[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"                    "-OPAGGREGRATED_CLUSTER"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"                 "AGGREGRATED_CLUSTER"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/BRCA-TP/10005900/BRCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/BRCA-TP/10667987/BRCA-TP.mergedcluster.txt"

nPatients in clinical file=1017, in cluster file=1065, common to both=1013
[1]   12 1013
[1] "MRNA_CNMF"
[1] 3
  1   2   3   4   5   6   7   8 
 21  39 121 101 110  74  20  40 
  1   2   3   4   5   6   7   8 
 21  39 121 101 110  74  20  40 
[1] "MRNA_CHIERARCHICAL"
[1] 3
  1   2   3   4   5 
102 156 118  92  58 
  1   2   3   4   5 
102 156 118  92  58 
[1] "CN_CNMF"
[1] 3
  1   2   3   4   5 
375 234  92 253  41 
  1   2   3   4   5 
375 234  92 253  41 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3   4   5 
127 193 169  85 116 
  1   2   3   4   5 
127 193 169  85 116 
[1] "RPPA_CNMF"
[1] 3
  1   2   3 
154 135 120 
  1   2   3 
154 135 120 
[1] "RPPA_CHIERARCHICAL"
[1] 3
  1   2   3   4   5 
 64 111  93 109  32 
  1   2   3   4   5 
 64 111  93 109  32 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3   4   5   6   7 
186 141 224 158 237  48  16 
  1   2   3   4   5   6   7 
186 141 224 158 237  48  16 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5   6 
174 229 194 176 181  56 
  1   2   3   4   5   6 
174 229 194 176 181  56 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
281 425 287 
  1   2   3 
281 425 287 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5 
155 182 401 129 126 
  1   2   3   4   5 
155 182 401 129 126 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3 
250 227 194 
  1   2   3 
250 227 194 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3   4   5   6 
118  66 188 123 110  66 
  1   2   3   4   5   6 
118  66 188 123 110  66 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "HISTOLOGICALTYPE"                      
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "NUMBER.OF.LYMPH.NODES"                 
[18] "RACE"                                  
[19] "ETHNICITY"                             
[20] "BATCHNUMBER"                           

Input Data has 20 rows and 1013 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
         259          437         1321         1463          434         1437 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
         635          416           NA          242         1196          852 
TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R 
         584          554         3188           NA         1276         2499 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
        2246          671           NA         1948         1686         1099 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
        3820         1964           NA         3409         2813         2695 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW 
        3283         2298         2289           NA         1930         1948 
TCGA-A2-A0CX TCGA-A2-A0CY TCGA-A2-A0CZ TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 
        1728         1673         1616          643         1051         1027 
TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP 
         875          767         3094         2718         2442         3273 
TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV 
        2426         2263         1127         1066         1043          968 
TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV 
         905          752          735         3017         1662           NA 
TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 
          NA         1534         1347          533          521           NA 
TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC 
         569          624          531          575          631          990 
TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI 
         769          554          469          666          659          441 
TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV 
         566          588          445          965           NA          714 
TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 
         528         1119          683          616          584          595 
TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D 
         501         1596         3276          496          523          552 
TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT 
        2796          322          635         1206           NA         2525 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ 
          NA          428         1505         1168         1064          973 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 
        1167          222          274          268          271          365 
TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH 
         205          104         1165         1074         1043         1079 
TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E 
         931         1139         1085         1007          965          326 
TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G 
         387          718          899          954          738          722 
TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ 
         724          661          627          679          345          322 
TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA 
         313          343          408          447          364          454 
TCGA-A7-A4SB TCGA-A7-A4SC TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D 
         418          446          441          644          545          448 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX 
         368          326          336          313          285          317 
TCGA-A7-A6VY TCGA-A8-A06N TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R 
         266           NA          396          396           31          547 
TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 
        1249           NA           NA          791           31          518 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07C TCGA-A8-A07E TCGA-A8-A07F 
        1642          274         1004          580          608          577 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P 
         577          426          365          518          304          334 
TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A081 
         273          243          303          304          853           NA 
