
       23.51         0.69        27.22         1.94         0.95         0.72 
TCGA-E9-A3HO TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP 
       26.07         0.62        15.72         0.26        13.81        14.40 
TCGA-EW-A1OV TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P8 TCGA-EW-A1PC 
       25.94        29.85        40.41        41.13         7.86         6.15 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A3E8 TCGA-GM-A2DH 
       19.96        55.00        52.73        25.91        21.27        42.28 
TCGA-GM-A3XL TCGA-JL-A3YX TCGA-LL-A441 TCGA-LL-A5YN TCGA-LL-A5YP TCGA-LL-A6FP 
       69.30        11.57        11.44        14.70        14.79        11.57 
TCGA-LL-A6FR TCGA-LL-A8F5 TCGA-OL-A5D7 TCGA-OL-A66I TCGA-OL-A66K TCGA-S3-A6ZF 
        3.88         6.21        46.55        23.47        33.57        16.50 
TCGA-S3-A6ZG TCGA-S3-AA10 TCGA-S3-AA17 TCGA-Z7-A8R5 
        6.81         7.92         3.91       100.01 

$`15Q LOSS WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        0.39         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SQ 
       47.24        13.68        31.79         7.96        39.32        18.21 
TCGA-A2-A04N TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK 
      104.81        82.16        63.12        55.43        36.13       136.73 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CU TCGA-A2-A0CV 
      112.08        92.48        88.60       107.93         5.19        63.45 
TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EP 
       34.55        33.76        28.77        25.22       101.72       107.61 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
       74.40        37.05        34.29        31.82        29.75        24.72 
TCGA-A2-A0ST TCGA-A2-A0SY TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 
       99.19        44.28        17.13         8.38        18.71        20.52 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG 
       17.46        18.90        32.55        25.28        15.42        21.90 
TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FV 
       21.67        14.50        19.33        48.46        23.77        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-A3XT TCGA-A2-A3XV TCGA-A2-A3XW 
       10.59        20.88        39.65        83.01        32.75        49.48 
TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 
       34.98        31.99        24.39        21.30        23.21        21.14 
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-A26G TCGA-A7-A26H TCGA-A7-A26J 
       12.72        23.61        29.56        23.74        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-A4SB TCGA-A7-A4SE TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX 
       14.93        13.74        21.17        12.10        10.72        11.05 
TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06T TCGA-A8-A06X 
        8.75        13.02        13.02         1.02        53.06        31.00 
TCGA-A8-A075 TCGA-A8-A079 TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J 
       17.03         9.01        19.99        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        24.99         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        38.01 
TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08R 
       28.96        33.01        19.96        37.05        31.00         0.99 
TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A095 TCGA-A8-A097 
       33.01        93.04        40.01        33.01        41.98        12.00 
TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K 
        9.99        12.00        50.04        49.05        45.07        29.98 
TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09X 
       33.07        25.02         8.98        19.04        15.02        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-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-A2FO TCGA-AC-A2QH 
       40.57        55.43        36.99        38.79        50.70         1.02 
TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 
        0.92         0.99         0.69        22.19         1.12        16.57 
TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y 
       19.79        23.24        24.79         1.55         0.07         1.81 
TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AN-A03X 
        1.18         0.43         1.68         1.12         1.32         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-A0AL TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FF TCGA-AN-A0FJ 
        6.51         0.16         0.33         0.33         4.64         7.96 
TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0XL TCGA-AN-A0XP TCGA-AN-A0XR 
        7.59         7.17         6.28         0.33         0.30         0.33 
TCGA-AN-A0XT 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-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A0J2 TCGA-AO-A0J3 
       84.69        68.75        47.87        59.05        32.78        21.40 
TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J8 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC 
       52.18        24.16        22.36        21.53        50.70        50.86 
TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JM 
       76.77        21.37        26.24        50.24        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       108.72       106.78        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-A1KR TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       70.39        26.93       130.09         5.65        15.62        32.52 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TW TCGA-AR-A0TZ 
        9.99       111.32        49.32        74.79        98.93        76.14 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM 
       83.87       114.02        85.97        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        37.81        76.21        61.28 
TCGA-AR-A1AX TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       62.14       109.58        50.89        73.02        96.89        78.51 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A251 
       84.20         0.85        76.01        53.36        83.77        78.48 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       73.18        72.76        58.92       128.65        20.25        62.86 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QM 
        7.36        40.04        38.17        39.39        40.54        54.74 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 
       16.04        20.45        10.59       143.38       149.59        12.13 
TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IM 
      220.90        50.70        65.72       146.50        18.77       126.12 
TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL 
       84.59       110.93       140.88       189.01       234.28        81.17 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV 
       78.02       172.96       162.05       140.48        89.46       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 
       97.48       188.68        17.98       129.57       129.70       186.48 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 
       28.27        68.94        58.88       139.17       170.17        85.35 
TCGA-B6-A40B TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 
      103.63        38.79        20.45        25.55        28.50        46.95 
TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B7 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       39.55        39.16        56.98        32.02        18.21        25.71 
TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ 
       24.85        21.70        61.68        35.67        48.69        27.19 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0C3 TCGA-BH-A0DD 
       53.69        53.95        49.94        11.67        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-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DZ 
       17.26         3.22         2.56        38.47        45.17        16.27 
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-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-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       24.56        52.96        26.50        20.38         5.85         2.50 
TCGA-BH-A0HQ TCGA-BH-A0HW TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0WA 
       36.85        51.32        23.93        24.95        42.35        23.05 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q 
        2.01         7.23        72.56        37.74        30.28        55.63 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18V TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW 
       37.55        66.05        51.16        82.85        42.28        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-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-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-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-A130 TCGA-C8-A131 
        0.07        12.66        12.66        12.66         3.12         1.78 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HG TCGA-C8-A1HI 
        1.45         0.69         3.85        12.33        11.34        11.34 
TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X 
        0.16        10.42         2.30         0.30         0.23         0.36 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A27B TCGA-C8-A3M7 
        8.28         9.67         0.03         0.03         0.99         0.03 
TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A145 
        0.23        11.90        13.25        20.58        14.17        13.48 
TCGA-D8-A147 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JH 
       19.20        16.50        18.71        15.78        18.15        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-A1XC TCGA-D8-A1XD 
       16.73        25.74        23.90        27.58         2.66        17.16 
TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XM TCGA-D8-A1XR TCGA-D8-A1XT TCGA-D8-A1XV 
       14.73        14.50        17.69        15.85         6.35        15.16 
TCGA-D8-A1XW TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F 
       12.66        15.52        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-A27N 
       13.45        13.05        14.43         9.44        16.41         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-A10A 
       18.51         7.33        43.00        34.42        27.52        40.41 
TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q 
       37.51        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-A153 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 
       28.60        17.03        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-A15I 
       23.34        22.82        17.29        20.71        21.63        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-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-A1IG TCGA-E2-A1IH 
       32.35        28.50        16.47        38.30        32.78        33.73 
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-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH 
       54.18        19.66        40.47        28.90        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        30.61 
TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1NE TCGA-E9-A1NF 
        9.21        19.20        36.82        12.00        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-A1RD 
        1.38         2.76        21.21        32.09        20.81         0.66 
TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       35.64         0.79        12.53        13.32        39.09        22.75 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A245 TCGA-E9-A24A TCGA-E9-A2JS TCGA-E9-A2JT 
       24.10        17.06         0.85        24.56        17.75         0.76 
TCGA-E9-A3Q9 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A6HE TCGA-EW-A1IW 
       18.41        12.33         0.23        14.70        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 
       43.73        66.38        72.03        13.55        18.12        11.84 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 
       21.24         6.67         4.08         4.60         8.75         9.53 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A6FQ 
       10.95         7.59        17.06        15.32        14.47         2.63 
TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A9Q3 
        4.14         4.50         4.50         5.59         3.22         7.36 
TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA 
       27.91         2.79         2.10        12.66        31.99        58.62 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       27.65        34.92        36.36        16.87        24.72        22.32 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O 
       20.38        26.70        65.62        31.07        26.04         7.23 
TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PL-A8LV TCGA-PL-A8LX TCGA-PL-A8LY 
       14.07        28.21        19.73         0.23         0.16         0.26 
TCGA-PL-A8LZ TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 
        3.95         8.65        10.59         5.56         8.52         7.17 
TCGA-S3-AA15 TCGA-W8-A86G TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
        6.87         5.29         9.60         9.14       105.04 

  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 
            24.375             22.090 
[1] "0.0 - 211.6 (24.4)" "0.0 - 234.3 (22.1)"
[1] "hr=" "1.3"
D67V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  15Q LOSS MUTATED        19       20        1        0       114        68
  15Q LOSS WILD-TYPE      64       60        8        5       228       166
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  15Q LOSS MUTATED           1         48          5         16        6
  15Q LOSS WILD-TYPE         1         94         24         47       12
                    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                 64
  STAGE IA                 20                 60
  STAGE IB                  1                  8
  STAGE II                  0                  5
  STAGE IIA               114                228
  STAGE IIB                68                166
  STAGE III                 1                  1
  STAGE IIIA               48                 94
  STAGE IIIB                5                 24
  STAGE IIIC               16                 47
  STAGE IV                  6                 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
  15Q LOSS MUTATED    59 200  34   9
  15Q LOSS WILD-TYPE 206 394  90  30
D67V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1               59                206
  T2              200                394
  T3               34                 90
  T4                9                 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
  15Q LOSS MUTATED   154  84  42  20
  15Q LOSS WILD-TYPE 327 255  71  54
D67V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0              154                327
  N1               84                255
  N2               42                 71
  N3               20                 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
  15Q LOSS MUTATED          1 260   6  36
  15Q LOSS WILD-TYPE        4 594  13 111
D67V6, multiclass
          clus
vv         15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CM0 (I+)                1                  4
  M0                    260                594
  M1                      6                 13
  MX                     36                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"
D67V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED   300   3
  15Q LOSS WILD-TYPE 714   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    300    3
  15Q LOSS WILD-TYPE  714    8
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE              300                714
  MALE                  3                  8
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  15Q LOSS MUTATED                            0                           246
  15Q LOSS WILD-TYPE                          1                           508
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  15Q LOSS MUTATED                               29                   3
  15Q LOSS WILD-TYPE                            146                   3
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  15Q LOSS MUTATED                                  9                  2
  15Q LOSS WILD-TYPE                               20                 13
                    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                 246                508
  INFILTRATING LOBULAR CARCINOMA                 29                146
  MEDULLARY CARCINOMA                             3                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)                9                 20
  MUCINOUS CARCINOMA                              2                 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"
D67V9, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    95 208
  15Q LOSS WILD-TYPE 187 535
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     95  208
  15Q LOSS WILD-TYPE  187  535
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                95                187
  YES              208                535
[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                          54   209
  15Q LOSS WILD-TYPE                       104   508
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                      54                104
  WHITE                                         209                508
[1] 4 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     8 247
  15Q LOSS WILD-TYPE  28 579
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      8  247
  15Q LOSS WILD-TYPE   28  579
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    8                 28
  NOT HISPANIC OR LATINO              247                579
[1] 2 2
[1] FALSE

Clustering(68) Variable = 16P LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED   142  19
  16P LOSS WILD-TYPE 744 100
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               161                844 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                19                100 
$`16P LOSS MUTATED`
TCGA-A1-A0SE TCGA-A1-A0SK TCGA-A1-A0SN TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A0CR 
       43.43        31.79        39.32        73.84        22.06       107.93 
TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0D0 TCGA-A2-A0D4 TCGA-A2-A0EQ TCGA-A2-A0EY 
       75.25        63.45        21.14        25.22        79.76        24.16 
TCGA-A2-A0SX TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A1FX TCGA-A2-A3XT TCGA-A2-A4RY 
       50.43        20.75        32.55        36.79        83.01        21.30 
TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A13D 
       38.30        34.29        35.47        30.61        35.67        31.73 
TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A26J TCGA-A7-A4SD TCGA-A7-A56D TCGA-A7-A5ZW 
       12.72        23.61        20.61        14.50        14.73        10.72 
TCGA-A7-A6VW TCGA-A8-A06O TCGA-A8-A075 TCGA-A8-A07B TCGA-A8-A07L TCGA-A8-A08J 
        9.37        13.02        17.03        43.00        17.03        37.05 
TCGA-A8-A08X TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09W TCGA-AC-A2BK 
       43.00        33.07         1.02        25.02         0.99        38.53 
TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A6IW TCGA-AC-A8OP TCGA-AC-A8OQ 
       38.20        40.57        55.43         0.69         1.74         1.12 
TCGA-AN-A046 TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0FN TCGA-AN-A0XN TCGA-AN-A0XR 
        0.33         6.51         0.33         7.17         0.33         0.33 
TCGA-AO-A0JD TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12G TCGA-AO-A1KT TCGA-AQ-A1H3 
       72.00        96.10        77.56        41.62        17.79        32.52 
TCGA-AQ-A54N TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A24H 
        2.56       114.02        75.55        43.07        17.23       109.58 
TCGA-AR-A24K TCGA-AR-A24O TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A251 TCGA-AR-A2LR 
       50.89        84.20        53.36        85.35        78.48        20.38 
TCGA-B6-A0I5 TCGA-B6-A0IJ TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RL TCGA-B6-A0X0 
      149.59       176.98       211.56       189.01        81.17       129.70 
TCGA-B6-A1KC TCGA-B6-A2IU TCGA-B6-A402 TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0BO 
       43.59       170.17        54.28        39.16        56.94        35.67 
TCGA-BH-A0C0 TCGA-BH-A0DE TCGA-BH-A0E0 TCGA-BH-A0E2 TCGA-BH-A0H5 TCGA-BH-A0HP 
       41.75        31.17         4.41        14.30        35.51        13.61 
TCGA-BH-A0HW TCGA-BH-A0HY TCGA-BH-A18K TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1ET 
       51.32        50.79        90.84        51.39        69.93        82.85 
TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FL TCGA-BH-A203 
       42.28        55.69       114.15        33.17        55.00        38.60 
TCGA-BH-A209 TCGA-BH-A28Q TCGA-C8-A130 TCGA-C8-A1HG TCGA-C8-A26X TCGA-C8-A278 
      130.16         6.44         3.12        11.34         0.36         0.03 
TCGA-C8-A27B TCGA-C8-A3M7 TCGA-D8-A1JC TCGA-D8-A1JN TCGA-D8-A1JT TCGA-D8-A1JU 
        0.99         0.03        15.78        20.38        13.32        14.70 
TCGA-D8-A27V TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A150 
       12.53        18.51         7.33        32.02        28.60        25.41 
TCGA-E2-A159 TCGA-E2-A15J TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ 
       25.05        19.40        17.06        14.07        14.99        60.53 
TCGA-E2-A1II TCGA-E2-A1IL TCGA-E2-A1L7 TCGA-E2-A1LK TCGA-E2-A573 TCGA-E2-A574 
       33.70         3.88        27.42         8.75        34.92        19.89 
TCGA-E9-A1ND TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A248 TCGA-EW-A1J5 TCGA-EW-A1J6 
       12.59        23.51         0.69         1.94        15.68        28.77 
TCGA-EW-A1P8 TCGA-EW-A1PC TCGA-EW-A3U0 TCGA-EW-A423 TCGA-GM-A2D9 TCGA-GM-A2DC 
        7.86         6.15        17.49        10.16        59.57        53.52 
TCGA-GM-A2DH TCGA-GM-A2DO TCGA-GM-A3NY TCGA-GM-A3XL TCGA-GM-A4E0 TCGA-LL-A50Y 
       42.28        53.36        38.20        69.30        72.03         7.59 
TCGA-LL-A5YN TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-OL-A5D7 TCGA-OL-A5RW TCGA-OL-A66L 
       14.70         3.22         6.21        46.55        36.36        31.07 
TCGA-OL-A6VO TCGA-PL-A8LV TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA12 
       28.21         0.23        10.59         7.92         8.52 

$`16P LOSS WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        0.39         8.52        14.37        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ 
       20.88        13.68         7.96        28.01        19.20        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-A0CM TCGA-A2-A0CO 
       55.43        36.13       136.73        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        48.46        31.73 
TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 
       23.77        23.47        17.36        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-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ 
       29.98        32.75        49.48        38.40        34.98        31.99 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 
       38.37         7.30        24.39        23.21        26.96        21.14 
TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13E TCGA-A7-A13H 
       21.90        35.31        37.45        33.11        10.72        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-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-A4SE TCGA-A7-A4SF TCGA-A7-A5ZV 
       11.97        14.93        13.74        21.17        17.92        12.10 
TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q 
       11.05        10.29        10.42         8.75        13.02         1.02 
TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z 
       17.98        53.06        29.03        31.00        26.01         1.02 
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-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U 
       12.00         9.99        10.98         8.98         7.99        24.99 
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        38.01        28.96        33.01        19.96        12.00 
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        33.01        93.04 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 
       40.01        33.01        30.97        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        50.04        49.05 
TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09X 
       45.07        29.98         8.98        19.04        15.02        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-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH 
        1.48        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        22.19 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS 
        1.12        16.57        19.79        23.24        24.79         1.55 
TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO 
        0.07         1.12         1.81         1.18         0.43         1.68 
TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A04A 
        1.32         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        52.18        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        50.24        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       108.72       106.78        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        32.91         9.99       111.32        49.32         5.26 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
       74.79        86.66        29.75        98.93        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       101.95        83.87        85.97        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        37.81        76.21        61.28        63.62        62.14 
TCGA-AR-A1AY TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24P TCGA-AR-A24Q 
       20.22        73.02        96.89        78.51         0.85       101.52 
TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 
       87.22        76.01        50.96        83.77        79.00        56.15 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH 
       73.18        72.76        58.92        93.83       128.65        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       62.86        42.87         7.36        40.04        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       40.54        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-A401 TCGA-B6-A408 TCGA-B6-A40B 
      101.52        73.51       139.17        85.35        49.94       103.63 
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-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 
       46.95        40.83        39.55        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-A0BL TCGA-BH-A0BM TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       44.05        61.68        48.69        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-A0C7 TCGA-BH-A0DD TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       42.90        45.83        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-A0E6 TCGA-BH-A0E7 
       45.17        47.41        16.27        15.68         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-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 
       10.78        15.16        37.78        24.56        23.08        41.00 
TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HQ 
       52.96        26.50        20.38         5.85         2.50        36.85 
TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 
       12.89        27.25         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-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-A26Y TCGA-C8-A26Z TCGA-C8-A273 
        3.25         0.30         0.23         0.43         8.28         9.67 
TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A13Z 
        0.03         0.03        12.20         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-A1JD 
       19.20        14.17        17.49        16.50        18.71        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-A1JP TCGA-D8-A1JS TCGA-D8-A1X5 
       20.12        20.09        19.40        21.01        12.20        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-A1XZ 
        6.35        12.99        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-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-A27W TCGA-D8-A3Z5 
        4.80         0.76        10.09        13.08        12.26        14.50 
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-A14X TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 
       31.96        17.03        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-A15K TCGA-E2-A15L 
       21.63        18.21        12.92        17.42         9.04        20.58 
TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 
        7.73        13.02        19.56        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-A1IN TCGA-E2-A1IO 
       32.78        33.73        28.44        22.65        22.19        20.98 
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-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LL TCGA-E2-A2P5 
       28.90        18.87       106.75       102.61        43.04        16.93 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A576 TCGA-E2-A9RU 
        5.52        15.72         7.20        30.61        19.00         9.21 
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-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-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-A245 TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
       17.06         0.85        27.22         0.95        24.56         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-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP 
       12.33         0.23        14.70         0.26        13.81        14.40 
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-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY 
       13.25        16.57        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-A1PA TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE 
       18.48        30.08        18.90        19.99        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-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2DA 
       22.09        21.27        10.59         7.40       109.87       194.27 
TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       53.13        43.04        42.71        61.91        62.33        90.84 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A5PV 
       76.64        77.33       110.50        43.73        66.38        13.55 
TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 
       18.12        11.84        11.57        21.24         6.67         4.08 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A5YL 
        4.60         8.75         9.53        11.44        10.95        17.06 
TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR 
       15.32        14.47        14.79        11.57         2.63         3.88 
TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A9Q3 TCGA-LQ-A4E4 
        4.14         4.50         4.50         5.59         7.36        27.91 
TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.79         2.10        12.66        31.99        58.62        27.65 
TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H 
       34.92        16.87        24.72        22.32        20.38        26.70 
TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P 
       23.47        65.62        33.57        26.04         7.23        14.07 
TCGA-OL-A6VQ TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG 
       19.73         0.16         0.26         3.95        16.50         6.81 
TCGA-S3-A6ZH TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-W8-A86G 
        8.65         5.56         7.17         6.87         3.91         5.29 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        9.60         9.14       100.01       105.04 