TCGA-A8-A082 TCGA-A8-A083 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A 
         549           NA          458         1124          396           30 
TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08H TCGA-A8-A08I 
         702          608          549          607           NA          365 
TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S 
          NA           NA          943          943           30          580 
TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A090 TCGA-A8-A091 TCGA-A8-A092 
        2830         1034         1217           NA          580          487 
TCGA-A8-A093 TCGA-A8-A094 TCGA-A8-A095 TCGA-A8-A096 TCGA-A8-A097 TCGA-A8-A099 
         546           NA         1277           NA          365          304 
TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09G 
         304          365           31          396          943           NA 
TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R 
        1006          912          457           31          761          273 
TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A09Z TCGA-A8-A0A1 
         579          457           30           NA           NA          365 
TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB 
         579          396          640           30          396          518 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 
        1157           29           72          330           81           45 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
        1172         1162         1234         1686         1125         1180 
TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB 
          NA         1542           31           28           69           30 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 
          21          451          286           34           55           51 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y 
          47           40           47            2           34           55 
TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A03Y 
          36           21           13           53           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-A0G0 TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO 
          10           10           16           10           10          375 
TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV 
           9           10           10           10           10          162 
TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P 
         170         2442         1455         2031           NA         2576 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 
        2091         1456           NA          886          997          651 
TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 
         537          735         1140          618          680         1613 
TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF 
         655         1542         1547         2190         2335          650 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 
         798         1172         1887         1683         2184         3120 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B 
        3019         2850         2877         2923         2755         2359 
TCGA-AO-A12C TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
        1994         1948         1743         1471         1266          863 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT 
         448         2513         1882         2141           16          541 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 
         754          819         3957           NA          475          402 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
          78          665          304         2521         1500           NA 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TU TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX 
        1138         1730          360          905          739         1972 
TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 
          NA         2316         1988         2134           NA         2317 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL 
        1684         2298         1881         1605         1559         1485 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR 
        1903         1330         1325         1216         1310           NA 
TCGA-AR-A1AS TCGA-AR-A1AT TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX 
        1242           NA         1409         1295         1072         1103 
TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
         615         3333         1548         2221         1991         2074 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T 
        1998           26         2009         1746         1888         1620 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 
        1623         1648         1550         1465         1574         1708 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE 
        1374         1236         1212         1059           NA         3913 
TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
          NA         1304          224         1218          520          633 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
         516          620         1665          488          622           NA 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I6 TCGA-B6-A0I8 TCGA-B6-A0I9 
          NA         4361         4550           NA           NA           NA 
TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH 
        6719           NA           NA           NA           NA           NA 
TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP 
        5383           NA         3836           NA         3350         3374 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL 
        4285         6435         2082         5749         7126           NA 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS 
          NA         5261         4929           NA           NA           NA 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV 
        2721         3991         4788           NA         5739           NA 
TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 
         547           NA           NA         3941           NA         5672 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI 
          NA           NA           NA         1326         3088         2236 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B 