  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 
             31.07              21.65 
[1] "0.0 - 211.6 (31.1)" "0.0 - 234.3 (21.6)"
[1] "hr=" "1.3"
D68V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16P LOSS MUTATED        20        9        1        0        66        29
  16P LOSS WILD-TYPE      63       71        8        5       276       205
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16P LOSS MUTATED           0         20          5         11        1
  16P LOSS WILD-TYPE         2        122         24         52       17
                    vv
clus                 STAGE TIS STAGE X
  16P LOSS MUTATED           0       1
  16P LOSS WILD-TYPE         1      15
D68V3, multiclass
            clus
vv           16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                  20                 63
  STAGE IA                  9                 71
  STAGE IB                  1                  8
  STAGE II                  0                  5
  STAGE IIA                66                276
  STAGE IIB                29                205
  STAGE III                 0                  2
  STAGE IIIA               20                122
  STAGE IIIB                5                 24
  STAGE IIIC               11                 52
  STAGE IV                  1                 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
  16P LOSS MUTATED    42  94  19   7
  16P LOSS WILD-TYPE 223 500 105  32
D68V4, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1               42                223
  T2               94                500
  T3               19                105
  T4                7                 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
  16P LOSS MUTATED    91  42  16  13
  16P LOSS WILD-TYPE 390 297  97  61
D68V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0               91                390
  N1               42                297
  N2               16                 97
  N3               13                 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
  16P LOSS MUTATED          0 142   1  20
  16P LOSS WILD-TYPE        5 712  18 127
D68V6, multiclass
          clus
vv         16P LOSS MUTATED 16P LOSS WILD-TYPE
  CM0 (I+)                0                  5
  M0                    142                712
  M1                      1                 18
  MX                     20                127
[1] 4 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   161   2
  16P LOSS WILD-TYPE 853   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED    161    2
  16P LOSS WILD-TYPE  853    9
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE              161                853
  MALE                  2                  9
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  16P LOSS MUTATED                            0                           131
  16P LOSS WILD-TYPE                          1                           623
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  16P LOSS MUTATED                               21                   3
  16P LOSS WILD-TYPE                            154                   3
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  16P LOSS MUTATED                                  3                  0
  16P LOSS WILD-TYPE                               26                 15
                    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                 131                623
  INFILTRATING LOBULAR CARCINOMA                 21                154
  MEDULLARY CARCINOMA                             3                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)                3                 26
  MUCINOUS CARCINOMA                              0                 15
  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    41 122
  16P LOSS WILD-TYPE 241 621
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     41  122
  16P LOSS WILD-TYPE  241  621
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                41                241
  YES              122                621
[1] 2 2
[1] FALSE
D68V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P LOSS MUTATED                                  0    11
  16P LOSS WILD-TYPE                                1    45
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED                          41   101
  16P LOSS WILD-TYPE                       117   616
D68V11, multiclass
                                  clus
vv                                 16P LOSS MUTATED 16P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          11                 45
  BLACK OR AFRICAN AMERICAN                      41                117
  WHITE                                         101                616
[1] 4 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     7 135
  16P LOSS WILD-TYPE  29 691
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      7  135
  16P LOSS WILD-TYPE   29  691
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    7                 29
  NOT HISPANIC OR LATINO              135                691
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16Q LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED   490  57
  16Q LOSS WILD-TYPE 396  62
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               547                458 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                57                 62 
$`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-A04T TCGA-A2-A04U 
       39.32        28.01       104.81        82.16        73.84        22.06 
TCGA-A2-A04V TCGA-A2-A0CK TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
       63.12       136.73       112.08        92.48        88.60       107.93 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D3 
       75.55        75.25        63.45        21.14        34.55        28.77 
TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EQ TCGA-A2-A0EU 
       25.22       101.72        89.36        80.28        79.76        34.29 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0SU TCGA-A2-A0SY TCGA-A2-A0T1 TCGA-A2-A0T4 
       24.72        24.16        54.64        44.28        17.13        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-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV 
       15.42        21.67        19.33        48.46        31.73        23.47 
TCGA-A2-A1FX TCGA-A2-A1G0 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A3KC TCGA-A2-A3KD 
       36.79        20.25        52.47       107.70        20.88        39.65 
TCGA-A2-A3XT TCGA-A2-A4RY TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH 
       83.01        21.30        21.90        38.30        34.29        35.47 
TCGA-A7-A0CJ TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H 
       30.61        33.11        31.73        12.72        23.61        29.56 
TCGA-A7-A26E TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IZ TCGA-A7-A3J1 
       31.36        21.73        20.61        22.32        10.59        11.28 
TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZW 
       14.93        13.74        14.50        21.17        14.73        10.72 
TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q 
       11.05        10.29         9.37        13.02        13.02         1.02 
TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E 
       29.03        31.00        17.03         9.01        43.00        19.99 
TCGA-A8-A07F TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S 
       18.97        12.00        17.03        10.98         8.98         7.99 
TCGA-A8-A084 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08G 
       15.06        13.02         0.99        38.01        28.96        19.96 
TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X 
       37.05        31.00        31.00        33.01        93.04        43.00 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 
       40.01        33.01        30.97        17.95        41.98         9.99 
TCGA-A8-A09B TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R 
       12.00        29.98        33.07         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-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23E 
       13.02        21.04        13.02        17.03        38.04         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-A2FM TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3HN TCGA-AC-A3OD 
       36.99        26.04        50.70         0.92         0.69        14.83 
TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A5XS TCGA-AC-A62X 
       22.19         1.12        16.57        19.79         1.55         1.12 
TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AN-A03X 
        0.69         0.43         1.68         1.74         1.12         0.33 
TCGA-AN-A03Y TCGA-AN-A046 TCGA-AN-A0AK TCGA-AN-A0AR TCGA-AN-A0FK TCGA-AN-A0FN 
        0.33         0.33         7.36         0.33         7.00         7.17 
TCGA-AN-A0FS TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS 
        6.28         0.33         0.33         0.30         0.33         0.33 
TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P 
        0.33         0.33        80.28        66.77        81.63        84.69 
TCGA-AO-A03R TCGA-AO-A0J3 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA 
       68.75        21.40        20.32        22.36        53.03        21.53 
TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A125 TCGA-AO-A126 
       72.00        21.37        50.24        62.04        99.25       108.72 
TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A1KP 
       96.10        90.58        77.56        57.30        41.62        82.62 
TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AR-A0TV 
        0.53        17.79        15.62        32.52         2.56        29.75 
TCGA-AR-A0TZ TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AK TCGA-AR-A1AL 
       76.14        83.87       114.02        75.55        51.25        48.82 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A24H 
       62.56        43.73        39.98        43.07        17.23       109.58 
TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24T 
       50.89        73.02        78.51        84.20         0.85        76.01 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24X TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A2LE 
       53.36        85.35        83.77        78.48        72.76       128.65 
TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       62.86        42.87         7.36        40.04        38.17        39.39 
TCGA-AR-A5QN TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IH 
       16.04       149.59       220.90       129.57        50.70       112.37 
TCGA-B6-A0IM TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH 
      126.12       110.93       140.88       211.56        68.45       189.01 
TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RV TCGA-B6-A0WS 
      234.28        81.17       172.96       102.77       157.41        97.48 
TCGA-B6-A0WW TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A2IU 
       17.98       129.57       129.70        58.88        43.59       170.17 
TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV 
       54.28        49.94       103.63        55.00        24.53        38.79 
TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 
       25.55        46.95        40.83        39.16        48.36        56.94 
TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BF TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP 
       56.98        37.22        25.71        61.68        35.67        48.69 
TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 
       27.19        53.95        41.75        44.02        48.13        42.90 
TCGA-BH-A0DE TCGA-BH-A0DH TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DS 
       31.17        38.01        13.91        17.26        15.65         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 
       38.47        45.17        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-A0GY TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0HI TCGA-BH-A0HK 
       30.35        15.16        37.78        35.51        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-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F 
       50.79        23.93        24.95        44.81        23.05         8.81 
TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18T TCGA-BH-A18U 
       20.12        90.84        37.74        30.28         7.36        51.39 
TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW 
       69.93        91.99        82.85        42.28        12.00        55.69 
TCGA-BH-A1EY TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE 
       17.69        31.53        89.16       114.15        33.17        74.73 
TCGA-BH-A1FG TCGA-BH-A1FL TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A209 TCGA-BH-A28Q 
      122.89        55.00         0.72        38.60       130.16         6.44 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42V TCGA-C8-A12N TCGA-C8-A130 TCGA-C8-A137 
       20.12         0.99         8.94        11.77         3.12         3.85 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HM 
        3.75        12.33        10.92        11.34        11.34         2.30 
TCGA-C8-A1HN TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A274 TCGA-C8-A278 TCGA-C8-A27B 
        3.25         0.23         0.36         0.03         0.03         0.99 
TCGA-C8-A3M7 TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A141 TCGA-D8-A1J8 TCGA-D8-A1J9 
        0.03        11.90        20.88        20.58        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-E2-A576 
        5.52        15.72        30.61        34.92        19.89        19.00 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1NG 
       19.20        36.82        12.00        12.59        20.05        21.57 
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        24.56         0.72        26.07 
TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IY 
       15.72         0.23        14.40        15.39        12.20         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV 
       18.21        13.25        16.57        15.68        28.77        25.94 
TCGA-EW-A1OZ TCGA-EW-A1P3 TCGA-EW-A1P6 TCGA-EW-A1P8 TCGA-EW-A1PC TCGA-EW-A1PE 
       40.41        52.96        18.48         7.86         6.15        10.52 
TCGA-EW-A1PG TCGA-EW-A2FS TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 
       34.55        52.73        21.27        17.49        10.16        10.59 
TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DC TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DN 
        7.40        59.57        53.52        42.28        61.91        77.33 
TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XL TCGA-GM-A4E0 TCGA-GM-A5PV 
       53.36       110.50        38.20        69.30        72.03        13.55 
TCGA-GM-A5PX TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A50Y 
       18.12        11.57        21.24         6.67         4.60         7.59 
TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A6FP TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LQ-A4E4 
       17.06        14.70        11.57         3.22         6.21        27.91 
TCGA-MS-A51U TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV 
        2.79        12.66        46.55        31.99        58.62        34.92 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5S0 TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L 
       36.36        16.87        20.38        65.62        33.57        31.07 
TCGA-OL-A66N TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PL-A8LV TCGA-S3-A6ZF TCGA-S3-A6ZG 
       26.04        28.21        19.73         0.23        16.50         6.81 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA12 TCGA-W8-A86G TCGA-XX-A899 TCGA-XX-A89A 
       10.59         7.92         8.52         5.29         9.60         9.14 
TCGA-Z7-A8R6 
      105.04 

$`16Q LOSS WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SG TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SP 
        0.39         8.52        14.27        20.88        13.68        19.20 
TCGA-A1-A0SQ TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
       18.21        18.02        41.95        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-A0YG TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YT TCGA-A2-A1FW 
       18.71        21.90        14.50        18.61        23.77        17.36 
TCGA-A2-A1FZ TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A25B TCGA-A2-A25C 
       22.45        19.20        19.56        16.47        16.31        17.19 
TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XV 
       18.15        91.92        10.59        33.93        29.98        32.75 
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-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CE TCGA-A7-A0D9 
       24.39        23.21        26.96        21.14        35.31        37.45 
TCGA-A7-A0DA TCGA-A7-A13E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A3IY 
       35.67        10.72        24.26        23.74        23.80        11.34 
TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SF TCGA-A7-A5ZV 
       10.29        13.41        14.70        11.97        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        53.06        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        24.99         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        33.01        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        50.04        49.05 
TCGA-A8-A09I TCGA-A8-A0A7 TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A2FK TCGA-AC-A2QH 
       45.07         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        23.24        24.79         0.07         1.81 
TCGA-AC-A6IV TCGA-AC-A8OR TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C 
        1.18         1.32         0.23         0.62         2.96         1.78 
TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0AT 
        1.71         8.02         6.51         0.16         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FT TCGA-AN-A0FV 
        6.44         4.64         7.96         7.59         6.02         0.33 
TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XO TCGA-AN-A0XV 
        0.36         0.33         0.33         0.33        12.33         5.33 
TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 
        5.59        47.84        47.87        59.05        29.13        32.78 
TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE 
       52.18        24.16        37.48        50.70        50.86        76.77 
TCGA-AO-A0JG TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A128 TCGA-AO-A12D 
       26.24        55.33        71.80       102.58       106.78        64.04 
TCGA-AO-A12F TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AQ-A04H 
       48.36        28.37        14.73        61.87        70.39        24.79 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP 
       26.93       130.09         5.65        32.91         9.99       111.32 
TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0TX 
       49.32         5.26        74.79        86.66        98.93        64.83 
TCGA-AR-A0TY TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AJ 
       55.86        65.36       101.95        85.97        61.84        52.77 
TCGA-AR-A1AO TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX 
       43.56        37.81        76.21        61.28        63.62        62.14 
TCGA-AR-A1AY TCGA-AR-A24M TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24W TCGA-AR-A24Z 
       20.22        96.89       101.52        87.22        50.96        79.00 
TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LH TCGA-AR-A2LQ 
       56.15        73.18        58.92        93.83        20.25        40.54 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 
       20.38        54.74        20.45        10.59        77.62       143.38 
TCGA-B6-A0I9 TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IN 
       12.13        65.72       146.50       176.98        18.77        84.59 
TCGA-B6-A0IO TCGA-B6-A0RM TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT 
      110.14        78.02       162.05       140.48       100.70        89.46 
TCGA-B6-A0RU TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0X1 
      131.21       188.68        79.63        21.47       113.79       186.48 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A401 
       28.27        68.94       101.52        73.51       139.17        85.35 
TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B3 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD 
       20.45        28.50        39.55        51.68        32.02        18.21 
TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BR TCGA-BH-A0BT TCGA-BH-A0BV 
       24.85        21.70        44.05        53.69        45.57        49.94 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0DD TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DL 
       11.67        49.05        45.83        23.44        22.13        48.23 
TCGA-BH-A0DQ TCGA-BH-A0DX TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H6 TCGA-BH-A0H7 
        3.22        47.41        24.43        10.78        24.56        23.08 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0RX TCGA-BH-A0W5 TCGA-BH-A18G 
       41.00        52.96        26.50         5.59        42.35         2.01 
TCGA-BH-A18I TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S 
        7.23        26.66        72.56        55.63        37.55        66.05 
TCGA-BH-A18V TCGA-BH-A1ES TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1F6 TCGA-BH-A1F8 
       51.16       113.82        49.58        25.81        97.48        24.66 
TCGA-BH-A1FB TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR 
      120.62        36.92        63.35        45.63        72.07       144.59 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A28O TCGA-BH-A42U 
       72.07         6.90        83.31        57.83        10.65       109.28 
TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U 
       11.93        11.77        12.66        11.77         0.07        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-A135 TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A26V TCGA-C8-A26Y 
        0.62         0.16        12.03        10.42         0.30         0.43 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A3M8 TCGA-D8-A140 
        8.28         9.67         0.03        12.20         0.23        13.25 
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-A1JF TCGA-D8-A1JH TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM 
       18.71        12.03        14.01        20.12        20.09        19.40 
TCGA-D8-A1X7 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD 
       16.73        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-A1XT 
       15.22        14.73        21.83        19.92        17.69         6.35 
TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y2 TCGA-D8-A27E 
       12.99        15.16        12.66        15.32        14.24        17.42 
TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27R 
       16.04        13.05        14.43        13.48         4.80        10.09 
TCGA-D8-A27W TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10B TCGA-E2-A10F 
       12.26        43.00        27.52        46.59        37.51        28.87 
TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14R TCGA-E2-A14T TCGA-E2-A14V TCGA-E2-A14X 
       47.15        40.96        38.60        33.30        34.26        31.96 
TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A158 TCGA-E2-A15A TCGA-E2-A15F TCGA-E2-A15M 
       27.12        19.43        14.79        23.34        21.63         7.73 
TCGA-E2-A15P TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1IG 
       19.56        53.62        53.03        32.35        28.50        32.78 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1L9 TCGA-E2-A1LB 
       28.44        22.65        22.19        20.98        19.66        40.47 
TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LL TCGA-E2-A56Z TCGA-E2-A9RU 
       28.90       106.75       102.61        43.04         7.20         9.21 
TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NI 
       13.48        13.12        36.56        39.55        35.77         9.86 
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-A54X TCGA-E9-A5FK TCGA-E9-A5FL 
        0.76        18.41         0.62        12.33        14.70         0.26 
TCGA-E9-A5UO TCGA-EW-A1IX TCGA-EW-A1J1 TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY 
       13.81        39.72        18.90        22.82        29.95        29.85 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P7 TCGA-EW-A1PA 
       41.13        39.78        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        43.73        66.38        11.84 
TCGA-LD-A7W5 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A5YM 
        4.08         8.75         9.53        11.44        10.95        15.32 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z 
       14.47        14.79         2.63         3.88         4.14         4.50 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A9Q3 TCGA-OK-A5Q2 TCGA-OL-A5RU TCGA-OL-A5RY 
        4.50         5.59         7.36         2.10        27.65        24.72 
TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66O TCGA-OL-A66P TCGA-PL-A8LX 
       22.32        26.70        23.47         7.23        14.07         0.16 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZH TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 
        0.26         3.95         8.65         5.56         7.17         6.87 
TCGA-S3-AA17 TCGA-Z7-A8R5 
        3.91       100.01 

  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 
            22.060             22.785 
[1] "0.0 - 234.3 (22.1)" "0.0 - 194.3 (22.8)"
[1] "hr=" "1.3"
D69V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16Q LOSS MUTATED        53       40        4        4       197       122
  16Q LOSS WILD-TYPE      30       40        5        1       145       112
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16Q LOSS MUTATED           1         74         13         35        6
  16Q LOSS WILD-TYPE         1         68         16         28       12
                    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                  53                 30
  STAGE IA                 40                 40
  STAGE IB                  4                  5
  STAGE II                  4                  1
  STAGE IIA               197                145
  STAGE IIB               122                112
  STAGE III                 1                  1
  STAGE IIIA               74                 68
  STAGE IIIB               13                 16
  STAGE IIIC               35                 28
  STAGE IV                  6                 12
  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   148 321  71  18
  16Q LOSS WILD-TYPE 117 273  53  21
D69V4, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1              148                117
  T2              321                273
  T3               71                 53
  T4               18                 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
  16Q LOSS MUTATED   278 172  58  44
  16Q LOSS WILD-TYPE 203 167  55  30
D69V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0              278                203
  N1              172                167
  N2               58                 55
  N3               44                 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                 CM0 (I+)  M0  M1  MX
  16Q LOSS MUTATED          0 466   7  86
  16Q LOSS WILD-TYPE        5 388  12  61
D69V6, multiclass
          clus
vv         16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CM0 (I+)                0                  5
  M0                    466                388
  M1                      7                 12
  MX                     86                 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"
D69V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED   555   4
  16Q LOSS WILD-TYPE 459   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED    555    4
  16Q LOSS WILD-TYPE  459    7
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE              555                459
  MALE                  4                  7
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  16Q LOSS MUTATED                            0                           386
  16Q LOSS WILD-TYPE                          1                           368
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  16Q LOSS MUTATED                              136                   3
  16Q LOSS WILD-TYPE                             39                   3
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  16Q LOSS MUTATED                                 18                  1
  16Q LOSS WILD-TYPE                               11                 14
                    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                 386                368
  INFILTRATING LOBULAR CARCINOMA                136                 39
  MEDULLARY CARCINOMA                             3                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)               18                 11
  MUCINOUS CARCINOMA                              1                 14
  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   143 416
  16Q LOSS WILD-TYPE 139 327
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED    143  416
  16Q LOSS WILD-TYPE  139  327
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO               143                139
  YES              416                327
[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                          82   389
  16Q LOSS WILD-TYPE                        76   328
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                      82                 76
  WHITE                                         389                328
[1] 4 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    18 437
  16Q LOSS WILD-TYPE  18 389
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     18  437
  16Q LOSS WILD-TYPE   18  389
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   18                 18
  NOT HISPANIC OR LATINO              437                389
[1] 2 2
[1] FALSE

Clustering(70) Variable = 17P LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED   464  70
  17P LOSS WILD-TYPE 422  49
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               534                471 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                70                 49 
$`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       136.73 
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        48.46        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        32.75        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        24.39        26.96        21.90        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        43.00        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        38.01 
TCGA-A8-A08F TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A092 
       33.01         9.99        31.00         0.99        43.00        30.97 
TCGA-A8-A093 TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M 
       17.95         9.99         1.02        45.07        29.98        33.07 
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 
       16.57        19.79         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-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN 
        0.36         0.33         0.33         0.33         0.33         0.33 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XW 
       12.33         0.30         0.33         0.33         0.33         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-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0JA TCGA-AO-A0JB 
       29.13        32.78        21.40        52.18        21.53        50.70 
TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A126 TCGA-AO-A129 
       72.00        76.77        62.04        71.80       108.72        96.10 
TCGA-AO-A12D TCGA-AO-A12G TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04J 
       64.04        41.62        70.39         0.53        24.79        26.93 
TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0TP 
      130.09         5.65        32.52         2.56        32.91       111.32 
TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 
        5.26        86.66        98.93        55.86        76.14       101.95 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ 
       83.87       114.02        85.97        75.55        61.84        52.77 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU 
       62.56        43.73        43.07        17.23        37.81        76.21 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24O TCGA-AR-A24P 
       62.14        20.22       109.58        73.02        84.20         0.85 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A254 
       76.01        53.36        85.35        79.00        56.15        72.76 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A5QM 
       58.92        93.83       128.65        62.86        40.04        54.74 
TCGA-B6-A0I9 TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ 
       12.13       129.57        65.72       146.50       112.37       176.98 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IQ TCGA-B6-A0RE 
       18.77       126.12        84.59       110.14       140.88       211.56 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0RV 
       68.45       189.01       234.28       100.70       131.21       157.41 
TCGA-B6-A0WS TCGA-B6-A0WV TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X7 TCGA-B6-A1KN 
       97.48        79.63       113.79       129.57        58.88       139.17 
TCGA-B6-A402 TCGA-B6-A408 TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0B2 
       54.28        49.94        38.79        25.55        46.95        40.83 
TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BF 
       48.36        56.94        51.68        37.22        32.02        25.71 
TCGA-BH-A0BM TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BW TCGA-BH-A0BZ 
       61.68        48.69        27.19        53.69        11.67        49.05 
TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL 
       44.02        45.83        31.17        22.13        13.91        48.23 
TCGA-BH-A0DP TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E2 TCGA-BH-A0E6 
       15.65        47.41        16.27         4.41        14.30         9.63 
TCGA-BH-A0E9 TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0H0 TCGA-BH-A0H7 TCGA-BH-A0HA 
       46.19        31.00        24.43        15.16        23.08        52.96 
TCGA-BH-A0HB TCGA-BH-A0HK TCGA-BH-A0HP TCGA-BH-A0HU TCGA-BH-A0W4 TCGA-BH-A0WA 
       26.50         5.85        13.61        12.89        24.95        23.05 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18L TCGA-BH-A18P 
        8.81         2.01         7.23        20.12        26.66        30.28 
TCGA-BH-A18Q TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN 
       55.63        66.05         7.36        51.39        51.16        69.93 
TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EY TCGA-BH-A1F6 
       91.99       113.82        42.28        12.00        17.69        97.48 
TCGA-BH-A1F8 TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
       24.66        33.17        74.73       122.89        36.92        63.35 
TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 
       45.63        72.07         6.90         0.72        38.60        57.83 
TCGA-BH-A209 TCGA-BH-A42T TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12O TCGA-C8-A12P 
      130.16         0.99        11.93        11.77        12.66        11.77 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 
        0.07        12.66         1.78         0.69         0.62         3.85 
TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL 
        3.75        10.92        11.34         0.16        12.03        10.42 
TCGA-C8-A1HM TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z 
        2.30         0.30         0.23         0.36         0.43         8.28 
TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-D8-A13Y TCGA-D8-A13Z 
        0.03        12.20         0.99         0.03        11.90        20.88 
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-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JK TCGA-D8-A1JM 
       15.78        18.15        18.90        12.03        20.12        19.40 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JT TCGA-D8-A1X5 TCGA-D8-A1X7 TCGA-D8-A1X9 
       20.38        21.01        13.32        18.58        16.73        23.90 
TCGA-D8-A1XA TCGA-D8-A1XF TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM 
       27.58        15.22        21.83        14.50        19.92        17.69 
TCGA-D8-A1XQ TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 
       16.41         6.35        12.99        16.54        15.32        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27M 
        3.81        14.24        14.14        13.45        13.05        13.48 
TCGA-D8-A27N TCGA-D8-A27R TCGA-D8-A27T TCGA-E2-A105 TCGA-E2-A10C TCGA-E2-A10F 
        4.80        10.09        13.08        43.00        40.11        28.87 
TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A14Y 
       38.24        38.60        33.17        34.26        31.96        28.60 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A158 
       17.03        25.41        27.12        23.24        21.04        14.79 
TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I 
       25.05        23.34        20.71        18.21        12.92        17.42 
TCGA-E2-A15M TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1IE TCGA-E2-A1IG 
        7.73        14.07        14.99        60.53        38.30        32.78 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A1L8 
       33.73        33.70        28.44        20.98        27.42        39.62 
TCGA-E2-A1LA TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 
       24.59        28.90        18.87        43.04        16.93         5.52 
TCGA-E2-A56Z TCGA-E2-A573 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N5 TCGA-E9-A1N6 
        7.20        34.92        19.00         9.21        36.82        13.48 
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-A1R4 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RE TCGA-E9-A1RF 
        6.12        21.21        32.09        20.81        34.65         6.58 
TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A228 TCGA-E9-A22A TCGA-E9-A22B 
       21.27        35.64        34.13        12.53        39.09        22.75 
TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A3HO 
       23.51         0.69        27.22         0.72        17.75        26.07 
TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP 
        0.62        15.72        12.33         0.26        13.81        14.40 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
       15.39        12.20        18.90        13.25        16.57        15.68 
TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OZ TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 
       28.77        25.94        40.41        52.96        29.82        23.11 
TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A2FR 
        7.86        18.90        13.94        10.52        14.43        55.00 
TCGA-EW-A2FV TCGA-EW-A3E8 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2DA TCGA-GM-A2DB 
       25.91        21.27         7.40       109.87       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-A3XL TCGA-JL-A3YW TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A9QF TCGA-LL-A5YM 
       69.30        11.84         6.67         4.08         8.75        15.32 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7T0 TCGA-LL-A8F5 
       14.70        14.47         4.50         4.50         3.22         6.21 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA 
        7.36        27.91        12.66        46.55        31.99        58.62 
TCGA-OL-A5RW TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66I TCGA-PL-A8LV TCGA-S3-A6ZF 
       36.36        22.32        20.38        23.47         0.23        16.50 
TCGA-S3-A6ZH TCGA-S3-AA10 TCGA-S3-AA17 TCGA-W8-A86G TCGA-XX-A89A TCGA-Z7-A8R6 
        8.65         7.92         3.91         5.29         9.14       105.04 

$`17P LOSS WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SG TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A2-A04N 
        0.39         8.52        14.27        13.68         7.96       104.81 
TCGA-A2-A04Q TCGA-A2-A04X TCGA-A2-A0CL TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CS 
       41.95        55.43        64.57        92.48        88.60        75.55 
TCGA-A2-A0CX TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EP TCGA-A2-A0ER 
       56.81        33.76        28.77       101.72       107.61        74.40 
TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0ST 
       37.05        35.05        34.29        31.82        29.75        99.19 
TCGA-A2-A0SU TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YD 
       54.64        17.52         8.38        17.46        18.90        25.28 
TCGA-A2-A0YF TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FX 
       15.42        14.50        18.61        31.73        23.77        36.79 
TCGA-A2-A1FZ TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25C TCGA-A2-A25E TCGA-A2-A25F 
       22.45        16.47        52.47        17.19        91.92        10.59 
TCGA-A2-A3KC TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XX TCGA-A2-A3XZ TCGA-A2-A4RY 
       20.88        33.93        29.98        38.40        31.99        21.30 
TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CH TCGA-A7-A0DB 
       23.21        21.14        38.30        35.31        35.47        33.11 
TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 
       10.72        23.61        20.61        11.34        10.59        10.29 
TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A5ZV TCGA-A7-A5ZW 
       11.28        13.41        14.70        11.97        12.10        10.72 
TCGA-A7-A6VV TCGA-A8-A06P TCGA-A8-A06T TCGA-A8-A06Y TCGA-A8-A07F TCGA-A8-A07J 
       10.29        13.02        53.06        26.01        18.97        12.00 
TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07Z TCGA-A8-A082 
        9.99        10.98         7.99        24.99        28.04        18.05 
TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08P 
        0.99        28.96        19.96        12.00        37.05        31.00 
TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A095 TCGA-A8-A097 
       33.01        93.04        40.01        33.01        41.98        12.00 
TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09Q TCGA-A8-A09T 
        9.99        12.00        50.04        49.05        25.02        19.04 
TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A6 TCGA-A8-A0A9 TCGA-AC-A23G 
       15.02         0.99        12.00        21.04        13.02        10.85 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM 
        2.66         1.48        55.43        36.99        38.79        26.04 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A3HN TCGA-AC-A3QP TCGA-AC-A3YI TCGA-AC-A3YJ 
       50.70         1.02         0.69        22.19        23.24        24.79 
TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO 
        1.55         0.07         1.18         0.69         0.43         1.68 
TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A049 
        1.74         1.12         1.32         0.33         0.33         0.62 
TCGA-AN-A04A TCGA-AN-A0AK TCGA-AN-A0AR TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FN 
        2.96         7.36         0.33         4.64         7.00         7.17 
TCGA-AN-A0FS TCGA-AN-A0XS TCGA-AN-A0XV TCGA-AO-A03L TCGA-AO-A03U TCGA-AO-A0J5 
        6.28         0.33         5.33        80.28        59.05        24.16 
TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JC TCGA-AO-A0JF 
       37.48        20.32        22.36        53.03        50.86        21.37 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A128 
       26.24        50.24        55.33       102.58        99.25       106.78 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12H TCGA-AO-A1KO 
       90.58        77.56        57.30        48.36        28.37        14.73 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KT TCGA-AQ-A1H2 TCGA-AQ-A7U7 TCGA-AR-A0TQ 
       82.62        61.87        17.79        15.62         9.99        49.32 
TCGA-AR-A0TS TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0U0 TCGA-AR-A1AK TCGA-AR-A1AL 
       74.79        29.75        64.83        65.36        51.25        48.82 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A24K TCGA-AR-A24M 
       43.56        39.98        61.28        63.62        50.89        96.89 
TCGA-AR-A24N TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A251 
       78.51       101.52        87.22        50.96        83.77        78.48 
TCGA-AR-A252 TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LN TCGA-AR-A2LO 
       73.18        20.25        42.87         7.36        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       40.54        20.38        16.04        20.45        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IP TCGA-B6-A0RL 
      143.38       149.59       220.90        50.70       110.93        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-A0WT TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
      188.68        17.98        21.47       129.70       186.48        28.27 
TCGA-B6-A0X5 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A401 
       68.94        43.59       101.52        73.51       170.17        85.35 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B3 
      103.63        55.00        24.53        20.45        28.50        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B7 TCGA-BH-A0BD TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL 
       39.16        56.98        18.21        24.85        21.70        44.05 
TCGA-BH-A0BO TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0C0 TCGA-BH-A0C3 
       35.67        53.95        45.57        49.94        41.75        48.13 
TCGA-BH-A0C7 TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DO TCGA-BH-A0DQ TCGA-BH-A0DS 
       42.90        23.44        38.01        17.26         3.22         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0E1 TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EB 
       38.47        45.17        15.68        44.81        32.65        24.49 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 
       30.35        10.78        37.78        35.51        24.56        41.00 
TCGA-BH-A0HI TCGA-BH-A0HO TCGA-BH-A0HQ TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY 
       20.38         2.50        36.85        51.32        27.25        50.79 
TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18K TCGA-BH-A18M 
        5.59        23.93        42.35        44.81        90.84        72.56 
TCGA-BH-A18N TCGA-BH-A18R TCGA-BH-A1ET TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F0 
       37.74        37.55        82.85        55.69        49.58        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FL TCGA-BH-A1FR 
       31.53        89.16       120.62       114.15        55.00       144.59 
TCGA-BH-A1FU TCGA-BH-A204 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42U 
       72.07        83.31        10.65         6.44        20.12       109.28 
TCGA-BH-A42V TCGA-C8-A12N TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 
        8.94        11.77        12.66        12.66        12.66         3.12 
TCGA-C8-A132 TCGA-C8-A1HE TCGA-C8-A1HI TCGA-C8-A1HN TCGA-C8-A273 TCGA-C8-A274 
        1.45        12.33        11.34         3.25         9.67         0.03 
TCGA-C8-A275 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-A1JB TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JL 
       18.71        12.03        14.01        18.97        20.09        20.09 
TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X6 TCGA-D8-A1X8 TCGA-D8-A1XB TCGA-D8-A1XC 
       12.20        14.70        17.79        25.74        18.15         2.66 
TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XV 
       17.16        14.73         7.96        15.85        16.31        15.16 
TCGA-D8-A1XW TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       12.66        17.42        16.04        14.43         9.44        16.41 
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-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-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14W 
       47.15        44.68        40.96        33.30        43.33        32.02 
TCGA-E2-A154 TCGA-E2-A156 TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15J 
       19.43        23.87        22.82        17.29        21.63        19.40 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A1B0 
        9.04        20.58        13.02        19.56        17.06        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-A1IF TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L6 
       37.41        22.65         3.88        22.19        11.08        54.18 
TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A3DX 
       19.66        40.47       106.75       102.61         8.75        15.72 
TCGA-E2-A570 TCGA-E2-A574 TCGA-E9-A1N4 TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NI 
       30.61        19.89        19.20        35.77        21.57         9.86 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1R6 
       11.90        14.30         0.62         2.10         1.38         2.76 
TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RH TCGA-E9-A227 TCGA-E9-A229 TCGA-E9-A22E 
       40.24         0.66        34.59         0.79        13.32        12.89 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A245 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A 
       24.10        17.06         0.85         1.94         0.95        24.56 
TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A54Y TCGA-E9-A5FK TCGA-EW-A1IX TCGA-EW-A1IY 
        0.76        18.41         0.23        14.70        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P1 
       18.21        22.82        29.95        29.85        41.13        39.78 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PG TCGA-EW-A1PH 
       18.48        30.08        19.99         6.15        34.55        19.96 
TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-GM-A2D9 
       52.73        22.09        17.49        10.16        10.59        59.57 
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-JL-A3YX 
       43.73        66.38        72.03        13.55        18.12        11.57 
TCGA-LD-A66U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y 
       21.24         4.60         9.53        11.44        10.95         7.59 
TCGA-LL-A5YL TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y 
       17.06        14.79        11.57         2.63         3.88         4.14 
TCGA-LL-A7SZ TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX 
        5.59         2.79         2.10        27.65        34.92        16.87 
TCGA-OL-A5RY TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       24.72        26.70        65.62        33.57        31.07        26.04 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PL-A8LX TCGA-PL-A8LY 
        7.23        14.07        28.21        19.73         0.16         0.26 
TCGA-PL-A8LZ TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 
        3.95         6.81        10.59         5.56         8.52         7.17 
TCGA-S3-AA15 TCGA-XX-A899 TCGA-Z7-A8R5 
        6.87         9.60       100.01 

  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 
            22.095             22.820 
[1] "0.0 - 234.3 (22.1)" "0.0 - 220.9 (22.8)"
[1] "hr=" "1.2"
D70V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17P LOSS MUTATED        42       36        2        3       179       134
  17P LOSS WILD-TYPE      41       44        7        2       163       100
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17P LOSS MUTATED           0         80         11         37       10
  17P LOSS WILD-TYPE         2         62         18         26        8
                    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                  42                 41
  STAGE IA                 36                 44
  STAGE IB                  2                  7
  STAGE II                  3                  2
  STAGE IIA               179                163
  STAGE IIB               134                100
  STAGE III                 0                  2
  STAGE IIIA               80                 62
  STAGE IIIB               11                 18
  STAGE IIIC               37                 26
  STAGE IV                 10                  8
  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   120 338  70  16
  17P LOSS WILD-TYPE 145 256  54  23
D70V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1              120                145
  T2              338                256
  T3               70                 54
  T4               16                 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
  17P LOSS MUTATED   258 173  63  41
  17P LOSS WILD-TYPE 223 166  50  33
D70V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0              258                223
  N1              173                166
  N2               63                 50
  N3               41                 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          2 462  11  71
  17P LOSS WILD-TYPE        3 392   8  76
D70V6, multiclass
          clus
vv         17P LOSS MUTATED 17P LOSS WILD-TYPE
  CM0 (I+)                2                  3
  M0                    462                392
  M1                     11                  8
  MX                     71                 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"
D70V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   542   4
  17P LOSS WILD-TYPE 472   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    542    4
  17P LOSS WILD-TYPE  472    7
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE              542                472
  MALE                  4                  7
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  17P LOSS MUTATED                            0                           420
  17P LOSS WILD-TYPE                          1                           334
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  17P LOSS MUTATED                               77                   5
  17P LOSS WILD-TYPE                             98                   1
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  17P LOSS MUTATED                                 18                  4
  17P LOSS WILD-TYPE                               11                 11
                    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                 420                334
  INFILTRATING LOBULAR CARCINOMA                 77                 98
  MEDULLARY CARCINOMA                             5                  1
  MIXED HISTOLOGY (PLEASE SPECIFY)               18                 11
  MUCINOUS CARCINOMA                              4                 11
  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   152 394
  17P LOSS WILD-TYPE 130 349
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    152  394
  17P LOSS WILD-TYPE  130  349
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO               152                130
  YES              394                349
[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                          88   372
  17P LOSS WILD-TYPE                        70   345
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                      88                 70
  WHITE                                         372                345
[1] 4 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    19 446
  17P LOSS WILD-TYPE  17 380
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     19  446
  17P LOSS WILD-TYPE   17  380
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                   19                 17
  NOT HISPANIC OR LATINO              446                380
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17Q LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED   221  30
  17Q LOSS WILD-TYPE 665  89
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
               251                754 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                30                 89 
$`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       136.73        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        32.75        34.98        38.37        24.39 
TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CG TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A13D 
       26.96        21.90        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        43.00 
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 
       38.01        12.00        43.00        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 
       16.57        19.79         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-A0FX TCGA-AN-A0FY TCGA-AN-A0XR TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AO-A03N 
        0.33         0.33         0.33         0.33         0.33        66.77 
TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0JD TCGA-AO-A0JL 
       29.13        32.78        21.40        52.18        72.00        55.33 
TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A0Y5 TCGA-AQ-A54N 
       96.10        64.04        70.39         0.53         5.65         2.56 
TCGA-AR-A0TP TCGA-AR-A0TY TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AI 
      111.32        55.86       101.95       114.02        75.55        61.84 
TCGA-AR-A1AJ TCGA-AR-A1AN TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AY TCGA-AR-A24U 
       52.77        43.73        43.07        17.23        20.22        53.36 
TCGA-AR-A250 TCGA-B6-A0IB TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IO TCGA-B6-A0IQ 
       56.15       129.57       112.37       176.98       110.14       140.88 
TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WY 
      211.56        68.45       189.01       100.70       131.21       113.79 
TCGA-B6-A1KN TCGA-B6-A408 TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0B5 
      139.17        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-A0HU TCGA-BH-A18F 
       31.00        23.08        26.50        13.61        12.89         8.81 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18V TCGA-BH-A1EN 
        2.01         7.23        30.28        55.63        51.16        69.93 
TCGA-BH-A1ES TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EY TCGA-BH-A1F6 TCGA-BH-A1FD 
      113.82        42.28        12.00        17.69        97.48        33.17 
TCGA-BH-A1FH TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A208 TCGA-C8-A12L TCGA-C8-A12M 
       36.92        45.63        72.07        57.83        11.93        11.77 
TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A131 TCGA-C8-A137 
       12.66        11.77         0.07        12.66         1.78         3.85 
TCGA-C8-A1HK TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A278 TCGA-C8-A27B 
       12.03         0.23         0.36         8.28         0.03         0.99 
TCGA-C8-A3M7 TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J8 
        0.03        11.90        20.88        13.48        19.20        14.17 
TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JC TCGA-D8-A1JK TCGA-D8-A1JM TCGA-D8-A1JN 
       17.49        16.50        15.78        20.12        19.40        20.38 
TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XQ TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XZ 
       21.83        14.50        16.41         6.35        12.99        15.32 
TCGA-D8-A27M TCGA-E2-A105 TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z 
       13.48        43.00        34.26        31.96        28.60        17.03 
TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15G 
       25.41        27.12        23.24        14.79        25.05        18.21 
TCGA-E2-A15M TCGA-E2-A1AZ TCGA-E2-A1II TCGA-E2-A1L7 TCGA-E2-A1LL TCGA-E2-A2P5 
        7.73        60.53        33.70        27.42        43.04        16.93 
TCGA-E2-A573 TCGA-E2-A576 TCGA-E9-A1N6 TCGA-E9-A1RA TCGA-E9-A1RF TCGA-E9-A1RG 
       34.92        19.00        13.48        32.09         6.58        21.27 
TCGA-E9-A244 TCGA-E9-A295 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A5FL TCGA-EW-A1J6 
        0.69         0.72         0.62        15.72         0.26        28.77 
TCGA-EW-A1OV TCGA-EW-A1OZ TCGA-EW-A1P4 TCGA-EW-A1P8 TCGA-EW-A2FV TCGA-GI-A2C8 
       25.94        40.41        29.82         7.86        25.91         7.40 
TCGA-GI-A2C9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DI TCGA-JL-A3YW 
      109.87       194.27        53.13        43.04        61.91        11.84 
TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A9QF TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A73Z 
        6.67         4.08         8.75        14.70        14.47         4.50 
TCGA-OL-A5D7 TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-OL-A66I TCGA-XX-A89A 
       46.55        36.36        20.38        23.47         9.14 

$`17Q LOSS WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        0.39         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SQ TCGA-A2-A04N 
       47.24        20.88        13.68         7.96        18.21       104.81 
TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
       41.95        82.16        63.12        64.04        55.43        36.13 
TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CS TCGA-A2-A0CU 
       64.57       112.08        92.48        88.60        75.55         5.19 
TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM 
       64.04        56.81        33.76        28.77        25.22       101.72 
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-A0SY TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0T3 
       54.64        27.12        44.28        17.52         8.38        18.71 
TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YD TCGA-A2-A0YF 
       20.52        17.46        18.90        20.75        25.28        15.42 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YL TCGA-A2-A0YM 
       21.90        21.67        14.50        18.61        48.46        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-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
       16.47        52.47        17.19        18.15        91.92        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XW TCGA-A2-A3XX 
       20.88        39.65        33.93        29.98        49.48        38.40 
TCGA-A2-A3XZ TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A7-A0CD 
       31.99         7.30        21.30        23.21        21.14        38.30 
TCGA-A7-A0CE TCGA-A7-A0CH TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13E TCGA-A7-A13F 
       35.31        35.47        35.67        33.11        10.72        12.72 
TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY 
       23.61        29.56        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-A4SF TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A8-A06O 
       14.93        17.92        12.10        10.72        11.05        13.02 
TCGA-A8-A06P TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 
       13.02        53.06        29.03        26.01         1.02        17.03 
TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07J TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S 
       18.97        18.97        12.00         9.99        10.98         7.99 
TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A08A 
       24.99         9.99        28.04        18.05        36.95         0.99 
TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O 
       28.96        33.01        19.96        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        33.01        93.04        40.01        33.01 
TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B 
       30.97        41.98        12.00         9.99         9.99        12.00 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09Q 
        1.02        50.04        49.05        45.07        33.07        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-A0A9 TCGA-A8-A0AD TCGA-AC-A23C 
       19.04        13.02        21.04        13.02        38.04         0.95 
TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2FB TCGA-AC-A2FF 
        2.37        10.85         2.66         1.48        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-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3YI TCGA-AC-A3YJ 
        0.69        14.83        22.19         1.12        23.24        24.79 
TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX 
        1.55         0.07         1.12         1.18         0.69         0.43 
TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y 
        1.68         1.74         1.12         1.32         0.33         0.33 
TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK 
        0.23         0.62         2.96         1.71         8.02         7.36 
TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK 
        0.16         0.33         0.33         6.44         4.64         7.00 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO 
        7.17         6.28         0.33         0.33         0.33        12.33 
TCGA-AN-A0XP TCGA-AN-A0XS TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M 
        0.30         0.33         5.33         5.59        80.28        47.84 
TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A0J5 
       81.63        84.69        68.75        47.87        59.05        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-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ 
       50.86        76.77        21.37        26.24        50.24        62.04 
TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A 
       71.80       102.58        99.25       108.72       106.78        90.58 
TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
       77.56        57.30        48.36        41.62        28.37        14.73 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       82.62        61.87        17.79        24.79        26.93       130.09 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TQ TCGA-AR-A0TR 
       15.62        32.52        32.91         9.99        49.32         5.26 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TZ 
       74.79        86.66        29.75        98.93        64.83        76.14 
TCGA-AR-A0U0 TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM 
       65.36        83.87        85.97        51.25        48.82        62.56 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       43.56        39.98        37.81        76.21        61.28        63.62 
TCGA-AR-A1AX TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       62.14       109.58        50.89        73.02        96.89        78.51 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24V 
       84.20         0.85       101.52        87.22        76.01        85.35 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 
       50.96        83.77        79.00        78.48        73.18        72.76 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK 
       58.92        93.83       128.65        20.25        62.86        42.87 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
        7.36        40.04        38.17        39.39        40.54        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-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-A0RI TCGA-B6-A0RL 
       18.77       126.12        84.59       110.93       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-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-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-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B2 
      103.63        55.00        24.53        20.45        28.50        40.83 
TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B7 TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG 
       39.55        39.16        56.98        18.21        25.71        24.85 
TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BS 
       21.70        44.05        61.68        35.67        27.19        53.95 
TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 
       45.57        49.94        49.05        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-A0E1 TCGA-BH-A0E7 TCGA-BH-A0EA 
       45.17        47.41        16.27        15.68        44.81        32.65 
TCGA-BH-A0EB TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       24.49        24.43        30.35        10.78        15.16        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HI TCGA-BH-A0HK 
       35.51        24.56        41.00        52.96        20.38         5.85 
TCGA-BH-A0HO TCGA-BH-A0HQ TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX 
        2.50        36.85        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-A18J 
       23.93        24.95        42.35        44.81        23.05        20.12 
TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18R TCGA-BH-A18S 
       90.84        26.66        72.56        37.74        37.55        66.05 
TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1EW TCGA-BH-A1EX 
        7.36        51.39        91.99        82.85        55.69        49.58 
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-A1FE TCGA-BH-A1FG TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FR TCGA-BH-A1FU 
       74.73       122.89        63.35        55.00       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-A12N 
        6.44        20.12         0.99       109.28         8.94        11.77 
TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A132 TCGA-C8-A134 
       12.66        12.66        12.66         3.12         1.45         0.69 
TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI 
        0.62         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-A26Y 
        0.16        10.42         2.30         3.25         0.30         0.43 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A3M8 TCGA-D8-A140 
        9.67         0.03         0.03        12.20         0.23        13.25 
TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A146 TCGA-D8-A1JB TCGA-D8-A1JD 
       20.58        13.97        14.17        21.14        18.71        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-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 
       20.09        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-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-A1XV TCGA-D8-A1XW TCGA-D8-A1XY 
        7.96        15.85        16.31        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-A27N 
       13.45        13.05        14.43         9.44        16.41         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-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A 
       18.51         7.33        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-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15A TCGA-E2-A15C 
       32.02        19.43        21.04        23.87        23.34        22.82 
TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J 
       17.29        20.71        21.63        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-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-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-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-A2P6 TCGA-E2-A3DX 
       18.87       106.75       102.61         8.75         5.52        15.72 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1N5 
        7.20        30.61        19.89         9.21        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-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RB 
        2.10         6.12         1.38         2.76        21.21        20.81 
TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 
       40.24         0.66        34.65        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-A245 TCGA-E9-A247 TCGA-E9-A248 
       23.51        24.10        17.06         0.85        27.22         1.94 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 
        0.95        24.56        17.75         0.76        26.07        18.41 
TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE 
       12.33         0.23        14.70        13.81        14.40        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-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1P0 
       16.57        15.68        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-A1PA 
       39.78        52.96        23.11        18.48        30.08        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-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-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        43.73        69.30        66.38        72.03        13.55 
TCGA-GM-A5PX TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 
       18.12        11.57        21.24         4.60         9.53        11.44 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YP TCGA-LL-A6FP 
       10.95         7.59        17.06        15.32        14.79        11.57 
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-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
        6.21         7.36        27.91         2.79         2.10        12.66 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY 
       31.99        58.62        27.65        34.92        16.87        24.72 
TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       22.32        26.70        65.62        33.57        31.07        26.04 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PL-A8LV TCGA-PL-A8LX 
        7.23        14.07        28.21        19.73         0.23         0.16 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z 
        0.26         3.95        16.50         6.81         8.65        10.59 
TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 
        7.92         5.56         8.52         7.17         6.87         3.91 
TCGA-W8-A86G TCGA-XX-A899 TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        5.29         9.60       100.01       105.04 