        4233         5176         2596         1651         1519         2521 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ 
        1673          746         1180          622          777          867 
TCGA-BH-A0B0 TCGA-BH-A0B1 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 
        1428         1148         1242         1203         1191         1471 
TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B8 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC 
        1732         1733         1569         1572         1132          974 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM 
         554          782          756          660         1340         1876 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT 
        1085         1481          827         1633         1641         1386 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 
        1519          355         1492         1270         1339         1464 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI 
        1305         1394          948          713         1156          673 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS 
         423         1467          525          476           98           78 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 
        1170         1374         1442          495          134          477 
TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB 
         435          293         1363         1405           NA          745 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
         943          743          923          328          461         1149 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB 
        1080          747          702         1247         1611          806 
TCGA-BH-A0HF TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HL TCGA-BH-A0HN TCGA-BH-A0HO 
         727          620          178           72          516           76 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY 
         414         1121          392         1561          829         1545 
TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA 
         170          728          759         1288         1363          701 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18H TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K 
         268           61           NA          220           NA           NA 
TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 
         210           22           NA           NA           NA           NA 
TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V 
         324          196          612           30         3324          272 
TCGA-C8-A12K TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P 
          NA          363          358          358          385          358 
TCGA-C8-A12Q TCGA-C8-A12T TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X 
           2           NA          385          385          385          385 
TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A133 
          NA           NA           95           54           44           NA 
TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF 
          21           19          117          114          375          332 
TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM 
         345          345            5          366          317           70 
TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y 
          99           NA            9            7           11           13 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A 
         252          294            1            1            1          371 
TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 
          30            1            7          362          635          403 
TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 
         626          425          431          410          643          584 
TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD 
         431          532          502          569          480          552 
TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ 
         575          366          366          426          577          611 
TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS 
         612          611          590          620          639          371 
TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 
         405          447          565          541          509          783 
TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF 
         727          839          552           81          522          463 
TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO 
         448          664          441          606          538          242 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV 
         499          482          496          193          395          461 
TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 
         385          503          466          472          116          433 
TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I 
         430          530          488          409          397          439 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R 
         287          499          410          146           23          307 
TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 
         398          381          373          441          563          223 
TCGA-E2-A105 TCGA-E2-A106 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A 
        1308         1807         1047          837         1417         1229 
TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O 
        1141         1220          865          878         1434         1359 
TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U 
        1246         1163         1174         1009         1013         1318 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 
        1042          974          972          870          518          773 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 
         825          707          591          640          726          450 
TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F 
         762          710          694          526          630          658 
TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
         554          393          530          590          275          626 
TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
         235          396          595          519          428          456 
TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