  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 
             21.83              22.70 
[1] "0.0 - 211.6 (21.8)" "0.0 - 234.3 (22.7)"
[1] "hr=" "1"  
D71V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17Q LOSS MUTATED        19       20        1        0        89        57
  17Q LOSS WILD-TYPE      64       60        8        5       253       177
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17Q LOSS MUTATED           0         39          6         16        5
  17Q LOSS WILD-TYPE         2        103         23         47       13
                    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                  19                 64
  STAGE IA                 20                 60
  STAGE IB                  1                  8
  STAGE II                  0                  5
  STAGE IIA                89                253
  STAGE IIB                57                177
  STAGE III                 0                  2
  STAGE IIIA               39                103
  STAGE IIIB                6                 23
  STAGE IIIC               16                 47
  STAGE IV                  5                 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
  17Q LOSS MUTATED    59 154  34  10
  17Q LOSS WILD-TYPE 206 440  90  29
D71V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1               59                206
  T2              154                440
  T3               34                 90
  T4               10                 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
  17Q LOSS MUTATED   131  72  33  19
  17Q LOSS WILD-TYPE 350 267  80  55
D71V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0              131                350
  N1               72                267
  N2               33                 80
  N3               19                 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
  17Q LOSS MUTATED          1 225   5  27
  17Q LOSS WILD-TYPE        4 629  14 120
D71V6, multiclass
          clus
vv         17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CM0 (I+)                1                  4
  M0                    225                629
  M1                      5                 14
  MX                     27                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"
D71V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED   258   0
  17Q LOSS WILD-TYPE 756  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED    258    0
  17Q LOSS WILD-TYPE  756   11
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE              258                756
  MALE                  0                 11
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  17Q LOSS MUTATED                            0                           211
  17Q LOSS WILD-TYPE                          1                           543
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  17Q LOSS MUTATED                               29                   3
  17Q LOSS WILD-TYPE                            146                   3
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  17Q LOSS MUTATED                                  4                  0
  17Q LOSS WILD-TYPE                               25                 15
                    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                 211                543
  INFILTRATING LOBULAR CARCINOMA                 29                146
  MEDULLARY CARCINOMA                             3                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)                4                 25
  MUCINOUS CARCINOMA                              0                 15
  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    74 184
  17Q LOSS WILD-TYPE 208 559
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     74  184
  17Q LOSS WILD-TYPE  208  559
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                74                208
  YES              184                559
[1] 2 2
[1] FALSE
D71V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q LOSS MUTATED                                  1    20
  17Q LOSS WILD-TYPE                                0    36
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED                          49   164
  17Q LOSS WILD-TYPE                       109   553
D71V11, multiclass
                                  clus
vv                                 17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                          20                 36
  BLACK OR AFRICAN AMERICAN                      49                109
  WHITE                                         164                553
[1] 4 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     9 205
  17Q LOSS WILD-TYPE  27 621
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      9  205
  17Q LOSS WILD-TYPE   27  621
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    9                 27
  NOT HISPANIC OR LATINO              205                621
[1] 2 2
[1] FALSE

Clustering(72) Variable = 18P LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED   244  52
  18P LOSS WILD-TYPE 642  67
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               296                709 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                52                 67 
$`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        48.46        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        26.96        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        38.01        37.05         9.99        30.97 
TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q 
       12.00        50.04        49.05        33.07         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        16.57        19.79         0.07         1.74 
TCGA-AC-A8OQ TCGA-AN-A03X TCGA-AN-A04A TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL 
        1.12         0.33         2.96         8.02         7.36         6.51 
TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XP 
        0.16         0.33         0.33         0.36         0.33         0.30 
TCGA-AN-A0XU TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A0J4 
        0.33        80.28        47.84        66.77        81.63        52.18 
TCGA-AO-A0J5 TCGA-AO-A0J7 TCGA-AO-A0JA TCGA-AO-A0JG TCGA-AO-A129 TCGA-AO-A12E 
       24.16        20.32        21.53        26.24        96.10        57.30 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A54O 
       24.79        26.93       130.09         5.65        15.62        32.91 
TCGA-AR-A0TT TCGA-AR-A0TX TCGA-AR-A0U2 TCGA-AR-A1AI TCGA-AR-A1AP TCGA-AR-A1AV 
       86.66        64.83        83.87        61.84        39.98        61.28 
TCGA-AR-A1AW TCGA-AR-A24H TCGA-AR-A24R TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A252 
       63.62       109.58        87.22        85.35        50.96        73.18 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QQ TCGA-B6-A0IJ 
       58.92        93.83        54.74        16.04        10.59       176.98 
TCGA-B6-A0IK TCGA-B6-A0IO TCGA-B6-A0RH TCGA-B6-A0RL TCGA-B6-A0RP TCGA-B6-A0RS 
       18.77       110.14       189.01        81.17       102.77       100.70 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WY TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A402 
       79.63        17.98       113.79        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        34.92 
TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1NA TCGA-E9-A1ND TCGA-E9-A1NG 
       19.89         9.21        19.20        36.56        12.59        21.57 
TCGA-E9-A1R6 TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A22E TCGA-E9-A248 
        2.76         6.58        21.27        35.64        12.89         1.94 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A54Y TCGA-E9-A5FL TCGA-EW-A1IW TCGA-EW-A1J1 
        0.72        17.75         0.23         0.26        12.20        18.90 
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-LD-A7W5 TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YM 
       11.84         6.67         4.08         8.75        11.44        15.32 
TCGA-LL-A6FP TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OL-A5D6 TCGA-OL-A5S0 
       11.57         3.22         7.36        27.91        12.66        20.38 
TCGA-OL-A66N TCGA-OL-A6VQ TCGA-PL-A8LV TCGA-PL-A8LX TCGA-S3-A6ZF TCGA-S3-A6ZH 
       26.04        19.73         0.23         0.16        16.50         8.65 
TCGA-S3-AA10 TCGA-XX-A89A 
        7.92         9.14 

$`18P LOSS WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        0.39         8.52        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-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 
      136.73        64.57        24.79       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-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ 
       33.76        28.77       101.72        80.28       107.61        79.76 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST 
       74.40        37.05        35.05        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-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD 
        8.38        18.71        17.46        18.90        32.55        25.28 
TCGA-A2-A0YF TCGA-A2-A0YH TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FZ 
       15.42        21.67        18.61        31.73        23.47        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-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        32.75 
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 
       24.39        21.30        23.21        21.14        21.90        38.30 
TCGA-A7-A0CE TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB 
       35.31        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-A26G 
       31.73        10.72        23.61        29.56        31.36        23.74 
TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 
       23.80        21.73        20.61        11.34        10.59        10.29 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A5ZV 
       13.41        14.70        11.97        14.50        21.17        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-A06T TCGA-A8-A06X TCGA-A8-A06Z TCGA-A8-A075 
       13.02         1.02        53.06        31.00         1.02        17.03 
TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07J 
        9.01        43.00        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        24.99        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        28.96        33.01 
TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S 
       19.96        12.00        31.00        31.00         0.99        33.01 
TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 
       93.04        43.00        40.01        33.01        17.95        41.98 
TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09I TCGA-A8-A09K 
       12.00         9.99         9.99         1.02        45.07        29.98 
TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A4 
        8.98        19.04        15.02         0.99        12.00        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-A2FG TCGA-AC-A2FK TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3HN TCGA-AC-A3OD 
       36.99        38.79         1.02         0.92         0.69        14.83 
TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62X 
       22.19         1.12        23.24        24.79         1.55         1.12 
TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OR 
        1.81         1.18         0.69         0.43         1.68         1.32 
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-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-A0FX TCGA-AN-A0FY 
        7.59         7.17         6.28         6.02         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT 
        0.33         0.33        12.33         0.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U 
        5.33         5.59        84.69        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-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        50.24 
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       108.72 
TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A12G 
      106.78        90.58        77.56        64.04        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-A1H3 TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ 
       17.79        32.52         2.56         9.99       111.32        49.32 
TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0TZ 
        5.26        74.79        29.75        98.93        55.86        76.14 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AJ 
       65.36       101.95       114.02        85.97        75.55        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-A1AU TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K 
       17.23        37.81        76.21        62.14        20.22        50.89 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q 
       73.02        96.89        78.51        84.20         0.85       101.52 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 
       76.01        53.36        83.77        79.00        56.15        78.48 
TCGA-AR-A254 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL 
       72.76       128.65        20.25        62.86        42.87         7.36 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QP 
       40.04        38.17        39.39        40.54        20.38        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-A0IM TCGA-B6-A0IN 
       50.70        65.72       146.50       112.37       126.12        84.59 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RI TCGA-B6-A0RM 
      110.93       140.88       211.56        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-A1KF TCGA-B6-A2IU 
       28.27        68.94        58.88        43.59       101.52       170.17 
TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW 
       85.35        49.94       103.63        55.00        24.53        20.45 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 
       28.50        46.95        40.83        39.16        48.36        56.98 
TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL 
       51.68        32.02        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-A0BV 
       61.68        35.67        27.19        53.69        53.95        49.94 
TCGA-BH-A0BW TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG 
       11.67        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-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-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE 
       14.30        44.81        46.19        32.65        24.49        31.00 
TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H9 
       24.43        10.78        15.16        37.78        35.51        41.00 
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-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA 
       51.32         5.59        24.95        42.35        44.81        23.05 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P 
        2.01         7.23        20.12        72.56        37.74        30.28 
TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A1ES TCGA-BH-A1ET 
       55.63        37.55        66.05         7.36       113.82        82.85 
TCGA-BH-A1EX TCGA-BH-A1F5 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FG 
       49.58        89.16       120.62       114.15        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-A202 TCGA-BH-A208 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T 
        0.72        57.83        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-A12U 
      109.28         8.94        11.93        11.77        11.77        12.66 
TCGA-C8-A12V 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-A26V TCGA-C8-A26W TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A27B 
       10.42         0.30         0.23         0.03        12.20         0.99 
TCGA-C8-A3M8 TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A145 
        0.23        20.88        13.25        20.58        14.17        13.48 
TCGA-D8-A147 TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JF TCGA-D8-A1JK TCGA-D8-A1JL 
       19.20        18.71        15.78        12.03        20.12        20.09 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X6 TCGA-D8-A1X7 
       21.01        12.20        13.32        14.70        17.79        16.73 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF 
       25.74        23.90        18.15         2.66        17.16        15.22 
TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XS 
       14.73        14.50        17.69         7.96        16.41        16.31 
TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 
        6.35        15.16        12.66        15.32        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-A27T TCGA-D8-A27V 
        9.44        16.41         4.80         0.76        13.08        12.53 
TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A10A 
       12.26        14.50         7.33        43.00        27.52        40.41 
TCGA-E2-A10B TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14S TCGA-E2-A14T 
       37.51        28.87        47.15        40.96        33.17        33.30 
TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A153 
       43.33        32.02        31.96        28.60        25.41        23.24 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F 
       21.04        23.87        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-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-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       37.41        32.78        33.70        28.44        22.65         3.88 
TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 
       22.19        11.08        54.18        27.42        39.62        19.66 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A2P5 
       24.59        40.47        18.87       106.75       102.61        16.93 
TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A576 TCGA-E9-A1N5 TCGA-E9-A1N6 
       15.72         7.20        30.61        19.00        36.82        13.48 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NI 
       12.00        13.12        39.55        35.77        20.05         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-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-A1RH TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       34.59        34.13         0.79        12.53        13.32        39.09 
TCGA-E9-A22B TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A245 
       22.75        23.51        24.10        17.06         0.69         0.85 
TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 
       27.22         0.95        24.56         0.76        26.07        18.41 
TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A5UP 
        0.62        15.72        12.33        14.70        13.81        14.40 
TCGA-E9-A6HE TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1J3 
       15.39        39.72         8.48        18.21        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1P0 
       15.68        28.77        22.82        29.95        40.41        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-GI-A2C9 TCGA-GM-A2D9 
       22.09        21.27        17.49        10.59       109.87        59.57 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DI 
      194.27        53.13        53.52        43.04        42.71        61.91 
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-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX 
       43.73        69.30        66.38        72.03        13.55        18.12 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y 
       11.57        21.24         4.60         9.53        10.95         7.59 
TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A6FR 
       17.06        14.70        14.47        14.79         2.63         3.88 
TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-MS-A51U 
        4.14         4.50         4.50         5.59         6.21         2.79 
TCGA-OK-A5Q2 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
        2.10        46.55        31.99        58.62        27.65        34.92 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I 
       36.36        16.87        24.72        22.32        26.70        23.47 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO 
       65.62        33.57        31.07         7.23        14.07        28.21 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA12 
        0.26         3.95         6.81        10.59         5.56         8.52 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-W8-A86G TCGA-XX-A899 TCGA-Z7-A8R5 
        7.17         6.87         3.91         5.29         9.60       100.01 
TCGA-Z7-A8R6 
      105.04 

  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 
             20.38              23.51 
[1] "0.0 - 189.0 (20.4)" "0.0 - 234.3 (23.5)"
[1] "hr=" "2.4"
D72V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18P LOSS MUTATED        23       23        0        0        96        66
  18P LOSS WILD-TYPE      60       57        9        5       246       168
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18P LOSS MUTATED           0         47         16         25        5
  18P LOSS WILD-TYPE         2         95         13         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                  23                 60
  STAGE IA                 23                 57
  STAGE IB                  0                  9
  STAGE II                  0                  5
  STAGE IIA                96                246
  STAGE IIB                66                168
  STAGE III                 0                  2
  STAGE IIIA               47                 95
  STAGE IIIB               16                 13
  STAGE IIIC               25                 38
  STAGE IV                  5                 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    66 180  37  21
  18P LOSS WILD-TYPE 199 414  87  18
D72V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1               66                199
  T2              180                414
  T3               37                 87
  T4               21                 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
  18P LOSS MUTATED   134  98  39  26
  18P LOSS WILD-TYPE 347 241  74  48
D72V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0              134                347
  N1               98                241
  N2               39                 74
  N3               26                 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          0 255   5  44
  18P LOSS WILD-TYPE        5 599  14 103
D72V6, multiclass
          clus
vv         18P LOSS MUTATED 18P LOSS WILD-TYPE
  CM0 (I+)                0                  5
  M0                    255                599
  M1                      5                 14
  MX                     44                103
[1] 4 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   301   3
  18P LOSS WILD-TYPE 713   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    301    3
  18P LOSS WILD-TYPE  713    8
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE              301                713
  MALE                  3                  8
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  18P LOSS MUTATED                            0                           242
  18P LOSS WILD-TYPE                          1                           512
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  18P LOSS MUTATED                               41                   3
  18P LOSS WILD-TYPE                            134                   3
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  18P LOSS MUTATED                                  6                  0
  18P LOSS WILD-TYPE                               23                 15
                    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                 242                512
  INFILTRATING LOBULAR CARCINOMA                 41                134
  MEDULLARY CARCINOMA                             3                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)                6                 23
  MUCINOUS CARCINOMA                              0                 15
  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    84 220
  18P LOSS WILD-TYPE 198 523
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     84  220
  18P LOSS WILD-TYPE  198  523
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                84                198
  YES              220                523
[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                          46   204
  18P LOSS WILD-TYPE                       112   513
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                      46                112
  WHITE                                         204                513
[1] 4 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    11 248
  18P LOSS WILD-TYPE  25 578
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     11  248
  18P LOSS WILD-TYPE   25  578
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                   11                 25
  NOT HISPANIC OR LATINO              248                578
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18Q LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED   251  44
  18Q LOSS WILD-TYPE 635  75
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               295                710 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                44                 75 
$`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        48.46        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 
       26.96        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        38.01        37.05        31.00         0.99        30.97 
TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09M TCGA-A8-A09N 
        9.99        12.00        50.04        49.05        33.07         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        16.57        19.79         0.07 
TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AN-A03X TCGA-AN-A04A TCGA-AN-A0AK 
        0.43         1.74         1.12         0.33         2.96         7.36 
TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0FL TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FZ 
        6.51         0.16         7.59         0.33         0.36         0.33 
TCGA-AN-A0XP TCGA-AN-A0XU TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A0J2 TCGA-AO-A0J4 
        0.30         0.33        80.28        66.77        32.78        52.18 
TCGA-AO-A0J7 TCGA-AO-A0JA TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A1KT 
       20.32        21.53        96.10        64.04        57.30        17.79 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A54O 
       24.79        26.93       130.09         5.65        15.62        32.91 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A1AP 
       74.79        86.66        98.93       101.95        83.87        39.98 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A24H TCGA-AR-A24R TCGA-AR-A24V TCGA-AR-A24W 
       61.28        63.62       109.58        87.22        85.35        50.96 
TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A2LR TCGA-AR-A5QM 
       56.15        78.48        73.18        58.92        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-A18F 
       52.96        20.38        12.89        27.25        23.93         8.81 
TCGA-BH-A18K TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1EU 
       90.84        51.39        51.16        69.93        91.99        42.28 
TCGA-BH-A1EV TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1F8 
       12.00        17.69        25.81        31.53        97.48        24.66 
TCGA-BH-A1FM TCGA-BH-A201 TCGA-BH-A204 TCGA-BH-A209 TCGA-C8-A12P TCGA-C8-A12Q 
       45.63         6.90        83.31       130.16        11.77         0.07 
TCGA-C8-A12W TCGA-C8-A132 TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HI 
       12.66         1.45         0.62         3.75        12.33        11.34 
TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z 
        0.16        12.03         2.30         0.36         0.43         8.28 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A3M7 TCGA-D8-A13Z 
        9.67         0.03         0.03         0.03         0.03        20.88 
TCGA-D8-A142 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JC 
       13.97        21.14        14.17        17.49        16.50        15.78 
TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JN 
       18.90        12.03        14.01        18.97        20.09        20.38 
TCGA-D8-A1X5 TCGA-D8-A1XA TCGA-D8-A1XJ TCGA-D8-A1XL TCGA-D8-A1XR TCGA-D8-A1XU 
       18.58        27.58        21.83        19.92        15.85        12.99 
TCGA-D8-A1XY TCGA-D8-A1Y3 TCGA-D8-A27M TCGA-D8-A27R TCGA-D8-A3Z6 TCGA-E2-A107 
       16.54        14.14        13.48        10.09        18.51        34.42 
TCGA-E2-A109 TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A14O TCGA-E2-A14Z TCGA-E2-A150 
       46.59        40.11        28.44        44.68        17.03        25.41 
TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15E TCGA-E2-A15M 
       27.12        19.43        25.05        23.34        20.71         7.73 
TCGA-E2-A1AZ TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1IO TCGA-E2-A1LE TCGA-E2-A1LK 
       60.53        17.10        33.73        20.98        28.90         8.75 
TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N4 
       43.04         5.52        34.92        19.89         9.21        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-A1OV TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P3 
       12.20        18.90        25.94        29.85        40.41        52.96 
TCGA-EW-A1P8 TCGA-EW-A1PC TCGA-EW-A1PF TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A423 
        7.86         6.15        14.43        55.00        25.91        10.16 
TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2DH TCGA-GM-A2DL TCGA-JL-A3YW TCGA-LD-A74U 
        7.40       109.87        42.28        90.84        11.84         6.67 
TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A6FP 
        8.75        11.44        17.06        15.32        14.47        11.57 
TCGA-LL-A6FR TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OL-A5D6 TCGA-OL-A5S0 TCGA-OL-A66N 
        3.88         7.36        27.91        12.66        20.38        26.04 
TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PL-A8LV TCGA-PL-A8LX TCGA-S3-A6ZF TCGA-S3-A6ZH 
       28.21        19.73         0.23         0.16        16.50         8.65 
TCGA-XX-A89A 
        9.14 