        2329         1631         1613          911          984          867 
TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
         501          520         1165         1138          997         1026 
TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO 
        1025          865          689          118          675          638 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA 
         337         1648          834         1205          598          748 
TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK 
        1231           NA          574         3247         3121           NA 
TCGA-E2-A1LL TCGA-E2-A1LS TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z 
        1309          470          515          168          478          219 
TCGA-E2-A570 TCGA-E2-A572 TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N3 TCGA-E9-A1N4 
         549          831          677          605           NA          584 
TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC 
        1120          410          365          399         1112         1203 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI 
         383         1088          610          656           NA          300 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 
         362          435           19           64          186           42 
TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD 
          84          645          976          633         1224           20 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 
        1054          200          647         1052         1084         1038 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D 
          24          381          405         1189          692           NA 
TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A245 
         392          715          733          519           21           26 
TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS 
         828           59           29          382           22          540 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X 
          23          793          560           19          478           NA 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE 
           7           12            8            7           NA          468 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 
         371         1208          258          554          575          403 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX 
         504          477          875          789          694          911 
TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 
         908         1229         1251         1210         1611          907 
TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB 
         703          562          915           NA          575          608 
TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH 
         187          424          320          439         1051          607 
TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 
        1673         1604          788          672          647          532 
TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
         309          322          225         3342           NA         5909 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI 
        1616         1628         1309         1299         1286         1883 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
        1896         2763         2331         2352         1623         3361 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV 
        1162          982         2108         1641         1753          412 
TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 
         551          360          352          252          203          140 
TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM 
          20           91          109          210          169          143 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y 
         111           97           99           80          118          126 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LQ-A4E4 
         137          137          170           98          189          484 
TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA 
          85           64          385         1416          229         1357 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
         841          733          797          513          429          313 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L 
         298          449          721         1658         1031          945 
TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-S3-A6ZG TCGA-W8-A86G 
         554          220          135          207          161 
Variable 1:'AGE':	nDistinctValues=65,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=114,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=662,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=16,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=26,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=29,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'BATCH.NUMBER':	nDistinctValues=39,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "NEOPLASM.DISEASESTAGE"                 
 [3] "PATHOLOGY.T.STAGE"                     
 [4] "PATHOLOGY.N.STAGE"                     
 [5] "PATHOLOGY.M.STAGE"                     
 [6] "GENDER"                                
 [7] "HISTOLOGICAL.TYPE"                     
 [8] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [9] "NUMBER.OF.LYMPH.NODES"                 
[10] "RACE"                                  
[11] "ETHNICITY"                             
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 1013 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 
265 591 118  36 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
265 591 118  36 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
265 591 118  36 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
265 591 118  36 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
478 336 112  70 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
478 336 112  70 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2  N3 
478 336 112  70 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
478 336 112  70 
PATHOLOGY.M.STAGE, nv=4, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=7, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=29, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = MRNA_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 17  3