$`18Q LOSS WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        0.39         8.52        43.43        48.10        14.27        47.24 
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-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-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
       36.13       136.73        64.57        24.79       112.08        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CX 
       88.60       107.93        75.55        75.25        63.45        56.81 
TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EO 
       34.55        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-A0EW 
      107.61        79.76        74.40        37.05        35.05        29.75 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SY 
       24.72        24.16        99.19        54.64        44.88        44.28 
TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.52        17.13         8.38        18.71        17.46        18.90 
TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YH TCGA-A2-A0YJ TCGA-A2-A0YM 
       32.55        25.28        15.42        21.67        18.61        31.73 
TCGA-A2-A1FV TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       23.47        22.45        20.25        19.56        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS 
      107.70        91.92        10.59        20.88        39.65        33.93 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 
       32.75        49.48        38.40        34.98        31.99        38.37 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 
        7.30        24.39        21.30        23.21        21.14        21.90 
TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DB 
       38.30        35.31        35.47        30.61        37.45        33.11 
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-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VW 
       14.70        11.97        14.50        10.72        11.05         9.37 
TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06T TCGA-A8-A06X 
        8.75        13.02        13.02         1.02        53.06        31.00 
TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07J 
        9.01        43.00        19.99        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        24.99 
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        28.96 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08S 
       33.01        19.96        12.00         9.99        31.00        33.01 
TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 
       93.04        43.00        40.01        33.01        17.95        41.98 
TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09C TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09R 
       12.00         9.99         1.02        45.07        29.98         8.98 
TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A0A1 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 
       19.04        15.02        12.00        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-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FG TCGA-AC-A2FK 
        1.48        38.53        38.20        40.57        36.99        38.79 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
       50.70         1.02         0.92         0.69        14.83        22.19 
TCGA-AC-A3TN TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62X TCGA-AC-A62Y 
        1.12        23.24        24.79         1.55         1.12         1.81 
TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6NO TCGA-AC-A8OR TCGA-AN-A03Y TCGA-AN-A041 
        1.18         0.69         1.68         1.32         0.33         0.23 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AR 
        0.33         0.62         1.78         1.71         8.02         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-A0FX TCGA-AN-A0FY TCGA-AN-A0XL 
        7.17         6.28         6.02         0.33         0.33         0.33 
TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XV 
        0.33        12.33         0.33         0.33         0.33         5.33 
TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T 
        5.59        47.84        81.63        84.69        68.75        47.87 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 
       59.05        29.13        21.40        24.16        37.48        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF 
       53.03        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        50.24        62.04        55.33        71.80       102.58 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12F 
       99.25       108.72       106.78        90.58        77.56        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-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ 
        0.53        32.52         2.56         9.99       111.32        49.32 
TCGA-AR-A0TR TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 
        5.26        29.75        64.83        55.86        76.14        65.36 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK 
      114.02        85.97        75.55        61.84        52.77        51.25 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AQ TCGA-AR-A1AR 
       48.82        62.56        43.73        43.56        43.07        17.23 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L 
       37.81        76.21        62.14        20.22        50.89        73.02 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24T 
       96.89        78.51        84.20         0.85       101.52        76.01 
TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LE 
       53.36        83.77        79.00        72.76        93.83       128.65 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN 
       20.25        62.86        42.87         7.36        40.04        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0I1 TCGA-B6-A0I2 
       39.39        40.54        16.04        20.45        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-A0IM TCGA-B6-A0IN TCGA-B6-A0IP 
      146.50       112.37       176.98       126.12        84.59       110.93 
TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
      140.88        68.45       234.28        78.02       172.96       162.05 
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-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
       21.47       129.57       129.70       186.48        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KN TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40B 
       58.88        43.59       139.17        85.35        49.94       103.63 
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-A0B7 TCGA-BH-A0B9 
       40.83        39.55        39.16        48.36        56.98        51.68 
TCGA-BH-A0BC TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO 
       32.02        25.71        21.70        44.05        61.68        35.67 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0C0 TCGA-BH-A0C1 
       27.19        53.69        53.95        49.94        41.75        44.02 
TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DK 
       48.13        45.83        31.17        23.44        22.13        13.91 
TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       48.23        17.26        15.65         2.56        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-A0EE TCGA-BH-A0EI 
       44.81        46.19        32.65        24.49        31.00        24.43 
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-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HW TCGA-BH-A0HY 
        5.85         2.50        13.61        36.85        51.32        50.79 
TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18G 
        5.59        24.95        42.35        44.81        23.05         2.01 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P 
        7.23        20.12        26.66        72.56        37.74        30.28 
TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A1ES TCGA-BH-A1ET 
       55.63        37.55        66.05         7.36       113.82        82.85 
TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F5 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD 
       55.69        49.58        89.16       120.62       114.15        33.17 
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-A203 TCGA-BH-A208 TCGA-BH-A28O 
      144.59        72.07         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-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12X 
       11.77        11.77        12.66        12.66        12.66        12.66 
TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A1HF TCGA-C8-A1HG 
        3.12         1.78         0.69         3.85        10.92        11.34 
TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A27A TCGA-C8-A27B 
       10.42         3.25         0.30         0.23        12.20         0.99 
TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A145 
        0.23        11.90        13.25        20.58        14.17        13.48 
TCGA-D8-A147 TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JF TCGA-D8-A1JK TCGA-D8-A1JL 
       19.20        18.71        18.15        12.03        20.12        20.09 
TCGA-D8-A1JM TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X6 
       19.40        21.01        12.20        13.32        14.70        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-A1XK TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ 
       15.22        14.73        14.50        17.69         7.96        16.41 
TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y0 
       16.31         6.35        15.16        12.66        15.32        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H 
        3.81        14.24        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-A27T 
       14.43         9.44        16.41         4.80         0.76        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-A10A TCGA-E2-A10B TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q 
       40.41        37.51        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-A153 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 
       31.96        28.60        23.24        21.04        23.87        14.79 
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-A15O TCGA-E2-A15P TCGA-E2-A15R 
       19.40         9.04        20.58        13.02        19.56        17.06 
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-A1II 
       28.50        16.47        38.30        37.41        32.78        33.70 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L6 
       28.44        22.65         3.88        22.19        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-A2P5 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
      106.75       102.61        16.93        15.72         7.20        30.61 
TCGA-E2-A576 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NC 
       19.00        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 
       24.56         0.76        26.07        18.41         0.62        15.72 
TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IX 
       12.33        14.70        13.81        14.40        15.39        39.72 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 
        8.48        18.21        13.25        16.57        15.68        28.77 
TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P5 
       22.82        29.95        41.13        39.78        29.82        23.11 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE 
       18.48        30.08        18.90        19.99        13.94        10.52 
TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 
       34.55        19.96        52.73        22.09        21.27        17.49 
TCGA-EW-A424 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD 
       10.59        59.57       194.27        53.13        53.52        43.04 
TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO 
       42.71        61.91        62.33        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        43.73        69.30        66.38        72.03 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LD-A7W6 
       13.55        18.12        11.57        21.24         4.08         4.60 
TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YN TCGA-LL-A5YP TCGA-LL-A6FQ 
        9.53        10.95         7.59        14.70        14.79         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-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.79         2.10        46.55        31.99        58.62        27.65 
TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H 
       34.92        36.36        16.87        24.72        22.32        26.70 
TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P 
       23.47        65.62        33.57        31.07         7.23        14.07 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 
        0.26         3.95         6.81        10.59         7.92         5.56 
TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-W8-A86G TCGA-XX-A899 
        8.52         7.17         6.87         3.91         5.29         9.60 
TCGA-Z7-A8R5 TCGA-Z7-A8R6 
      100.01       105.04 

  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 
            20.320             23.885 
[1] "0.0 - 211.6 (20.3)" "0.2 - 234.3 (23.9)"
[1] "hr=" "1.7"
D73V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18Q LOSS MUTATED        22       24        0        0        93        65
  18Q LOSS WILD-TYPE      61       56        9        5       249       169
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18Q LOSS MUTATED           0         48         16         25        5
  18Q LOSS WILD-TYPE         2         94         13         38       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                  22                 61
  STAGE IA                 24                 56
  STAGE IB                  0                  9
  STAGE II                  0                  5
  STAGE IIA                93                249
  STAGE IIB                65                169
  STAGE III                 0                  2
  STAGE IIIA               48                 94
  STAGE IIIB               16                 13
  STAGE IIIC               25                 38
  STAGE IV                  5                 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    66 182  36  19
  18Q LOSS WILD-TYPE 199 412  88  20
D73V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1               66                199
  T2              182                412
  T3               36                 88
  T4               19                 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
  18Q LOSS MUTATED   135  93  42  27
  18Q LOSS WILD-TYPE 346 246  71  47
D73V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0              135                346
  N1               93                246
  N2               42                 71
  N3               27                 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
  18Q LOSS MUTATED          1 249   5  49
  18Q LOSS WILD-TYPE        4 605  14  98
D73V6, multiclass
          clus
vv         18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CM0 (I+)                1                  4
  M0                    249                605
  M1                      5                 14
  MX                     49                 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"
D73V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   301   3
  18Q LOSS WILD-TYPE 713   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    301    3
  18Q LOSS WILD-TYPE  713    8
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE              301                713
  MALE                  3                  8
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  18Q LOSS MUTATED                            1                           241
  18Q LOSS WILD-TYPE                          0                           513
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  18Q LOSS MUTATED                               43                   2
  18Q LOSS WILD-TYPE                            132                   4
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  18Q LOSS MUTATED                                  6                  0
  18Q LOSS WILD-TYPE                               23                 15
                    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                 241                513
  INFILTRATING LOBULAR CARCINOMA                 43                132
  MEDULLARY CARCINOMA                             2                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                6                 23
  MUCINOUS CARCINOMA                              0                 15
  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    89 215
  18Q LOSS WILD-TYPE 193 528
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     89  215
  18Q LOSS WILD-TYPE  193  528
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                89                193
  YES              215                528
[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                          50   200
  18Q LOSS WILD-TYPE                       108   517
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                      50                108
  WHITE                                         200                517
[1] 4 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    12 248
  18Q LOSS WILD-TYPE  24 578
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     12  248
  18Q LOSS WILD-TYPE   24  578
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   12                 24
  NOT HISPANIC OR LATINO              248                578
[1] 2 2
[1] FALSE

Clustering(74) Variable = 19P LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED   154  24
  19P LOSS WILD-TYPE 732  95
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               178                827 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                24                 95 
$`19P LOSS MUTATED`
TCGA-5T-A9QA TCGA-A1-A0SJ TCGA-A1-A0SQ TCGA-A2-A04P TCGA-A2-A04T TCGA-A2-A04U 
        0.39        13.68        18.21        18.02        73.84        22.06 
TCGA-A2-A04X TCGA-A2-A0CM TCGA-A2-A0CW TCGA-A2-A0D4 TCGA-A2-A0EO TCGA-A2-A0T3 
       55.43        24.79        64.04        25.22        80.28        18.71 
TCGA-A2-A0T7 TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A3XT 
       20.75        21.90        21.67        23.77        17.36        83.01 
TCGA-A2-A3XX TCGA-A2-A3XZ TCGA-A2-A4S1 TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A26I 
       38.40        31.99        26.96        31.73        10.72        21.73 
TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A6VX TCGA-A8-A06Q TCGA-A8-A06R 
       14.50        17.92        14.73        10.42         1.02        17.98 
TCGA-A8-A06T TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07G TCGA-A8-A07L TCGA-A8-A07O 
       53.06        17.03        53.98        18.97        17.03         9.99 
TCGA-A8-A07W TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08O 
        9.99        33.01        19.96        12.00        37.05        31.00 
TCGA-A8-A08S TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09I TCGA-A8-A09N TCGA-AC-A2BM 
       33.01         9.99         1.02        45.07         1.02        38.20 
TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A62V TCGA-AC-A6IX TCGA-AC-A8OQ TCGA-AN-A041 
       26.04         1.02         0.07         0.43         1.12         0.23 
TCGA-AN-A04A TCGA-AN-A0AS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FZ TCGA-AO-A03M 
        2.96         0.33         6.02         0.33         0.33        47.84 
TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0JD TCGA-AO-A0JM 
       66.77        84.69        21.40        52.18        72.00        71.80 
TCGA-AO-A1KQ TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AR-A0TQ TCGA-AR-A0TS 
       61.87        17.79         5.65         2.56        49.32        74.79 
TCGA-AR-A0TW TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AJ TCGA-AR-A1AQ TCGA-AR-A24H 
       98.93        83.87       114.02        52.77        43.07       109.58 
TCGA-AR-A24R TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A2LK TCGA-AR-A5QQ TCGA-B6-A0I1 
       87.22        56.15        73.18        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-A1Y3 TCGA-D8-A27M TCGA-E2-A109 
       16.41         6.35        16.54        14.14        13.48        46.59 
TCGA-E2-A14O TCGA-E2-A152 TCGA-E2-A159 TCGA-E2-A15H TCGA-E2-A15S TCGA-E2-A1AZ 
       44.68        27.12        25.05        12.92        14.07        60.53 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N6 TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R3 
       34.92        19.89        13.48         9.86        11.90         2.10 
TCGA-E9-A1RC TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A22G TCGA-E9-A2JS TCGA-E9-A5UO 
       40.24        34.59        34.13        23.51        17.75        13.81 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1P8 TCGA-EW-A1PA 
       25.94        22.82        29.95        40.41         7.86        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-A6FP TCGA-LL-A7T0 TCGA-MS-A51U TCGA-OL-A5D7 TCGA-OL-A5S0 
       42.28        11.57         3.22         2.79        46.55        20.38 
TCGA-OL-A6VO TCGA-PL-A8LX TCGA-S3-A6ZF TCGA-S3-AA14 
       28.21         0.16        16.50         7.17 

$`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 
      136.73        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        48.46        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 
       32.75        49.48        34.98        38.37         7.30        24.39 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE 
       21.30        23.21        21.14        21.90        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        43.00        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        24.99        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        38.01 
TCGA-A8-A08C TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X 
       28.96         9.99        31.00         0.99        93.04        43.00 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 
       40.01        33.01        30.97        17.95        41.98        12.00 
TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09M 
        9.99        12.00        50.04        49.05        29.98        33.07 
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-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
        1.48        38.53        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-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ 
       22.19         1.12        16.57        19.79        23.24        24.79 
TCGA-AC-A5XS TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6NO 
        1.55         1.12         1.81         1.18         0.69         1.68 
TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A046 TCGA-AN-A049 
        1.74         1.32         0.33         0.33         0.33         0.62 
TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM 
        1.78         1.71         8.02         7.36         6.51         0.16 
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-A0FW TCGA-AN-A0FX TCGA-AN-A0FY 
        7.59         7.17         6.28         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-A03O 
        0.33         0.33         5.33         5.59        80.28        81.63 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J5 
       68.75        47.87        59.05        29.13        32.78        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-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ 
       50.86        76.77        21.37        26.24        50.24        62.04 
TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 
       55.33       102.58        99.25       108.72       106.78        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-A1KR TCGA-AO-A1KS TCGA-AQ-A04H 
       28.37        14.73        82.62        70.39         0.53        24.79 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AQ-A7U7 
       26.93       130.09        15.62        32.52        32.91         9.99 
TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY 
      111.32         5.26        86.66        29.75        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       101.95        85.97        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        37.81        76.21        61.28        63.62        62.14 
TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       20.22        50.89        73.02        96.89        78.51        84.20 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W 
        0.85       101.52        76.01        53.36        85.35        50.96 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
       83.77        79.00        78.48        72.76        58.92        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN 
      128.65        20.25        62.86         7.36        40.04        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP 
       39.39        40.54        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-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-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-A0AW 
      170.17        85.35       103.63        55.00        24.53        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-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-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-A0BZ TCGA-BH-A0C0 
       27.19        53.69        53.95        49.94        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-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-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-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       24.43        30.35        10.78        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-A0RX TCGA-BH-A0W3 
       13.61        36.85        12.89        51.32         5.59        23.93 
TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18G TCGA-BH-A18J TCGA-BH-A18K 
       24.95        42.35        44.81         2.01        20.12        90.84 
TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18T 
       72.56        37.74        30.28        55.63        37.55         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-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-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-A1FR 
      122.89        36.92        63.35        55.00        45.63       144.59 
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-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-A12Q TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A131 
       12.66         0.07        12.66        12.66         3.12         1.78 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HG TCGA-C8-A1HI 
        1.45         0.69         3.85        12.33        11.34        11.34 
TCGA-C8-A1HJ TCGA-C8-A1HM TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A273 
        0.16         2.30         0.30         0.23         0.36         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-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-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JK 
       18.15        18.90        12.03        12.03        14.01        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-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-A1XU 
       19.92        17.69         7.96        15.85        16.31        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-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-A10C TCGA-E2-A10E TCGA-E2-A10F 
       27.52        40.41        37.51        40.11        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-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-A155 TCGA-E2-A156 TCGA-E2-A158 
       25.41        23.24        19.43        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-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-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-A576 TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1N5 
        7.20        30.61        19.00         9.21        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-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R5 
       20.05        21.57        14.30         0.62         6.12         1.38 
TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RE 
        2.76        21.21        32.09        20.81         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-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        24.56         0.72 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X 
        0.76        26.07        18.41         0.62        15.72        12.33 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW 
        0.23        14.70         0.26        14.40        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-A1OY TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 
       15.68        28.77        29.85        41.13        39.78        52.96 
TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PB TCGA-EW-A1PD 
       29.82        23.11        18.48        30.08        19.99        13.94 
TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 
       10.52        14.43        34.55        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-A2DF TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       53.13        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        43.73 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW 
       69.30        66.38        72.03        13.55        18.12        11.84 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF 
       11.57        21.24         6.67         4.08         4.60         8.75 
TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM 
        9.53        11.44        10.95         7.59        17.06        15.32 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y 
       14.70        14.47        14.79         2.63         3.88         4.14 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
        4.50         4.50         5.59         6.21         7.36        27.91 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
        2.10        12.66        31.99        58.62        27.65        34.92 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I 
       36.36        16.87        24.72        22.32        26.70        23.47 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P 
       65.62        33.57        31.07        26.04         7.23        14.07 
TCGA-OL-A6VQ TCGA-PL-A8LV TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZG TCGA-S3-A6ZH 
       19.73         0.23         0.26         3.95         6.81         8.65 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA15 TCGA-S3-AA17 
       10.59         7.92         5.56         8.52         6.87         3.91 
TCGA-W8-A86G TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        5.29         9.60         9.14       100.01       105.04 