  subtype2 36  3
  subtype3 98 18
  subtype4 87 13
  subtype5 97 11
  subtype6 55 15
  subtype7 16  3
  subtype8 33  6
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
      20       39      116      100      108       70       19       39 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
       3        3       18       13       11       15        3        6 
$subtype1
TCGA-A1-A0SD TCGA-A1-A0SH TCGA-A1-A0SM TCGA-A2-A0SV TCGA-A8-A06P TCGA-A8-A07G 
       14.37        47.24         7.96        27.12        13.02        18.97 
TCGA-A8-A07I TCGA-A8-A08Z TCGA-A8-A097 TCGA-AN-A03X TCGA-AN-A0AS TCGA-AN-A0XN 
       14.01        40.01        12.00         0.33         0.33         0.33 
TCGA-AN-A0XW TCGA-BH-A0DZ TCGA-BH-A0H6 TCGA-BH-A18J TCGA-BH-A1EO TCGA-C8-A12O 
        5.59        16.27        24.56        20.12        91.99        12.66 
TCGA-D8-A141 TCGA-E2-A153 
       20.58        23.24 

$subtype2
TCGA-A1-A0SE TCGA-A2-A0CP TCGA-A2-A0CV TCGA-A2-A0CZ TCGA-A2-A0EO TCGA-A2-A0ES 
       43.43        92.48        63.45        53.13        80.28        37.05 
TCGA-A2-A0EX TCGA-A2-A0SU TCGA-A2-A0T7 TCGA-A2-A0YL TCGA-A8-A08O TCGA-A8-A09A 
       24.72        54.64        20.75        14.63        31.00         9.99 
TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A0JA TCGA-AO-A0JB 
       13.02        21.04        80.28        47.84        21.53        50.70 
TCGA-AO-A12C TCGA-AO-A12E TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AU TCGA-B6-A0IE 
       65.56        57.30        43.73        43.56        46.32        65.72 
TCGA-B6-A0RQ TCGA-B6-A0RV TCGA-B6-A0WY TCGA-BH-A0AZ TCGA-BH-A0B1 TCGA-BH-A0DG 
      140.48       157.41       113.79        28.50        37.74        23.44 
TCGA-BH-A0DI TCGA-BH-A0E9 TCGA-BH-A0EI TCGA-C8-A132 TCGA-C8-A1HI TCGA-E2-A14Q 
       22.13        46.19        24.43         1.45        11.34        38.24 
TCGA-E2-A15E TCGA-E2-A15H TCGA-E2-A1B1 
       20.71        12.92        53.03 

$subtype3
TCGA-A1-A0SJ TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CT TCGA-A2-A0CU 
       13.68        82.16        63.12        36.13        75.25         5.19 
TCGA-A2-A0CW TCGA-A2-A0D4 TCGA-A2-A0ER TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0T3 
       64.04        25.22        74.40        35.05        34.29        18.71 
TCGA-A2-A0YH TCGA-A2-A0YT TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A13F 
       21.67        23.77        38.30        30.61        37.45        12.72 
TCGA-A8-A06O TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07L 
       13.02        29.03        31.00         1.02         9.01        17.03 
TCGA-A8-A07P TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A086 
       10.98         9.99        28.04        18.05        36.95        13.02 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A091 TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09K 
       18.05        19.96        19.07        13.02        31.00        29.98 
TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A04A 
       15.02        25.02         8.98         0.23         0.62         2.96 
TCGA-AN-A0AK TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ 
        7.36         6.44         4.64         0.36         0.33         0.33 
TCGA-AN-A0XT TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03V TCGA-AO-A0J3 
        0.33        84.69        68.75        47.87        29.13        21.40 
TCGA-AO-A0J7 TCGA-AO-A0JI TCGA-AO-A126 TCGA-AO-A12H TCGA-AQ-A04H TCGA-AR-A0TQ 
       20.32        38.53        93.70        28.37        24.79        49.32 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U2 TCGA-B6-A0IM 
       29.75        24.30        55.86        76.14        83.87       126.12 
TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0RG TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0WT 
       84.59       110.14        68.45        81.17        78.02       188.68 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0X5 TCGA-BH-A0AU TCGA-BH-A0B4 TCGA-BH-A0B8 
       79.63        17.98        68.94        24.53        39.16        51.58 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DH TCGA-BH-A0DK TCGA-BH-A0E2 TCGA-BH-A0GZ 
       42.90        45.83        38.01        13.91        14.30        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H7 TCGA-BH-A0HB TCGA-BH-A0HW TCGA-BH-A0HX 
       15.16        37.78        23.08        26.50        51.32        27.25 
TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18R TCGA-BH-A1ES TCGA-C8-A12M TCGA-C8-A12U 
       26.66        37.74        37.55       113.82        11.77        12.66 
TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A1HG TCGA-C8-A1HN TCGA-D8-A140 TCGA-E2-A105 
       12.66        12.66        11.34         3.25        13.25        43.00 
TCGA-E2-A106 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A14O TCGA-E2-A14S TCGA-E2-A14T 
       59.41        46.59        40.41        44.68        33.17        33.30 
TCGA-E2-A14W TCGA-E2-A155 TCGA-E2-A15A TCGA-E2-A15F TCGA-E2-A15O TCGA-E2-A15R 
       32.02        21.04        23.34        21.63        13.02        17.06 
TCGA-E2-A15S TCGA-E2-A15T 
       14.07        14.99 

$subtype4
TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04T 
       31.79        28.01        19.20        18.02        41.95        73.84 
TCGA-A2-A04U TCGA-A2-A0CM TCGA-A2-A0CY TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0ST 
       22.06        24.79        55.00        21.14        33.76        99.19 
TCGA-A2-A0SX TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0YE TCGA-A2-A0YJ TCGA-A2-A0YM 
       50.43        17.52         8.38        18.21        18.61        31.73 
TCGA-A7-A0CE TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A8-A07C TCGA-A8-A07O 
       35.31        35.67        31.73        10.72        19.07         9.99 
TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A08R TCGA-A8-A08X TCGA-AN-A04D TCGA-AN-A0AL 
        8.98         9.96         0.99        33.99         1.71         6.51 
TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FX 
        0.16         0.33         0.33         7.96         7.59         0.33 
TCGA-AN-A0G0 TCGA-AN-A0XU TCGA-AO-A03U TCGA-AO-A0J4 TCGA-AO-A0J6 TCGA-AO-A0JL 
        0.53         0.33        59.05        17.65        37.48        55.33 
TCGA-AO-A124 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12F TCGA-AQ-A04J TCGA-AR-A0TP 
      102.58        94.59        96.10        48.36        26.93        82.88 