  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 
            21.075             23.110 
[1] "0.1 - 139.2 (21.1)" "0.0 - 234.3 (23.1)"
[1] "hr=" "1.4"
D74V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19P LOSS MUTATED        14       12        2        0        61        41
  19P LOSS WILD-TYPE      69       68        7        5       281       193
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19P LOSS MUTATED           1         26          5         12        6
  19P LOSS WILD-TYPE         1        116         24         51       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                  14                 69
  STAGE IA                 12                 68
  STAGE IB                  2                  7
  STAGE II                  0                  5
  STAGE IIA                61                281
  STAGE IIB                41                193
  STAGE III                 1                  1
  STAGE IIIA               26                116
  STAGE IIIB                5                 24
  STAGE IIIC               12                 51
  STAGE IV                  6                 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    40 114  20   8
  19P LOSS WILD-TYPE 225 480 104  31
D74V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1               40                225
  T2              114                480
  T3               20                104
  T4                8                 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 LOSS MUTATED    78  68  17  15
  19P LOSS WILD-TYPE 403 271  96  59
D74V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0               78                403
  N1               68                271
  N2               17                 96
  N3               15                 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
  19P LOSS MUTATED          2 152   6  22
  19P LOSS WILD-TYPE        3 702  13 125
D74V6, multiclass
          clus
vv         19P LOSS MUTATED 19P LOSS WILD-TYPE
  CM0 (I+)                2                  3
  M0                    152                702
  M1                      6                 13
  MX                     22                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"
D74V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED   180   2
  19P LOSS WILD-TYPE 834   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED    180    2
  19P LOSS WILD-TYPE  834    9
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE              180                834
  MALE                  2                  9
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  19P LOSS MUTATED                            0                           162
  19P LOSS WILD-TYPE                          1                           592
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  19P LOSS MUTATED                                7                   1
  19P LOSS WILD-TYPE                            168                   5
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  19P LOSS MUTATED                                  3                  3
  19P LOSS WILD-TYPE                               26                 12
                    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                 162                592
  INFILTRATING LOBULAR CARCINOMA                  7                168
  MEDULLARY CARCINOMA                             1                  5
  MIXED HISTOLOGY (PLEASE SPECIFY)                3                 26
  MUCINOUS CARCINOMA                              3                 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"
D74V9, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    53 129
  19P LOSS WILD-TYPE 229 614
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     53  129
  19P LOSS WILD-TYPE  229  614
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                53                229
  YES              129                614
[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                          40   107
  19P LOSS WILD-TYPE                       118   610
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                      40                118
  WHITE                                         107                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"
D74V12, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     8 141
  19P LOSS WILD-TYPE  28 685
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      8  141
  19P LOSS WILD-TYPE   28  685
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    8                 28
  NOT HISPANIC OR LATINO              141                685
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19Q LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED   128  21
  19Q LOSS WILD-TYPE 758  98
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               149                856 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                21                 98 
$`19Q LOSS MUTATED`
TCGA-5T-A9QA TCGA-A1-A0SQ TCGA-A2-A04U TCGA-A2-A04X TCGA-A2-A0CM TCGA-A2-A0D1 
        0.39        18.21        22.06        55.43        24.79        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        53.06        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-A09A 
       33.01        19.96        12.00        31.00        33.01         9.99 
TCGA-A8-A09C TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09N TCGA-AC-A23C TCGA-AC-A2BM 
        1.02        45.07        33.07         1.02         0.95        38.20 
TCGA-AC-A2FM TCGA-AC-A62V TCGA-AC-A8OQ TCGA-AN-A041 TCGA-AN-A04A TCGA-AN-A0AS 
       26.04         0.07         1.12         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        52.18        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       114.02        52.77 
TCGA-AR-A1AQ TCGA-AR-A24H TCGA-AR-A24R TCGA-AR-A252 TCGA-AR-A2LK TCGA-AR-A5QQ 
       43.07       109.58        87.22        73.18        42.87        10.59 
TCGA-B6-A0I1 TCGA-B6-A0IB TCGA-B6-A0WX TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A402 
       77.62       129.57        21.47       101.52       139.17        54.28 
TCGA-B6-A408 TCGA-BH-A0BT TCGA-BH-A0C0 TCGA-BH-A0C7 TCGA-BH-A0DQ TCGA-BH-A0EB 
       49.94        45.57        41.75        42.90         3.22        24.49 
TCGA-BH-A0EE TCGA-BH-A0H0 TCGA-BH-A0H7 TCGA-BH-A0HY TCGA-BH-A0WA TCGA-BH-A18F 
       31.00        15.16        23.08        50.79        23.05         8.81 
TCGA-BH-A18I TCGA-BH-A18S TCGA-BH-A1FU TCGA-BH-A204 TCGA-BH-A209 TCGA-C8-A12M 
        7.23        66.05        72.07        83.31       130.16        11.77 
TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A1HF TCGA-C8-A1HL TCGA-C8-A26X 
       11.77         0.07        12.66        10.92        10.42         0.36 
TCGA-C8-A26Y TCGA-C8-A278 TCGA-C8-A27A TCGA-D8-A13Y TCGA-D8-A1JC TCGA-D8-A1JI 
        0.43         0.03        12.20        11.90        15.78        18.97 
TCGA-D8-A1JJ TCGA-D8-A1JM TCGA-D8-A1XA TCGA-D8-A1XQ TCGA-D8-A1XT TCGA-D8-A1XY 
       20.09        19.40        27.58        16.41         6.35        16.54 
TCGA-D8-A1Y3 TCGA-D8-A27M TCGA-E2-A109 TCGA-E2-A14O TCGA-E2-A159 TCGA-E2-A15H 
       14.14        13.48        46.59        44.68        25.05        12.92 
TCGA-E2-A15S TCGA-E2-A1AZ TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N6 TCGA-E9-A1NF 
       14.07        60.53        34.92        19.89        13.48        20.05 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R3 TCGA-E9-A1R7 TCGA-E9-A1RB TCGA-E9-A1RH 
        9.86        11.90         2.10        21.21        20.81        34.59 
TCGA-E9-A226 TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A2JS TCGA-E9-A5UO TCGA-EW-A1OW 
       34.13        23.51         0.69        17.75        13.81        22.82 
TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1PA TCGA-EW-A1PC TCGA-EW-A2FR TCGA-EW-A2FS 
       29.95        40.41        18.90         6.15        55.00        52.73 
TCGA-EW-A3U0 TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH TCGA-LL-A7T0 TCGA-OL-A5D7 
       17.49        53.52        42.71        42.28         3.22        46.55 
TCGA-OL-A5RY TCGA-OL-A6VO TCGA-PL-A8LX TCGA-S3-A6ZF TCGA-S3-AA14 
       24.72        28.21         0.16        16.50         7.17 

$`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       136.73        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-A0CX TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0D3 
       63.45        64.04        56.81        21.14        33.76        28.77 
TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER 
       25.22       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-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 
       17.52        17.13         8.38        18.71        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YH 
       18.90        32.55        25.28        18.21        15.42        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        48.46        31.73        23.47 
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-A3XS TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW 
       20.88        39.65        33.93        29.98        32.75        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        24.39 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD 
       21.30        23.21        26.96        21.14        21.90        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-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       33.11        31.73        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-A3IY 
       24.26        23.74        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-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-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z 
       13.02        13.02        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-A07I 
       17.03         9.01        43.00        19.99        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W 
       12.00        10.98         8.98         7.99        24.99         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-A08J TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08R 
       38.01        28.96        37.05         9.99        31.00         0.99 
TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 
       93.04        43.00        40.01        33.01        30.97        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        50.04        49.05 
TCGA-A8-A09K TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
       29.98        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-A23E TCGA-AC-A23G TCGA-AC-A23H 
       13.02        17.03        38.04         2.37        10.85         2.66 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
        1.48        38.53        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        22.19         1.12        16.57        19.79        23.24 
TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW 
       24.79         1.55         1.12         1.81         1.18         0.69 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y 
        0.43         1.68         1.74         1.32         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-A0AT TCGA-AN-A0FD TCGA-AN-A0FF 
        6.51         0.16         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-A0FW 
        7.96         7.00         7.59         7.17         6.28         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-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-A0J2 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 
       32.78        24.16        37.48        20.32        22.36        53.03 
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-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 
       50.24        62.04       102.58        99.25       108.72       106.78 
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-A1KR TCGA-AO-A1KS 
       41.62        28.37        14.73        82.62        70.39         0.53 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O 
       26.93       130.09        15.62        32.52         2.56        32.91 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT 
        9.99       111.32        49.32         5.26        74.79        86.66 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 
       29.75        98.93        64.83        55.86        76.14        65.36 
TCGA-AR-A0U1 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AL 
      101.95        85.97        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        37.81 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K 
       76.21        61.28        63.62        62.14        20.22        50.89 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q 
       73.02        96.89        78.51        84.20         0.85       101.52 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
       76.01        53.36        85.35        50.96        83.77        79.00 
TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE 
       56.15        78.48        72.76        58.92        93.83       128.65 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       20.25        62.86         7.36        40.04        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0I2 
       40.54        20.38        54.74        16.04        20.45       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-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-A1KC TCGA-B6-A1KI TCGA-B6-A2IU 
       28.27        68.94        58.88        43.59        73.51       170.17 
TCGA-B6-A401 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW 
       85.35       103.63        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-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-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-A0C1 TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE 
       11.67        49.05        44.02        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-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ 
       15.65         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-A0H3 TCGA-BH-A0H5 
       32.65        24.43        30.35        10.78        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-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-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P 
       20.12        90.84        26.66        72.56        37.74        30.28 
TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN 
       55.63        37.55         7.36        51.39        51.16        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-A1FM TCGA-BH-A1FN TCGA-BH-A1FR 
       36.92        63.35        55.00        45.63        72.07       144.59 
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-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-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-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE 
        1.45         0.69         0.62         3.85         3.75        12.33 
TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN 
       11.34        11.34         0.16        12.03         2.30         3.25 
TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
        0.30         0.23         8.28         9.67         0.03         0.03 
TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 
        0.99         0.03         0.23        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-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-A1JK TCGA-D8-A1JL TCGA-D8-A1JN TCGA-D8-A1JP 
       12.03        14.01        20.12        20.09        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-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF 
       25.74        23.90        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-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XZ 
       15.85        16.31        12.99        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-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        30.61 
TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 
       19.00         9.21        19.20        36.82        12.00        13.12 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1R0 
       36.56        39.55        12.59        35.77        21.57        14.30 
TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RC 
        0.62         6.12         1.38         2.76        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-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-A249 TCGA-E9-A24A 
       17.06         0.85        27.22         1.94         0.95        24.56 
TCGA-E9-A295 TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
        0.72         0.76        26.07        18.41         0.62        15.72 
TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UP TCGA-E9-A6HE 
       12.33         0.23        14.70         0.26        14.40        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-A1OY TCGA-EW-A1P0 
       16.57        15.68        28.77        25.94        29.85        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-A1PB TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
        7.86        19.99        13.94        10.52        14.43        34.55 
TCGA-EW-A1PH TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A423 TCGA-EW-A424 
       19.96        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-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        43.73        69.30        66.38        72.03 
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        21.24         6.67 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
        4.08         4.60         8.75         9.53        11.44        10.95 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP 
        7.59        17.06        15.32        14.70        14.47        14.79 
TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 
       11.57         2.63         3.88         4.14         4.50         4.50 
TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 
        5.59         6.21         7.36        27.91         2.79         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW 
       12.66        31.99        58.62        27.65        34.92        36.36 
TCGA-OL-A5RX TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J 
       16.87        22.32        20.38        26.70        23.47        65.62 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ 
       33.57        31.07        26.04         7.23        14.07        19.73 
TCGA-PL-A8LV TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z 
        0.23         0.26         3.95         6.81         8.65        10.59 
TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-W8-A86G 
        7.92         5.56         8.52         6.87         3.91         5.29 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        9.60         9.14       100.01       105.04 

  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 
            21.470             22.785 
[1] "0.0 - 139.2 (21.5)" "0.0 - 234.3 (22.8)"
[1] "hr=" "1.5"
D75V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19Q LOSS MUTATED        10       10        1        0        54        33
  19Q LOSS WILD-TYPE      73       70        8        5       288       201
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19Q LOSS MUTATED           1         26          3          7        5
  19Q LOSS WILD-TYPE         1        116         26         56       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                  10                 73
  STAGE IA                 10                 70
  STAGE IB                  1                  8
  STAGE II                  0                  5
  STAGE IIA                54                288
  STAGE IIB                33                201
  STAGE III                 1                  1
  STAGE IIIA               26                116
  STAGE IIIB                3                 26
  STAGE IIIC                7                 56
  STAGE IV                  5                 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    37  96  15   4
  19Q LOSS WILD-TYPE 228 498 109  35
D75V4, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1               37                228
  T2               96                498
  T3               15                109
  T4                4                 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
  19Q LOSS MUTATED    63  57  21   9
  19Q LOSS WILD-TYPE 418 282  92  65
D75V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0               63                418
  N1               57                282
  N2               21                 92
  N3                9                 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
  19Q LOSS MUTATED          2 124   5  21
  19Q LOSS WILD-TYPE        3 730  14 126
D75V6, multiclass
          clus
vv         19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CM0 (I+)                2                  3
  M0                    124                730
  M1                      5                 14
  MX                     21                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"
D75V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED   150   2
  19Q LOSS WILD-TYPE 864   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED    150    2
  19Q LOSS WILD-TYPE  864    9
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE              150                864
  MALE                  2                  9
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  19Q LOSS MUTATED                            0                           136
  19Q LOSS WILD-TYPE                          1                           618
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  19Q LOSS MUTATED                                4                   1
  19Q LOSS WILD-TYPE                            171                   5
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  19Q LOSS MUTATED                                  3                  3
  19Q LOSS WILD-TYPE                               26                 12
                    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                 136                618
  INFILTRATING LOBULAR CARCINOMA                  4                171
  MEDULLARY CARCINOMA                             1                  5
  MIXED HISTOLOGY (PLEASE SPECIFY)                3                 26
  MUCINOUS CARCINOMA                              3                 12
  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    50 102
  19Q LOSS WILD-TYPE 232 641
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     50  102
  19Q LOSS WILD-TYPE  232  641
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                50                232
  YES              102                641
[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                          31    91
  19Q LOSS WILD-TYPE                       127   626
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                      31                127
  WHITE                                          91                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"
D75V12, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     5 120
  19Q LOSS WILD-TYPE  31 706
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      5  120
  19Q LOSS WILD-TYPE   31  706
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                 31
  NOT HISPANIC OR LATINO              120                706
[1] 2 2
[1] FALSE

Clustering(76) Variable = 20P LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    74  14
  20P LOSS WILD-TYPE 812 105
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                88                917 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                14                105 
$`20P LOSS MUTATED`
TCGA-5T-A9QA TCGA-A1-A0SK TCGA-A2-A04T TCGA-A2-A0YE TCGA-A2-A3XU TCGA-A2-A4S3 
        0.39        31.79        73.84        18.21        29.98        21.90 
TCGA-A7-A0CE TCGA-A7-A26E TCGA-A7-A26I TCGA-A7-A4SE TCGA-A8-A06Q TCGA-A8-A079 
       35.31        31.36        21.73        21.17         1.02         9.01 
TCGA-A8-A07L TCGA-A8-A08F TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A0AB TCGA-AC-A3W5 
       17.03        33.01         9.99        31.00        17.03        16.57 
TCGA-AC-A62X TCGA-AN-A0AM TCGA-AN-A0XW TCGA-AO-A0J6 TCGA-AO-A1KT TCGA-AQ-A04J 
        1.12         0.16         5.59        37.48        17.79        26.93 
TCGA-AQ-A54N TCGA-AR-A0TZ TCGA-AR-A0U3 TCGA-AR-A1AR TCGA-AR-A24K TCGA-AR-A251 
        2.56        76.14       114.02        17.23        50.89        78.48 
TCGA-B6-A0I9 TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0RL TCGA-B6-A0RS TCGA-B6-A0X1 
       12.13       176.98        18.77        81.17       100.70       186.48 
TCGA-B6-A1KN TCGA-BH-A0AV TCGA-BH-A0B4 TCGA-BH-A0B9 TCGA-BH-A0BR TCGA-BH-A0DH 
      139.17        38.79        39.16        51.68        53.69        38.01 
TCGA-BH-A0E1 TCGA-BH-A18V TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FM TCGA-C8-A12M 
       15.68        51.16       114.15        33.17        45.63        11.77 
TCGA-C8-A134 TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1XA TCGA-D8-A1XJ 
        0.69        20.12        20.09        19.40        27.58        21.83 
TCGA-D8-A1XK TCGA-D8-A1XQ TCGA-D8-A1Y3 TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27R 
       14.50        16.41        14.14        16.04        13.05        10.09 
TCGA-E2-A14N TCGA-E2-A14R TCGA-E2-A15A TCGA-E2-A15E TCGA-E2-A2P5 TCGA-E2-A573 
       47.15        38.60        23.34        20.71        16.93        34.92 
TCGA-E9-A1N5 TCGA-E9-A1NC TCGA-E9-A1R6 TCGA-E9-A1RE TCGA-E9-A22G TCGA-E9-A244 
       36.82        39.55         2.76        34.65        23.51         0.69 
TCGA-EW-A1P4 TCGA-EW-A1P8 TCGA-EW-A2FR TCGA-EW-A2FW TCGA-EW-A3U0 TCGA-EW-A423 
       29.82         7.86        55.00        22.09        17.49        10.16 
TCGA-GM-A2DF TCGA-JL-A3YX TCGA-LL-A5YP TCGA-MS-A51U TCGA-OL-A5RW TCGA-OL-A5S0 
       42.71        11.57        14.79         2.79        36.36        20.38 
TCGA-OL-A66O TCGA-OL-A6VO TCGA-PL-A8LX TCGA-S3-AA0Z 
        7.23        28.21         0.16        10.59 

$`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       136.73        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        48.46        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        32.75        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        24.39        21.30        23.21        26.96 
TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 
       21.14        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        53.06        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        43.00 
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        24.99         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        38.01 
TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08R 
       28.96        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 
       33.01        93.04        43.00        40.01        33.01        30.97 
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        50.04        49.05        45.07        29.98        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-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        22.19         1.12        19.79 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV 
       23.24        24.79         1.55         0.07         1.81         1.18 
TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR 
        0.69         0.43         1.68         1.74         1.12         1.32 
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-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR 
        1.78         1.71         8.02         7.36         6.51         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-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        52.18 
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-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI 
       50.86        72.00        76.77        21.37        26.24        50.24 
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       108.72 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
      106.78        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-AQ-A04H TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 
       70.39         0.53        24.79       130.09         5.65        15.62 
TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
       32.52        32.91         9.99       111.32        49.32         5.26 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
       74.79        86.66        29.75        98.93        64.83        55.86 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
       65.36       101.95        83.87        85.97        75.55        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-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       39.98        43.07        37.81        76.21        61.28        63.62 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       62.14        20.22       109.58        73.02        96.89        78.51 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24U 
       84.20         0.85       101.52        87.22        76.01        53.36 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 
       85.35        50.96        83.77        79.00        56.15        73.18 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       72.76        58.92        93.83       128.65        20.25        62.86 
TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       42.87         7.36        40.04        38.17        39.39        40.54 
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-A0IH TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP 
      146.50       112.37       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-A0RM 
      140.88       211.56        68.45       189.01       234.28        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RU 
      172.96       162.05       102.77       140.48        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-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      113.79       129.57       129.70        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-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AY 
       49.94       103.63        55.00        24.53        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-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-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-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-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-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-A18M TCGA-BH-A18N TCGA-BH-A18P 
       20.12        90.84        26.66        72.56        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-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-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
       24.66       120.62        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-A202 
       55.00        72.07       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-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-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-A135 TCGA-C8-A137 
       12.66         3.12         1.78         1.45         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-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-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-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT 
       18.97        20.09        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-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-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-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-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-A14S TCGA-E2-A14T TCGA-E2-A14U 
       44.68        40.96        38.24        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-A15C TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H 
       25.05        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-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-A2P6 
       18.87       106.75       102.61         8.75        43.04         5.52 
TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU 
       15.72         7.20        30.61        19.89        19.00         9.21 
TCGA-E9-A1N4 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1ND 
       19.20        13.48        12.00        13.12        36.56        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-A1RA 
        0.62         2.10         6.12         1.38        21.21        32.09 
TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH 
       20.81        40.24         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-A22H TCGA-E9-A243 TCGA-E9-A245 TCGA-E9-A247 
       22.75        12.89        24.10        17.06         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        24.56         0.72        17.75         0.76 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y 
       26.07        18.41         0.62        15.72        12.33         0.23 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW 
       14.70         0.26        13.81        14.40        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-A1P5 TCGA-EW-A1P6 
       40.41        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-A2FS TCGA-EW-A2FV TCGA-EW-A3E8 
       14.43        34.55        19.96        52.73        25.91        21.27 
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        43.73 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW 
       69.30        66.38        72.03        13.55        18.12        11.84 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 
       21.24         6.67         4.08         4.60         8.75         9.53 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN 
       11.44        10.95         7.59        17.06        15.32        14.70 
TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z 
       14.47        11.57         2.63         3.88         4.14         4.50 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
        4.50         5.59         3.22         6.21         7.36        27.91 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.10        12.66        46.55        31.99        58.62        27.65 
TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I 
       34.92        16.87        24.72        22.32        26.70        23.47 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66P TCGA-OL-A6VQ 
       65.62        33.57        31.07        26.04        14.07        19.73 
TCGA-PL-A8LV TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH 
        0.23         0.26         3.95        16.50         6.81         8.65 
TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 
        7.92         5.56         8.52         7.17         6.87         3.91 
TCGA-W8-A86G TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        5.29         9.60         9.14       100.01       105.04 

  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 
             21.78              22.75 
[1] "0.2 - 186.5 (21.8)" "0.0 - 234.3 (22.8)"
[1] "hr=" "1.4"
D76V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20P LOSS MUTATED         3        5        1        0        36        18
  20P LOSS WILD-TYPE      80       75        8        5       306       216
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20P LOSS MUTATED           0         14          3          6        4
  20P LOSS WILD-TYPE         2        128         26         57       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                 80
  STAGE IA                  5                 75
  STAGE IB                  1                  8
  STAGE II                  0                  5
  STAGE IIA                36                306
  STAGE IIB                18                216
  STAGE III                 0                  2
  STAGE IIIA               14                128
  STAGE IIIB                3                 26
  STAGE IIIC                6                 57
  STAGE IV                  4                 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    15  63   8   4
  20P LOSS WILD-TYPE 250 531 116  35
D76V4, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1               15                250
  T2               63                531
  T3                8                116
  T4                4                 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
  20P LOSS MUTATED    40  29  11   8
  20P LOSS WILD-TYPE 441 310 102  66
D76V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0               40                441
  N1               29                310
  N2               11                102
  N3                8                 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
  20P LOSS MUTATED          0  71   5  14
  20P LOSS WILD-TYPE        5 783  14 133
D76V6, multiclass
          clus
vv         20P LOSS MUTATED 20P LOSS WILD-TYPE
  CM0 (I+)                0                  5
  M0                     71                783
  M1                      5                 14
  MX                     14                133
[1] 4 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    89   1
  20P LOSS WILD-TYPE 925  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     89    1
  20P LOSS WILD-TYPE  925   10
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE               89                925
  MALE                  1                 10
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  20P LOSS MUTATED                            0                            76
  20P LOSS WILD-TYPE                          1                           678
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  20P LOSS MUTATED                                7                   2
  20P LOSS WILD-TYPE                            168                   4
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  20P LOSS MUTATED                                  2                  0
  20P LOSS WILD-TYPE                               27                 15
                    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                  76                678
  INFILTRATING LOBULAR CARCINOMA                  7                168
  MEDULLARY CARCINOMA                             2                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                2                 27
  MUCINOUS CARCINOMA                              0                 15
  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  62
  20P LOSS WILD-TYPE 254 681
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     28   62
  20P LOSS WILD-TYPE  254  681
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                28                254
  YES               62                681
[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                          23    55
  20P LOSS WILD-TYPE                       135   662
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                      23                135
  WHITE                                          55                662
[1] 4 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  68
  20P LOSS WILD-TYPE  31 758
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      5   68
  20P LOSS WILD-TYPE   31  758
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                 31
  NOT HISPANIC OR LATINO               68                758
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED    43   8
  20Q LOSS WILD-TYPE 843 111
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                51                954 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 8                111 
$`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        43.00        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-AR-A251 TCGA-B6-A0RS 
        2.56       114.02        17.23        50.89        78.48       100.70 
TCGA-B6-A0X1 TCGA-BH-A0AV TCGA-BH-A18V TCGA-BH-A1FC TCGA-C8-A12M TCGA-C8-A27B 
      186.48        38.79        51.16       114.15        11.77         0.99 
TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-E2-A14N TCGA-E2-A15E 
       20.12        20.09        21.83        14.50        47.15        20.71 
TCGA-E2-A2P5 TCGA-E9-A1NC TCGA-E9-A22G TCGA-EW-A1P4 TCGA-EW-A1P8 TCGA-EW-A2FW 
       16.93        39.55        23.51        29.82         7.86        22.09 
TCGA-EW-A3U0 TCGA-JL-A3YX TCGA-LL-A5YP TCGA-MS-A51U TCGA-OL-A5RW TCGA-OL-A66O 
       17.49        11.57        14.79         2.79        36.36         7.23 
TCGA-OL-A6VO TCGA-PL-A8LV TCGA-S3-AA0Z 
       28.21         0.23        10.59 