TCGA-AR-A0TS TCGA-AR-A0TU TCGA-AR-A0U0 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
       37.41        11.84        65.36        55.36        75.55        61.84 
TCGA-AR-A1AJ TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AY TCGA-B6-A0I2 TCGA-B6-A0I6 
       52.77        43.07        17.23        20.22       143.38        32.78 
TCGA-B6-A0IJ TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0WX 
      176.98       140.88       211.56        89.46       131.21        21.47 
TCGA-B6-A0X1 TCGA-BH-A0AV TCGA-BH-A0B3 TCGA-BH-A0B9 TCGA-BH-A0BG TCGA-BH-A0BL 
      186.48        38.79        39.55        51.68        24.85        44.05 
TCGA-BH-A0BW TCGA-BH-A0DL TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0RX TCGA-BH-A0WA 
       11.67        48.23         4.41         9.63         5.59        23.05 
TCGA-BH-A18G TCGA-BH-A18K TCGA-BH-A18Q TCGA-BH-A18V TCGA-BH-A1F0 TCGA-C8-A12L 
        2.01        90.84        55.63        51.16        25.81        11.93 
TCGA-C8-A12V TCGA-C8-A131 TCGA-C8-A134 TCGA-D8-A13Y TCGA-D8-A142 TCGA-D8-A143 
       12.66         1.78         0.69        11.90        13.97        14.17 
TCGA-D8-A147 TCGA-E2-A14N TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A150 
       19.20        47.15        38.60        31.96        28.60        25.41 
TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A1AZ TCGA-E2-A1B5 
       14.79        25.05        60.53        32.35 

$subtype5
TCGA-A2-A04N TCGA-A2-A0CQ TCGA-A2-A0CS TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EV 
      104.81        88.60        75.55        28.77       101.72        31.82 
TCGA-A2-A0T5 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YI TCGA-A7-A0CH 
       17.46        32.55        25.28        15.42        14.50        35.47 
TCGA-A7-A0DB TCGA-A8-A06T TCGA-A8-A06Y TCGA-A8-A07F TCGA-A8-A07S TCGA-A8-A08A 
       33.11        41.06        26.01        18.97         7.99         0.99 
TCGA-A8-A08C TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 
       19.99        19.07        93.04        17.95        41.98         9.99 
TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A0A1 TCGA-A8-A0A2 
       12.00         1.02        19.04        15.02        12.00        19.04 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AN-A03Y TCGA-AN-A046 TCGA-AN-A0FK 
       13.02        17.03        38.04         0.33         0.33         7.00 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XV TCGA-AO-A0J8 TCGA-AO-A125 
       12.33         0.30         0.33         5.33        22.36        99.25 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12G TCGA-AR-A0TR TCGA-AR-A1AK TCGA-AR-A1AP 
       90.58        77.56        41.62         5.26        51.25        39.98 
TCGA-AR-A1AS TCGA-AR-A1AW TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC 
       40.83        35.24       149.59       220.90       129.57        50.70 
TCGA-B6-A0IP TCGA-B6-A0RI TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0WZ 
      110.93       234.28       172.96       162.05       102.77       129.57 
TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-BH-A0B5 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
      129.70        28.27        48.36        37.22        32.02        18.21 
TCGA-BH-A0BJ TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0DO 
       21.70        27.19        53.95        45.57        49.94        17.26 
TCGA-BH-A0DP TCGA-BH-A0DT TCGA-BH-A0E1 TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EB 
       15.65        38.47        15.68        44.81        32.65        24.49 
TCGA-BH-A0HA TCGA-BH-A0HF TCGA-BH-A0HI TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ 
       52.96        23.90        20.38         2.50        13.61        36.85 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A18I TCGA-BH-A18M TCGA-BH-A18S 
       23.93        24.95        42.35         7.23        72.56        66.05 
TCGA-BH-A1ET TCGA-C8-A12N TCGA-D8-A146 TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F 
       82.85        11.77        21.14        37.51        28.44        28.87 
TCGA-E2-A154 TCGA-E2-A156 TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15G TCGA-E2-A15I 
       19.43        23.87        22.82        17.29        18.21        17.42 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15P TCGA-E2-A1B4 TCGA-E2-A1BD 
       19.40         9.04        20.58        19.56        29.95        17.10 

$subtype6
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0EY TCGA-A2-A0SW 
       64.04        55.43        56.81        34.55        24.16        44.88 
TCGA-A2-A0T1 TCGA-A2-A0YG TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A075 TCGA-A8-A076 
       17.13        21.90         1.02        17.98        17.03        53.98 
TCGA-A8-A07B TCGA-A8-A084 TCGA-A8-A08B TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A092 
       33.01        15.06        23.08        37.05         9.99        16.01 
TCGA-A8-A09I TCGA-A8-A09N TCGA-A8-A09W TCGA-A8-A09X TCGA-AN-A04C TCGA-AN-A0FT 
       33.07         1.02         0.99        14.01         1.78         6.02 
TCGA-AN-A0FV TCGA-AO-A03N TCGA-AO-A0J2 TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JM 
        0.33        66.77        32.78        72.00        76.77        71.80 
TCGA-AO-A12D TCGA-AQ-A04L TCGA-AR-A0TX TCGA-AR-A0U3 TCGA-AR-A1AT TCGA-B6-A0I8 
       64.04       130.09        64.83        76.18        41.82        24.62 
TCGA-B6-A0I9 TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0RH TCGA-B6-A0RS TCGA-BH-A0AW 
       12.13       146.50        18.77       189.01       100.70        20.45 
TCGA-BH-A0B7 TCGA-BH-A0BR TCGA-BH-A0C1 TCGA-BH-A0DS TCGA-BH-A0EE TCGA-BH-A0GY 
       56.98        53.69        44.02         2.56        31.00        30.35 
TCGA-BH-A0H9 TCGA-BH-A0HU TCGA-BH-A0HY TCGA-BH-A18P TCGA-BH-A18T TCGA-BH-A18U 
       41.00        12.89        50.79        30.28         7.36        51.39 
TCGA-BH-A1EV TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A130 TCGA-C8-A135 TCGA-C8-A137 
       12.00        11.77         0.07         3.12         0.62         3.85 
TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HL TCGA-D8-A13Z TCGA-E2-A107 TCGA-E2-A10C 
        3.75        10.92        10.42        20.88        34.42        40.11 
TCGA-E2-A14P TCGA-E2-A14V TCGA-E2-A152 TCGA-E2-A1B0 
       40.96        34.26        27.12        53.62 

$subtype7
TCGA-A2-A0CL TCGA-A2-A0EQ TCGA-A8-A08I TCGA-A8-A08P TCGA-A8-A0A7 TCGA-AN-A0AJ 
       64.57        79.76        12.00        31.00         0.99         8.02 