$`20Q LOSS WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        0.39         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
       47.24        20.88        13.68         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 
      136.73        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-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-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-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX 
       24.16        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-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-A1FW TCGA-A2-A1FX 
       48.46        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-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-A3XV TCGA-A2-A3XW 
       20.88        39.65        33.93        83.01        32.75        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        24.39 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD 
       21.30        23.21        26.96        21.14        21.90        38.30 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13D 
       34.29        35.47        30.61        37.45        33.11        31.73 
TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26F TCGA-A7-A26G 
       10.72        12.72        23.61        29.56        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-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW 
       14.50        21.17        17.92        14.73        12.10        10.72 
TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P 
       11.05        10.29        10.42         8.75        13.02        13.02 
TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z 
       17.98        53.06        29.03        31.00        26.01         1.02 
TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G 
       17.03        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-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-A082 TCGA-A8-A084 
        7.99        24.99         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        38.01        28.96        33.01 
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 
       33.01        93.04        43.00        40.01        33.01        30.97 
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        50.04        49.05        45.07        29.98        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-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-A3W5 
        0.99         0.69        14.83        22.19         1.12        16.57 
TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y 
       19.79        23.24        24.79         1.55         0.07         1.81 
TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OQ 
        1.18         0.69         0.43         1.68         1.74         1.12 
TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 
        1.32         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-A0AL 
        2.96         1.78         1.71         8.02         7.36         6.51 
TCGA-AN-A0AM TCGA-AN-A0AS 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-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-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN 
        0.36         0.33         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-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03R 
        5.33        80.28        47.84        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        52.18 
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-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI 
       50.86        72.00        76.77        21.37        26.24        50.24 
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       108.72 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
      106.78        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-A1KT TCGA-AQ-A04H TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 
       70.39        17.79        24.79       130.09         5.65        15.62 
TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
       32.52        32.91         9.99       111.32        49.32         5.26 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
       74.79        86.66        29.75        98.93        64.83        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AH 
       76.14        65.36       101.95        83.87        85.97        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-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
       43.56        39.98        43.07        37.81        76.21        61.28 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M 
       63.62        62.14        20.22       109.58        73.02        96.89 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24T 
       78.51        84.20         0.85       101.52        87.22        76.01 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 
       53.36        85.35        50.96        83.77        79.00        56.15 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH 
       73.18        72.76        58.92        93.83       128.65        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       62.86        42.87         7.36        40.04        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       40.54        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-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-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC 
      129.57       129.70        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-A402 
      101.52        73.51       139.17       170.17        85.35        54.28 
TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AY 
       49.94       103.63        55.00        24.53        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-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-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-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW 
        5.85         2.50        13.61        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-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-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO 
       37.55        66.05         7.36        51.39        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-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-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-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-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-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-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-A1JF TCGA-D8-A1JG 
       18.71        15.78        18.15        18.90        12.03        12.03 
TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP 
       14.01        18.97        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-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ 
       15.22        14.73        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-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-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-A10C 
       34.42        27.52        46.59        40.41        37.51        40.11 
TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R 
       28.44        28.87        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-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-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-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z 
      102.61         8.75        43.04         5.52        15.72         7.20 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N4 
       30.61        34.92        19.89        19.00         9.21        19.20 
TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1ND 
       36.82        13.48        12.00        13.12        36.56        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-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-A249 TCGA-E9-A24A 
        0.69         0.85        27.22         1.94         0.95        24.56 
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-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO 
       15.72        12.33         0.23        14.70         0.26        13.81 
TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
       14.40        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-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-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-A3E8 TCGA-EW-A423 TCGA-EW-A424 
       55.00        52.73        25.91        21.27        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        43.73 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW 
       69.30        66.38        72.03        13.55        18.12        11.84 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 
       21.24         6.67         4.08         4.60         8.75         9.53 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN 
       11.44        10.95         7.59        17.06        15.32        14.70 
TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z 
       14.47        11.57         2.63         3.88         4.14         4.50 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
        4.50         5.59         3.22         6.21         7.36        27.91 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.10        12.66        46.55        31.99        58.62        27.65 
TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H 
       34.92        16.87        24.72        22.32        20.38        26.70 
TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66P 
       23.47        65.62        33.57        31.07        26.04        14.07 
TCGA-OL-A6VQ TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG 
       19.73         0.16         0.26         3.95        16.50         6.81 
TCGA-S3-A6ZH TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 
        8.65         7.92         5.56         8.52         7.17         6.87 
TCGA-S3-AA17 TCGA-W8-A86G TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        3.91         5.29         9.60         9.14       100.01       105.04 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              0.23               0.03 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            186.48             234.28 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             21.83              22.55 
[1] "0.2 - 186.5 (21.8)" "0.0 - 234.3 (22.5)"
[1] "hr=" "1.4"
D77V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20Q LOSS MUTATED         1        1        0        0        27        11
  20Q LOSS WILD-TYPE      82       79        9        5       315       223
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20Q LOSS MUTATED           0          7          1          2        2
  20Q LOSS WILD-TYPE         2        135         28         61       16
                    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                 82
  STAGE IA                  1                 79
  STAGE IB                  0                  9
  STAGE II                  0                  5
  STAGE IIA                27                315
  STAGE IIB                11                223
  STAGE III                 0                  2
  STAGE IIIA                7                135
  STAGE IIIB                1                 28
  STAGE IIIC                2                 61
  STAGE IV                  2                 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
  20Q LOSS MUTATED     6  40   5   1
  20Q LOSS WILD-TYPE 259 554 119  38
D77V4, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1                6                259
  T2               40                554
  T3                5                119
  T4                1                 38
[1] 4 2
[1] 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    27  17   5   3
  20Q LOSS WILD-TYPE 454 322 108  71
D77V5, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0               27                454
  N1               17                322
  N2                5                108
  N3                3                 71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CM0 (I+)  M0  M1  MX
  20Q LOSS MUTATED          0  42   2   8
  20Q LOSS WILD-TYPE        5 812  17 139
D77V6, multiclass
          clus
vv         20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CM0 (I+)                0                  5
  M0                     42                812
  M1                      2                 17
  MX                      8                139
[1] 4 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    52   0
  20Q LOSS WILD-TYPE 962  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED     52    0
  20Q LOSS WILD-TYPE  962   11
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE               52                962
  MALE                  0                 11
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  20Q LOSS MUTATED                            0                            39
  20Q LOSS WILD-TYPE                          1                           715
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  20Q LOSS MUTATED                                6                   3
  20Q LOSS WILD-TYPE                            169                   3
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  20Q LOSS MUTATED                                  1                  0
  20Q LOSS WILD-TYPE                               28                 15
                    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                  39                715
  INFILTRATING LOBULAR CARCINOMA                  6                169
  MEDULLARY CARCINOMA                             3                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)                1                 28
  MUCINOUS CARCINOMA                              0                 15
  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    16  36
  20Q LOSS WILD-TYPE 266 707
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED     16   36
  20Q LOSS WILD-TYPE  266  707
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                16                266
  YES               36                707
[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                          15    28
  20Q LOSS WILD-TYPE                       143   689
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                      15                143
  WHITE                                          28                689
[1] 4 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  40
  20Q LOSS WILD-TYPE  32 786
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      4   40
  20Q LOSS WILD-TYPE   32  786
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 32
  NOT HISPANIC OR LATINO               40                786
[1] 2 2
[1] FALSE

Clustering(78) Variable = 21Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED   146  21
  21Q LOSS WILD-TYPE 740  98
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               167                838 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                21                 98 
$`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        33.01        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 
       33.01         9.99        12.00        45.07        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-AC-A8OQ TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A0AM TCGA-AN-A0FF TCGA-AN-A0FJ 
        1.12         2.96         1.78         0.16         4.64         7.96 
TCGA-AN-A0FV TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AO-A03L TCGA-AO-A03P TCGA-AO-A03R 
        0.33         0.33         0.33        80.28        84.69        68.75 
TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J7 TCGA-AO-A0JD TCGA-AQ-A04L TCGA-AQ-A0Y5 
       21.40        52.18        20.32        72.00       130.09         5.65 
TCGA-AR-A0TP TCGA-AR-A0TT TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A1AP 
      111.32        86.66        76.14       101.95        83.87        39.98 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A256 
       53.36        85.35        50.96        56.15        73.18        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-OL-A6VQ 
       72.03        11.57        15.32        22.32        26.04        19.73 
TCGA-PL-A8LV TCGA-PL-A8LX TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-AA17 
        0.23         0.16        16.50         6.81         3.91 

$`21Q LOSS WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        0.39         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SO 
       47.24        20.88        13.68        31.79         7.96        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-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       136.73 
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-A0CX TCGA-A2-A0D1 
       75.55        75.25         5.19        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-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EV 
      107.61        79.76        74.40        37.05        35.05        31.82 
TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SV TCGA-A2-A0SW 
       29.75        24.72        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-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-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 
       48.46        31.73        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-A3XZ TCGA-A2-A4RW 
       29.98        32.75        49.48        38.40        31.99         7.30 
TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 
       24.39        21.30        23.21        26.96        21.14        21.90 
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-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-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD 
       31.36        24.26        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-A4SB TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D 
       11.97        14.93        13.74        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-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06X 
        8.75        13.02         1.02        17.98        53.06        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        43.00        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        24.99         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        38.01 
TCGA-A8-A08C TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X 
       28.96         9.99        31.00         0.99        93.04        43.00 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 
       40.01        33.01        30.97        17.95        41.98        12.00 
TCGA-A8-A099 TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09M 
        9.99         1.02        50.04        49.05        29.98        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-A0A6 TCGA-A8-A0A7 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E 
       21.04         0.99        17.03        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-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-A3W5 
        0.99         0.69        14.83        22.19         1.12        16.57 
TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X 
       19.79        23.24        24.79         1.55         0.07         1.12 
TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OR 
        1.81         1.18         0.69         0.43         1.68         1.32 
TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04D 
        0.33         0.33         0.23         0.33         0.62         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-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT 
        6.44         7.00         7.59         7.17         6.28         6.02 
TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN 
        0.36         0.33         0.33         0.33         0.33         0.33 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW 
       12.33         0.30         0.33         0.33         5.33         5.59 
TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V 
       47.84        66.77        81.63        47.87        59.05        29.13 
TCGA-AO-A0J2 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA 
       32.78        24.16        37.48        22.36        53.03        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        50.24 
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       108.72 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
      106.78        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-A1H2 
       70.39         0.53        17.79        24.79        26.93        15.62 
TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TQ TCGA-AR-A0TR 
       32.52         2.56        32.91         9.99        49.32         5.26 
TCGA-AR-A0TS TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0U0 
       74.79        29.75        98.93        64.83        55.86        65.36 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK 
      114.02        85.97        75.55        61.84        52.77        51.25 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AQ TCGA-AR-A1AR 
       48.82        62.56        43.73        43.56        43.07        17.23 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY 
       37.81        76.21        61.28        63.62        62.14        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        96.89        78.51        84.20 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24X TCGA-AR-A24Z 
        0.85       101.52        87.22        76.01        83.77        79.00 
TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       78.48        72.76        58.92       128.65        20.25        62.86 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
        7.36        40.04        38.17        39.39        40.54        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-A0IC TCGA-B6-A0IG TCGA-B6-A0IH 
      149.59        12.13       220.90        50.70       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-A0RO TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RU 
       78.02       172.96       162.05       140.48        89.46       131.21 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WX TCGA-B6-A0WY 
      157.41        97.48       188.68        79.63        21.47       113.79 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A1KF TCGA-B6-A1KI 
      129.57       129.70        28.27        68.94       101.52        73.51 
TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AW TCGA-BH-A0AY 
       85.35        54.28       103.63        55.00        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-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-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-A0DG TCGA-BH-A0DH 
       44.02        48.13        42.90        45.83        23.44        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DQ TCGA-BH-A0DS 
       22.13        13.91        48.23        17.26         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-A0EA TCGA-BH-A0EB TCGA-BH-A0EE 
       14.30         9.63        44.81        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-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-A0HW TCGA-BH-A0RX TCGA-BH-A0W4 
        2.50        13.61        36.85        51.32         5.59        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-A18N TCGA-BH-A18P TCGA-BH-A18Q 
       20.12        90.84        72.56        37.74        30.28        55.63 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES 
       37.55        66.05         7.36        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-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-A202 
       55.00        72.07       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-A12P TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A131 
       11.77        11.77        12.66        12.66         3.12         1.78 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A1HE TCGA-C8-A1HG TCGA-C8-A1HI 
        1.45         0.69         0.62        12.33        11.34        11.34 
TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A26V TCGA-C8-A26X TCGA-C8-A26Y 
        0.16        10.42         2.30         0.30         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-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-A143 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
       14.17        21.14        19.20        17.49        16.50        18.71 
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-A1JL TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT 
       20.12        20.09        20.38        21.01        12.20        13.32 
TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XC 
       14.70        18.58        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-A1XQ TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW 
       16.41        16.31         6.35        12.99        15.16        12.66 
TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G 
       15.52        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-A27R TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 
       10.09        12.53        14.50        18.51         7.33        43.00 
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-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-A155 TCGA-E2-A156 TCGA-E2-A158 
       25.41        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-A15I 
       25.05        23.34        22.82        17.29        21.63        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-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       37.41        32.78        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-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-A570 TCGA-E2-A573 
        8.75        16.93         5.52        15.72        30.61        34.92 
TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 
       19.00         9.21        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        24.56         0.72        17.75 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y 
        0.76        26.07        18.41        15.72        12.33         0.23 
TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IX TCGA-EW-A1IY 
       14.70        13.81        14.40        15.39        39.72         8.48 
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-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-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-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 
       34.55        19.96        55.00        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-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-A3XL TCGA-GM-A3XN TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW 
       43.73        69.30        66.38        13.55        18.12        11.84 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 
       21.24         6.67         4.08         4.60         8.75         9.53 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO 
       11.44        10.95         7.59        17.06        14.70        14.47 
TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z 
       14.79        11.57         2.63         3.88         4.14         4.50 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
        4.50         5.59         3.22         6.21         7.36        27.91 
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        31.99        58.62 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5S0 
       27.65        34.92        36.36        16.87        24.72        20.38 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66O 
       26.70        23.47        65.62        33.57        31.07         7.23 
TCGA-OL-A66P TCGA-OL-A6VO TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZH TCGA-S3-AA0Z 
       14.07        28.21         0.26         3.95         8.65        10.59 
TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-W8-A86G 
        7.92         5.56         8.52         7.17         6.87         5.29 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        9.60         9.14       100.01       105.04 

  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 
            22.320             22.405 
[1] "0.1 - 186.5 (22.3)" "0.0 - 234.3 (22.4)"
[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        0        51        43
  21Q LOSS WILD-TYPE      72       68        9        5       291       191
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  21Q LOSS MUTATED           1         27         10          5        6
  21Q LOSS WILD-TYPE         1        115         19         58       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                 72
  STAGE IA                 12                 68
  STAGE IB                  0                  9
  STAGE II                  0                  5
  STAGE IIA                51                291
  STAGE IIB                43                191
  STAGE III                 1                  1
  STAGE IIIA               27                115
  STAGE IIIB               10                 19
  STAGE IIIC                5                 58
  STAGE IV                  6                 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    38 102  18  11
  21Q LOSS WILD-TYPE 227 492 106  28
D78V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1               38                227
  T2              102                492
  T3               18                106
  T4               11                 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
  21Q LOSS MUTATED    70  59  29   9
  21Q LOSS WILD-TYPE 411 280  84  65
D78V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0               70                411
  N1               59                280
  N2               29                 84
  N3                9                 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
  21Q LOSS MUTATED          1 141   7  21
  21Q LOSS WILD-TYPE        4 713  12 126
D78V6, multiclass
          clus
vv         21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CM0 (I+)                1                  4
  M0                    141                713
  M1                      7                 12
  MX                     21                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"
D78V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED   170   0
  21Q LOSS WILD-TYPE 844  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED    170    0
  21Q LOSS WILD-TYPE  844   11
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE              170                844
  MALE                  0                 11
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  21Q LOSS MUTATED                            0                           141
  21Q LOSS WILD-TYPE                          1                           613
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  21Q LOSS MUTATED                               16                   2
  21Q LOSS WILD-TYPE                            159                   4
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  21Q LOSS MUTATED                                  6                  1
  21Q LOSS WILD-TYPE                               23                 14
                    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                 141                613
  INFILTRATING LOBULAR CARCINOMA                 16                159
  MEDULLARY CARCINOMA                             2                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                6                 23
  MUCINOUS CARCINOMA                              1                 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"
D78V9, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    51 119
  21Q LOSS WILD-TYPE 231 624
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     51  119
  21Q LOSS WILD-TYPE  231  624
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                51                231
  YES              119                624
[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                          30   108
  21Q LOSS WILD-TYPE                       128   609
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                      30                128
  WHITE                                         108                609
[1] 4 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     3 136
  21Q LOSS WILD-TYPE  33 690
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      3  136
  21Q LOSS WILD-TYPE   33  690
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 33
  NOT HISPANIC OR LATINO              136                690
[1] 2 2
[1] FALSE

Clustering(79) Variable = 22Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED   387  59
  22Q LOSS WILD-TYPE 499  60
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               446                559 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                59                 60 
$`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 
       21.30        21.90        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        53.06        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        43.00        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        33.01 
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        50.04         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        22.19         1.55         1.81 
TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AN-A041 TCGA-AN-A049 
        1.18         0.43         1.68         1.74         0.23         0.62 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FW 
        8.02         7.36         6.44         4.64         7.00         0.36 
TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XO TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT 
        0.33         0.33        12.33         0.33         0.33         0.33 
TCGA-AN-A0XU TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A0J3 TCGA-AO-A0J7 
        0.33        80.28        66.77        84.69        21.40        20.32 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JD TCGA-AO-A0JG 
       22.36        53.03        21.53        50.70        72.00        26.24 
TCGA-AO-A12A TCGA-AO-A12E TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AQ-A54N 
       90.58        57.30        82.62        61.87         0.53         2.56 
TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0TY 
       32.91         9.99         5.26        86.66        98.93        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AJ 
       76.14        65.36        83.87       114.02        75.55        52.77 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AV 
       62.56        43.73        39.98        43.07        17.23        61.28 
TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24O TCGA-AR-A24P 
       20.22       109.58        50.89        73.02        84.20         0.85 
TCGA-AR-A24R TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 
       87.22        50.96        83.77        79.00        56.15        73.18 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LK TCGA-AR-A2LO TCGA-AR-A5QN TCGA-AR-A5QP 
       58.92        93.83        42.87        39.39        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       103.63        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-E2-A576 
        8.75        16.93         7.20        34.92        19.89        19.00 
TCGA-E2-A9RU TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1ND 
        9.21        36.82        12.00        13.12        36.56        12.59 
TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1R2 TCGA-E9-A1R3 
       35.77        20.05        21.57         9.86         0.62         2.10 
TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE 
        2.76        32.09        20.81        40.24         0.66        34.65 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22E 
        6.58        21.27        35.64        13.32        39.09        12.89 
TCGA-E9-A22H TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A 
       24.10         0.69        27.22         1.94         0.95        24.56 
TCGA-E9-A3HO TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO 
       26.07        15.72         0.23        14.70         0.26        13.81 
TCGA-E9-A6HE TCGA-EW-A1IX TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J6 TCGA-EW-A1OW 
       15.39        39.72        18.90        13.25        28.77        22.82 
TCGA-EW-A1OY TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P8 TCGA-EW-A1PA 
       29.85        52.96        23.11        18.48         7.86        18.90 
TCGA-EW-A1PC TCGA-EW-A1PH TCGA-EW-A2FV TCGA-EW-A423 TCGA-GM-A2DA TCGA-GM-A2DB 
        6.15        19.96        25.91        10.16       194.27        53.13 
TCGA-GM-A2DC TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A3NY TCGA-GM-A3XN TCGA-GM-A4E0 
       53.52        62.33        90.84        38.20        66.38        72.03 
TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LL-A442 TCGA-LL-A5YN 
       11.84        11.57        21.24         4.08        10.95        14.70 
TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A7T0 TCGA-LQ-A4E4 TCGA-OL-A5D7 TCGA-OL-A5RV 
       14.47        11.57         3.22        27.91        46.55        34.92 
TCGA-OL-A5RW TCGA-OL-A5RZ TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A6VO TCGA-OL-A6VQ 
       36.36        22.32        33.57        31.07        28.21        19.73 
TCGA-PL-A8LX TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA10 
        0.16         3.95        16.50         6.81         8.65         7.92 
TCGA-XX-A89A TCGA-Z7-A8R5 
        9.14       100.01 

$`22Q LOSS WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SH TCGA-A1-A0SI 
        0.39         8.52        43.43        48.10        47.24        20.88 
TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04R TCGA-A2-A04T 
       31.79         7.96        19.20        18.21        82.16        73.84 
TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO 
       22.06        64.04        55.43       136.73        64.57       112.08 
TCGA-A2-A0CT TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM 
       75.25        56.81        34.55        33.76        28.77       101.72 
TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EX TCGA-A2-A0EY 
      107.61        79.76        74.40        37.05        24.72        24.16 
TCGA-A2-A0ST TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 
       99.19        44.88        44.28        17.52        17.13         8.38 
TCGA-A2-A0T5 TCGA-A2-A0YC TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL 
       17.46        32.55        14.50        18.61        19.33        48.46 
TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G1 TCGA-A2-A1G4 
       31.73        23.47        36.79        22.45        19.20        19.56 
TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
       16.47        52.47        17.19        18.15        91.92        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       20.88        39.65        32.75        49.48        38.40        34.98 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CD 
        7.30        24.39        23.21        26.96        21.14        38.30 
TCGA-A7-A0D9 TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H 
       37.45        12.72        23.61        24.26        23.74        23.80 
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-A4SA TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VX 
       14.93        12.10        10.72        11.05        10.29        10.42 
TCGA-A8-A06O TCGA-A8-A079 TCGA-A8-A07G TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S 
       13.02         9.01        18.97         9.99        10.98         7.99 
TCGA-A8-A07U TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B 
       24.99        28.04        18.05        13.02         0.99        38.01 
TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T 
       28.96        33.01         9.99        31.00         0.99        93.04 
TCGA-A8-A08X TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 
       43.00        33.01        30.97        17.95        41.98         9.99 
TCGA-A8-A09A TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09Q 
        9.99        49.05        45.07        29.98        33.07        25.02 
TCGA-A8-A09V TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0AD TCGA-AC-A23C 
       15.02        14.01        12.00        19.04        38.04         0.95 
TCGA-AC-A23E TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FG 
        2.37         2.66         1.48        38.20        40.57        36.99 
TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3OD TCGA-AC-A3TN 
       38.79        50.70         0.92         2.27        14.83         1.12 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A62V TCGA-AC-A62X 
       16.57        19.79        23.24        24.79         0.07         1.12 
TCGA-AC-A6IW TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A046 
        0.69         1.12         1.32         0.33         0.33         0.33 
TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR 
        2.96         1.78         1.71         6.51         0.16         0.33 
TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        0.33         0.33         7.96         7.59         7.17         6.28 
TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XP 
        6.02         0.33         0.33         0.33         0.33         0.30 
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-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       59.05        29.13        32.78        52.18        24.16        37.48 
TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL 
       50.86        76.77        21.37        50.24        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       108.72       106.78        96.10 
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-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-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TV 
       15.62        32.52       111.32        49.32        74.79        29.75 
TCGA-AR-A0TX TCGA-AR-A0U1 TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AL 
       64.83       101.95        85.97        61.84        51.25        48.82 
TCGA-AR-A1AO TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24M 
       43.56        37.81        76.21        63.62        62.14        96.89 
TCGA-AR-A24N TCGA-AR-A24Q TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A251 
       78.51       101.52        76.01        53.36        85.35        78.48 
TCGA-AR-A254 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LL TCGA-AR-A2LM 
       72.76       128.65        20.25        62.86         7.36        40.04 
TCGA-AR-A2LN TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QQ TCGA-B6-A0I1 
       38.17        40.54        20.38        54.74        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-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IP TCGA-B6-A0RH 
       65.72       176.98        18.77       126.12       110.93       189.01 
TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU 
      234.28        78.02       140.48       100.70        89.46       131.21 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WZ TCGA-B6-A0X0 
      157.41        97.48       188.68        79.63       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-A2IU TCGA-B6-A401 TCGA-B6-A402 TCGA-BH-A0AV TCGA-BH-A0AW 
       73.51       170.17        85.35        54.28        38.79        20.45 
TCGA-BH-A0AZ TCGA-BH-A0B2 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BG TCGA-BH-A0BM 
       28.50        40.83        32.02        18.21        24.85        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BW TCGA-BH-A0C0 
       35.67        48.69        27.19        53.95        11.67        41.75 
TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DK 
       44.02        45.83        31.17        23.44        22.13        13.91 
TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       48.23        17.26        15.65         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-A0EE TCGA-BH-A0EI TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       32.65        31.00        24.43        15.16        37.78        35.51 
TCGA-BH-A0H6 TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HW 
       24.56        20.38         5.85         2.50        13.61        51.32 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A18G TCGA-BH-A18N TCGA-BH-A18P 
       50.79         5.59        24.95         2.01        37.74        30.28 
TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO 
       55.63        37.55        66.05        51.39        69.93        91.99 
TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1FB 
       12.00        55.69        25.81        31.53        97.48       120.62 
TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FR TCGA-BH-A1FU 
       74.73       122.89        36.92        63.35       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-A12N TCGA-C8-A12O 
       20.12       109.28         8.94        11.93        11.77        12.66 
TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 
       11.77         0.07        12.66        12.66        12.66         3.12 
TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF 
        1.78         0.69         0.62         3.85        12.33        10.92 
TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y 
       11.34         0.16         0.30         0.23         0.36         0.43 
TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 
        9.67         0.03         0.03         0.99         0.03         0.23 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA 
       13.25        20.58        13.97        19.20        17.49        16.50 
TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JK 
       15.78        18.90        12.03        14.01        18.97        20.12 
TCGA-D8-A1JL TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X6 TCGA-D8-A1X7 
       20.09        12.20        13.32        14.70        17.79        16.73 
TCGA-D8-A1X8 TCGA-D8-A1XC TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XL 
       25.74         2.66        15.22        14.73        21.83        19.92 
TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ 
       16.41        16.31        15.16        12.66        16.54        15.32 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27K TCGA-D8-A27M 
       17.42        16.04        13.45        13.05         9.44        13.48 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z6 
        4.80         0.76        10.09        12.53        12.26        18.51 
TCGA-D8-A4Z1 TCGA-E2-A108 TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A14N TCGA-E2-A14P 
        7.33        27.52        37.51        28.44        47.15        40.96 
TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A152 TCGA-E2-A154 
       33.17        43.33        31.96        28.60        27.12        19.43 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15D TCGA-E2-A15J TCGA-E2-A15K 
       21.04        23.87        14.79        17.29        19.40         9.04 
TCGA-E2-A15L TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A1B0 TCGA-E2-A1B4 TCGA-E2-A1B6 
       20.58        17.06        14.07        53.62        29.95        28.50 
TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IG TCGA-E2-A1IK TCGA-E2-A1IU TCGA-E2-A1L6 
       16.47        38.30        32.78        22.65        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LG TCGA-E2-A1LH 
       27.42        19.66        24.59        40.47        18.87       106.75 
TCGA-E2-A1LI TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E9-A1N4 
      102.61        43.04         5.52        15.72        30.61        19.20 
TCGA-E9-A1N6 TCGA-E9-A1NC TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R4 TCGA-E9-A1R5 
       13.48        39.55        11.90        14.30         6.12         1.38 
TCGA-E9-A1R7 TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A22B 
       21.21        34.59        34.13         0.79        12.53        22.75 
TCGA-E9-A22G TCGA-E9-A243 TCGA-E9-A245 TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT 
       23.51        17.06         0.85         0.72        17.75         0.76 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54X TCGA-E9-A5UP TCGA-EW-A1IW TCGA-EW-A1IY 
       18.41         0.62        12.33        14.40        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        43.73        69.30        13.55        18.12 
TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A50Y 
        6.67         4.60         8.75         9.53        11.44         7.59 
TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y 
       17.06        15.32        14.79         2.63         3.88         4.14 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-MS-A51U 
        4.50         4.50         5.59         6.21         7.36         2.79 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RX 
        2.10        12.66        31.99        58.62        27.65        16.87 
TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66N 
       24.72        20.38        26.70        23.47        65.62        26.04 
TCGA-OL-A66O TCGA-OL-A66P TCGA-PL-A8LV TCGA-PL-A8LY TCGA-S3-AA0Z TCGA-S3-AA11 
        7.23        14.07         0.23         0.26        10.59         5.56 
TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-W8-A86G TCGA-XX-A899 
        8.52         7.17         6.87         3.91         5.29         9.60 
TCGA-Z7-A8R6 
      105.04 

  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 
             22.59              22.32 
[1] "0.0 - 211.6 (22.6)" "0.0 - 234.3 (22.3)"
[1] "hr=" "1.4"
D79V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  22Q LOSS MUTATED        34       35        2        1       143       113
  22Q LOSS WILD-TYPE      49       45        7        4       199       121
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  22Q LOSS MUTATED           1         64         12         35        7
  22Q LOSS WILD-TYPE         1         78         17         28       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                 49
  STAGE IA                 35                 45
  STAGE IB                  2                  7
  STAGE II                  1                  4
  STAGE IIA               143                199
  STAGE IIB               113                121
  STAGE III                 1                  1
  STAGE IIIA               64                 78
  STAGE IIIB               12                 17
  STAGE IIIC               35                 28
  STAGE IV                  7                 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   111 275  50  17
  22Q LOSS WILD-TYPE 154 319  74  22
D79V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1              111                154
  T2              275                319
  T3               50                 74
  T4               17                 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
  22Q LOSS MUTATED   205 153  51  41
  22Q LOSS WILD-TYPE 276 186  62  33
D79V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0              205                276
  N1              153                186
  N2               51                 62
  N3               41                 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
  22Q LOSS MUTATED          1 385   8  60
  22Q LOSS WILD-TYPE        4 469  11  87
D79V6, multiclass
          clus
vv         22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CM0 (I+)                1                  4
  M0                    385                469
  M1                      8                 11
  MX                     60                 87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED   448   6
  22Q LOSS WILD-TYPE 566   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED    448    6
  22Q LOSS WILD-TYPE  566    5
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE              448                566
  MALE                  6                  5
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  22Q LOSS MUTATED                            0                           344
  22Q LOSS WILD-TYPE                          1                           410
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  22Q LOSS MUTATED                               78                   2
  22Q LOSS WILD-TYPE                             97                   4
                    vv
clus                 MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  22Q LOSS MUTATED                                 17                  1
  22Q LOSS WILD-TYPE                               12                 14
                    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                 344                410
  INFILTRATING LOBULAR CARCINOMA                 78                 97
  MEDULLARY CARCINOMA                             2                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)               17                 12
  MUCINOUS CARCINOMA                              1                 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"
D79V9, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED   148 306
  22Q LOSS WILD-TYPE 134 437
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED    148  306
  22Q LOSS WILD-TYPE  134  437
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO               148                134
  YES              306                437
[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                          68   325
  22Q LOSS WILD-TYPE                        90   392
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                      68                 90
  WHITE                                         325                392
[1] 4 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    15 361
  22Q LOSS WILD-TYPE  21 465
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     15  361
  22Q LOSS WILD-TYPE   21  465
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   15                 21
  NOT HISPANIC OR LATINO              361                465
[1] 2 2
[1] FALSE

Clustering(80) Variable = XQ LOSS MUTATION ANALYSIS
D80V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED   145  22
  XQ LOSS WILD-TYPE 741  97
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              167               838 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               22                97 
$`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        21.90        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        53.06        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-AC-A8OQ TCGA-AN-A041 TCGA-AN-A0AJ 
       17.03        38.04        38.20         1.12         0.23         8.02 
TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0FD TCGA-AN-A0FJ TCGA-AN-A0FV 
        7.36         0.16         0.33         6.44         7.96         0.33 
TCGA-AN-A0XL TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AO-A03R TCGA-AO-A0J3 TCGA-AO-A0JA 
        0.33         0.33         0.33        68.75        21.40        21.53 
TCGA-AO-A0JE TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A124 TCGA-AO-A1KQ TCGA-AQ-A1H2 
       76.77        50.24        62.04       102.58        61.87        15.62 
TCGA-AQ-A54N TCGA-AR-A0TR TCGA-AR-A0TV TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U2 
        2.56         5.26        29.75        55.86        76.14        83.87 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A251 
      114.02        85.97        75.55        20.22       109.58        78.48 
TCGA-AR-A256 TCGA-AR-A2LO TCGA-AR-A2LR TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IK 
       93.83        39.39        20.38        65.72       146.50        18.77 
TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RL TCGA-B6-A0WX TCGA-B6-A1KN TCGA-BH-A0B0 
      140.88        68.45        81.17        21.47       139.17        46.95 
TCGA-BH-A0BV TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DX TCGA-BH-A0GZ TCGA-BH-A0HA 
       49.94        23.44        38.01        47.41        10.78        52.96 
TCGA-BH-A0HW TCGA-BH-A0W3 TCGA-BH-A1ES TCGA-BH-A1EY TCGA-BH-A1F8 TCGA-BH-A1FD 
       51.32        23.93       113.82        17.69        24.66        33.17 
TCGA-BH-A1FM TCGA-BH-A209 TCGA-BH-A42T TCGA-C8-A12Q TCGA-C8-A12X TCGA-C8-A135 
       45.63       130.16         0.99         0.07        12.66         0.62 
TCGA-C8-A1HF TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A26V TCGA-C8-A26W TCGA-D8-A13Y 
       10.92         0.16        10.42         0.30         0.23        11.90 
TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JI TCGA-D8-A1JJ 
       19.20        17.49        16.50        18.71        18.97        20.09 
TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JP TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XJ 
       20.09        19.40        21.01        23.90        27.58        21.83 
TCGA-D8-A1XO TCGA-D8-A1Y3 TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27T TCGA-E2-A152 
        7.96        14.14        16.04        13.05        13.08        27.12 
TCGA-E2-A155 TCGA-E2-A158 TCGA-E2-A15H TCGA-E2-A15K TCGA-E2-A15P TCGA-E2-A15S 
       21.04        14.79        12.92         9.04        19.56        14.07 
TCGA-E2-A1IE TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LH TCGA-E2-A576 TCGA-E9-A1N4 
       38.30        27.42        39.62       106.75        19.00        19.20 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1NF TCGA-E9-A1R4 
       12.00        13.12        36.56        39.55        20.05         6.12 
TCGA-E9-A1RG TCGA-E9-A22G TCGA-E9-A247 TCGA-E9-A5UO TCGA-EW-A1J1 TCGA-EW-A1J6 
       21.27        23.51        27.22        13.81        18.90        28.77 
TCGA-EW-A1OW TCGA-EW-A1OZ TCGA-EW-A1PA TCGA-EW-A1PD TCGA-GM-A2DH TCGA-GM-A3XL 
       22.82        40.41        18.90        13.94        42.28        69.30 
TCGA-JL-A3YX TCGA-LL-A6FR TCGA-LL-A7T0 TCGA-LQ-A4E4 TCGA-OL-A5DA TCGA-OL-A5RW 
       11.57         3.88         3.22        27.91        58.62        36.36 
TCGA-OL-A5RZ TCGA-PL-A8LX TCGA-S3-A6ZH TCGA-S3-AA14 TCGA-XX-A89A 
       22.32         0.16         8.65         7.17         9.14 

$`XQ LOSS WILD-TYPE`
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        0.39         8.52        14.37        43.43        48.10        14.27 
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-A04T TCGA-A2-A04V 
       18.21       104.81        18.02        41.95        73.84        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       136.73        64.57        24.79 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CU TCGA-A2-A0CV 
      112.08        92.48        88.60       107.93         5.19        63.45 
TCGA-A2-A0CX TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP 
       56.81        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-A0SW 
       29.75        24.72        24.16        99.19        54.64        44.88 
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-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-A1FW TCGA-A2-A1FX 
       48.46        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-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-A3XU TCGA-A2-A3XV TCGA-A2-A3XW 
       20.88        39.65        33.93        29.98        32.75        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        24.39 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CG 
       21.30        23.21        26.96        21.14        38.30        34.29 
TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F 
       35.47        37.45        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-A3J0 TCGA-A7-A3RF 
       21.73        20.61        22.32        11.34        10.29        13.41 
TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A5ZV 
       14.70        11.97        13.74        14.50        21.17        12.10 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A06P 
       10.72        11.05        10.29        10.42        13.02        13.02 
TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 
        1.02        17.98        31.00         1.02        53.98         9.01 
TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J 
       43.00        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        24.99 
TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B 
        9.99        28.04        18.05        13.02         0.99        38.01 
TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08R 
       28.96        33.01        19.96        37.05        31.00         0.99 
TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 
       33.01        93.04        43.00        40.01        33.01        30.97 
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-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09Q 
       50.04        49.05        45.07        29.98        33.07        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-AC-A23C 
       19.04        13.02        21.04         0.99        13.02         0.95 
TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2FB 
        2.37        10.85         2.66         1.48        38.53        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        22.19 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS 
        1.12        16.57        19.79        23.24        24.79         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-A6NO TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A046 
        1.68         1.74         1.32         0.33         0.33         0.33 
TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AL TCGA-AN-A0AS 
        0.62         2.96         1.78         1.71         6.51         0.33 
TCGA-AN-A0AT TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        0.33         4.64         7.00         7.59         7.17         6.28 
TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XN 
        6.02         0.36         0.33         0.33         0.33         0.33 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XV TCGA-AN-A0XW 
       12.33         0.30         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-A03T 
       80.28        47.84        66.77        81.63        84.69        47.87 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       59.05        29.13        32.78        52.18        24.16        37.48 
TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD 
       20.32        22.36        53.03        50.70        50.86        72.00 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 
       21.37        26.24        55.33        71.80        99.25       108.72 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
      106.78        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-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-A1H3 TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS 
       32.52        32.91         9.99       111.32        49.32        74.79 
TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A1AI 
       86.66        98.93        64.83        65.36       101.95        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-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
       39.98        43.07        17.23        37.81        76.21        61.28 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       63.62        62.14        50.89        73.02        96.89        78.51 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24U 
       84.20         0.85       101.52        87.22        76.01        53.36 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 
       85.35        50.96        83.77        79.00        56.15        73.18 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK 
       72.76        58.92       128.65        20.25        62.86        42.87 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN 
        7.36        40.04        38.17        40.54        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-A0IH TCGA-B6-A0IJ TCGA-B6-A0IM 
      220.90       129.57        50.70       112.37       176.98       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-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-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
       17.98       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-A2IU 
       68.94        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       103.63        55.00        24.53 
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-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-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 
       45.57        11.67        49.05        41.75        44.02        48.13 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL 
       42.90        45.83        31.17        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-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-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-A0HU TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A0W5 
       12.89        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-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-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-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-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-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-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V 
       57.83        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-A12U 
       11.93        11.77        11.77        12.66        11.77        12.66 
TCGA-C8-A12V TCGA-C8-A12W 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-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK 
        3.85         3.75        12.33        11.34        11.34        12.03 
TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 
        2.30         3.25         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-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 
        0.23        20.88        13.25        20.58        13.97        14.17 
TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE 
       13.48        21.14        14.17        15.78        18.15        18.90 
TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JK TCGA-D8-A1JN TCGA-D8-A1JS 
       12.03        12.03        14.01        20.12        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-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XK 
       18.15         2.66        17.16        15.22        14.73        14.50 
TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT 
       19.92        17.69        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-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-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27V 
       16.41        13.48         4.80         0.76        10.09        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-A14Z TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A156 
       28.60        17.03        25.41        23.24        19.43        23.87 
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-A15I TCGA-E2-A15J TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O 
       18.21        17.42        19.40        20.58         7.73        13.02 
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-A1IF TCGA-E2-A1IG 
       32.35        28.50        16.47        17.10        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-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB 
       20.98        11.08        54.18        19.66        24.59        40.47 
TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 
       28.90        18.87       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        30.61        34.92        19.89 
TCGA-E2-A9RU TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG 
        9.21        36.82        13.48        12.59        35.77        21.57 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R5 
        9.86        11.90        14.30         0.62         2.10         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-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-A22H 
       12.53        13.32        39.09        22.75        12.89        24.10 
TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A 
       17.06         0.69         0.85         1.94         0.95        24.56 
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-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UP 
       15.72        12.33         0.23        14.70         0.26        14.40 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J2 
       15.39        12.20        39.72         8.48        18.21        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1P0 
       16.57        15.68        25.94        29.95        29.85        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-A1PB TCGA-EW-A1PC TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
        7.86        19.99         6.15        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-A2DI 
      194.27        53.13        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-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX 
       38.20        43.73        66.38        72.03        13.55        18.12 
TCGA-JL-A3YW TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF 
       11.84        21.24         6.67         4.08         4.60         8.75 
TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM 
        9.53        11.44        10.95         7.59        17.06        15.32 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Y 
       14.70        14.47        14.79        11.57         2.63         4.14 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-MS-A51U 
        4.50         4.50         5.59         6.21         7.36         2.79 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5RU TCGA-OL-A5RV 
        2.10        12.66        46.55        31.99        27.65        34.92 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J 
       16.87        24.72        20.38        26.70        23.47        65.62 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO 
       33.57        31.07        26.04         7.23        14.07        28.21 
TCGA-OL-A6VQ TCGA-PL-A8LV TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG 
       19.73         0.23         0.26         3.95        16.50         6.81 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA15 TCGA-S3-AA17 
       10.59         7.92         5.56         8.52         6.87         3.91 
TCGA-W8-A86G TCGA-XX-A899 TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        5.29         9.60       100.01       105.04 

  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 
            21.27             23.16 
[1] "0.1 - 146.5 (21.3)" "0.0 - 234.3 (23.2)"
[1] "hr=" "1.2"
D80V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XQ LOSS MUTATED        13       13        0        0        63        43
  XQ LOSS WILD-TYPE      70       67        9        5       279       191
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XQ LOSS MUTATED           0         20          4          6        5
  XQ LOSS WILD-TYPE         2        122         25         57       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                 13                70
  STAGE IA                13                67
  STAGE IB                 0                 9
  STAGE II                 0                 5
  STAGE IIA               63               279
  STAGE IIB               43               191
  STAGE III                0                 2
  STAGE IIIA              20               122
  STAGE IIIB               4                25
  STAGE IIIC               6                57
  STAGE IV                 5                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    36 112  14   8
  XQ LOSS WILD-TYPE 229 482 110  31
D80V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1              36               229
  T2             112               482
  T3              14               110
  T4               8                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
  XQ LOSS MUTATED    83  61  17   9
  XQ LOSS WILD-TYPE 398 278  96  65
D80V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0              83               398
  N1              61               278
  N2              17                96
  N3               9                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
  XQ LOSS MUTATED          1 147   6  17
  XQ LOSS WILD-TYPE        4 707  13 130
D80V6, multiclass
          clus
vv         XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CM0 (I+)               1                 4
  M0                   147               707
  M1                     6                13
  MX                    17               130
[1] 4 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   168   3
  XQ LOSS WILD-TYPE 846   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED    168    3
  XQ LOSS WILD-TYPE  846    8
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE             168               846
  MALE                 3                 8
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  XQ LOSS MUTATED                            0                           138
  XQ LOSS WILD-TYPE                          1                           616
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  XQ LOSS MUTATED                               16                   1
  XQ LOSS WILD-TYPE                            159                   5
                   vv
clus                MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA
  XQ LOSS MUTATED                                  7                  2
  XQ LOSS WILD-TYPE                               22                 13
                   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                138               616
  INFILTRATING LOBULAR CARCINOMA                16               159
  MEDULLARY CARCINOMA                            1                 5
  MIXED HISTOLOGY (PLEASE SPECIFY)               7                22
  MUCINOUS CARCINOMA                             2                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"
D80V9, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    48 123
  XQ LOSS WILD-TYPE 234 620
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     48  123
  XQ LOSS WILD-TYPE  234  620
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               48               234
  YES             123               620
[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                          33   110
  XQ LOSS WILD-TYPE                       125   607
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                     33               125
  WHITE                                        110               607
[1] 4 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     6 140
  XQ LOSS WILD-TYPE  30 686
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      6  140
  XQ LOSS WILD-TYPE   30  686
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                30
  NOT HISPANIC OR LATINO             140               686
[1] 2 2
[1] FALSE