TCGA-AO-A03O TCGA-AO-A0JC TCGA-AR-A0TT TCGA-AR-A1AV TCGA-AR-A1AX TCGA-B6-A0WS 
       81.63        50.86        56.88        42.58        36.26        97.48 
TCGA-BH-A0BF TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0H5 TCGA-BH-A0W7 TCGA-C8-A1HM 
       25.71        49.05        41.75        35.51        44.81         2.30 
TCGA-E2-A14Z 
       17.03 

$subtype8
TCGA-A2-A0EN TCGA-A2-A0EW TCGA-A2-A0SY TCGA-A2-A0T4 TCGA-A2-A0T6 TCGA-A2-A0YK 
       89.36        29.75        44.28        20.52        18.90        19.33 
TCGA-A7-A0CG TCGA-A8-A07E TCGA-A8-A07J TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0XL 
       34.29        19.99        12.00         7.17         6.28         0.33 
TCGA-AN-A0XS TCGA-AO-A0J5 TCGA-AO-A0J9 TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ 
        0.33        24.16        53.03        21.37        26.24        62.04 
TCGA-AR-A1AL TCGA-B6-A0IH TCGA-B6-A0X7 TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0BM 
       48.82       112.37        58.88        25.55        46.95        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0C3 TCGA-BH-A0DE TCGA-BH-A0DQ TCGA-BH-A0DX 
       35.67        48.69        48.13        31.17         3.22        47.41 
TCGA-BH-A0HK TCGA-BH-A18F TCGA-BH-A1EU TCGA-BH-A1EW TCGA-D8-A145 TCGA-E2-A108 
        5.85         8.81        42.28        55.69        13.48        27.52 
TCGA-E2-A15M TCGA-E2-A1B6 TCGA-E2-A1BC 
        7.73        28.50        16.47 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
    0.33     1.45     0.23     0.16     0.30     0.07     0.99     0.33 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
   91.99   157.41   188.68   211.56   234.28   189.01    97.48   112.37 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
  15.320   43.430   26.580   27.470   25.645   30.315   41.750   27.520 
[1] "0.3 - 92.0 (15.3)"  "1.4 - 157.4 (43.4)" "0.2 - 188.7 (26.6)"
[4] "0.2 - 211.6 (27.5)" "0.3 - 234.3 (25.6)" "0.1 - 189.0 (30.3)"
[7] "1.0 - 97.5 (41.8)"  "0.3 - 112.4 (27.5)"
D1V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1       1        0        0         8         3          5          1
  subtype2       1        3        0        12        10          8          0
  subtype3       8        6        4        36        34         20          6
  subtype4       8       10        0        45        19          9          1
  subtype5      14       14        0        43        15         10          5
  subtype6       4        2        0        21        19         15          2
  subtype7       4        1        0         6         4          4          0
  subtype8       6        1        2        14         6          6          0
          vv
clus       STAGE IIIC STAGE IV STAGE TIS STAGE X
  subtype1          0        2         0       1
  subtype2          2        1         1       1
  subtype3          3        1         0       3
  subtype4          4        3         0       2
  subtype5          2        3         0       4
  subtype6          6        3         0       2
  subtype7          0        0         0       1
  subtype8          2        1         0       2
D1V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I           1        1        8        8       14        4        4
  STAGE IA          0        3        6       10       14        2        1
  STAGE IB          0        0        4        0        0        0        0
  STAGE IIA         8       12       36       45       43       21        6
  STAGE IIB         3       10       34       19       15       19        4
  STAGE IIIA        5        8       20        9       10       15        4
  STAGE IIIB        1        0        6        1        5        2        0
  STAGE IIIC        0        2        3        4        2        6        0
  STAGE IV          2        1        1        3        3        3        0
  STAGE TIS         0        1        0        0        0        0        0
  STAGE X           1        1        3        2        4        2        1
            clus
vv           subtype8
  STAGE I           6
  STAGE IA          1
  STAGE IB          2
  STAGE IIA        14
  STAGE IIB         6
  STAGE IIIA        6
  STAGE IIIB        0
  STAGE IIIC        2
  STAGE IV          1
  STAGE TIS         0
  STAGE X           2
[1] 11  8
[1] 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
  subtype1  6 13  0  2
  subtype2  8 21  9  0
  subtype3 25 75 14  6
  subtype4 23 67  8  2
  subtype5 40 55  9  6
  subtype6 11 49 12  2
  subtype7  7 10  3  0
  subtype8 13 21  4  2
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  T1        6        8       25       23       40       11        7       13
  T2       13       21       75       67       55       49       10       21
  T3        0        9       14        8        9       12        3        4
  T4        2        0        6        2        6        2        0        2
[1] 4 8
[1] 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
  subtype1  6  6  7  1
  subtype2 14 16  5  3
  subtype3 49 50 14  4
  subtype4 64 24  8  5
  subtype5 66 31  7  5
  subtype6 24 26 14  8
  subtype7 11  5  3  0
  subtype8 21 12  3  3
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  N0        6       14       49       64       66       24       11       21
  N1        6       16       50       24       31       26        5       12
  N2        7        5       14        8        7       14        3        3
  N3        1        3        4        5        5        8        0        3
[1] 4 8
[1] 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
  subtype1        0  19   2   0
  subtype2        1  37   1   0
  subtype3        0 116   1   4
  subtype4        0  97   3   1
  subtype5        1 101   3   5
  subtype6        0  70   3   1
  subtype7        0  19   0   1
  subtype8        0  37   1   2
D1V6, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  CM0 (I+)        0        1        0        0        1        0        0
  M0             19       37      116       97      101       70       19
  M1              2        1        1        3        3        3        0
  MX              0        0        4        1        5        1        1
          clus
vv         subtype8
  CM0 (I+)        0
  M0             37
  M1              1
  MX              2
[1] 4 8
[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
  subtype1  20   1
  subtype2  39   0
  subtype3 117   4
  subtype4 101   0
  subtype5 110   0
  subtype6  74   0
  subtype7  19   1
  subtype8  40   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20    1
  subtype2   39    0
  subtype3  117    4
  subtype4  101    0
  subtype5  110    0
  subtype6   74    0
  subtype7   19    1
  subtype8   40    0
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       20       39      117      101      110       74       19
  MALE          1        0        4        0        0        0        1
        clus
vv       subtype8
  FEMALE       40
  MALE          0
[1] 2 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA
  subtype1                            20                              0
  subtype2                            28                              8
  subtype3                           113                              1
  subtype4                            92                              1
  subtype5                            85                             14
  subtype6                            67                              5
  subtype7                            19                              1
  subtype8                            24                             11
          vv
clus       MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  subtype1                   0                                0
  subtype2                   0                                3
  subtype3                   0                                1
  subtype4                   1                                0
  subtype5                   0                                5
  subtype6                   0                                0
  subtype7                   0                                0
  subtype8                   0                                3
          vv
clus       MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                  0              1
  subtype2                  0              0
  subtype3                  1              5
  subtype4                  0              6
  subtype5                  1              5
  subtype6                  0              2
  subtype7                  0              0
  subtype8                  0              2
D1V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  INFILTRATING DUCTAL CARCINOMA          20       28      113       92       85
  INFILTRATING LOBULAR CARCINOMA          0        8        1        1       14
  MEDULLARY CARCINOMA                     0        0        0        1        0
  MIXED HISTOLOGY (PLEASE SPECIFY)        0        3        1        0        5
  MUCINOUS CARCINOMA                      0        0        1        0        1
  OTHER  SPECIFY                          1        0        5        6        5
                                  clus
vv                                 subtype6 subtype7 subtype8
  INFILTRATING DUCTAL CARCINOMA          67       19       24
  INFILTRATING LOBULAR CARCINOMA          5        1       11
  MEDULLARY CARCINOMA                     0        0        0
  MIXED HISTOLOGY (PLEASE SPECIFY)        0        0        3
  MUCINOUS CARCINOMA                      0        0        0
  OTHER  SPECIFY                          2        0        2
[1] 6 8
[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
  subtype1  3 18
  subtype2 14 25
  subtype3 35 86
  subtype4 41 60
  subtype5 33 77
  subtype6 22 52
  subtype7  8 12
  subtype8 12 28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   18
  subtype2   14   25
  subtype3   35   86
  subtype4   41   60
  subtype5   33   77
  subtype6   22   52
  subtype7    8   12
  subtype8   12   28
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  NO         3       14       35       41       33       22        8       12
  YES       18       25       86       60       77       52       12       28
[1] 2 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     2                         0
  subtype2                                0     4                         3
  subtype3                                0    10                        12
  subtype4                                0     6                        12
  subtype5                                0     2                         5
  subtype6                                1     9                         2
  subtype7                                0     1                         5
  subtype8                                0     0                         1
          vv
clus       WHITE
  subtype1    14
  subtype2    28
  subtype3    74
  subtype4    75
  subtype5    81
  subtype6    43
  subtype7    11
  subtype8    35
D1V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        0        0
  ASIAN                                   2        4       10        6        2
  BLACK OR AFRICAN AMERICAN               0        3       12       12        5
  WHITE                                  14       28       74       75       81
                                  clus
vv                                 subtype6 subtype7 subtype8
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0
  ASIAN                                   9        1        0
  BLACK OR AFRICAN AMERICAN               2        5        1
  WHITE                                  43       11       35
[1] 4 8
[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
  subtype1  0 14
  subtype2  1 32
  subtype3  0 83
  subtype4  1 83
  subtype5  2 70
  subtype6  2 46
  subtype7  1 14
  subtype8  0 30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   14
  subtype2    1   32
  subtype3    0   83
  subtype4    1   83
  subtype5    2   70
  subtype6    2   46
  subtype7    1   14
  subtype8    0   30
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            0        1        0        1        2        2
  NOT HISPANIC OR LATINO       14       32       83       83       70       46
                        clus
vv                       subtype7 subtype8
  HISPANIC OR LATINO            1        0
  NOT HISPANIC OR LATINO       14       30
[1] 2 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = MRNA_CHIERARCHICAL
D2V1, survival
          sevent
clus2        0   1
  subtype1  83  15
  subtype2 138  17
  subtype3  91  21
  subtype4  79  12
  subtype5  48   7
subtype1 subtype2 subtype3 subtype4 subtype5 
      98      155      112       91       55 
subtype1 subtype2 subtype3 subtype4 subtype5 
      15       17       21       12        7 
$subtype1
TCGA-A1-A0SD TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CT TCGA-A2-A0CU 
       14.37        82.16        63.12        36.13        75.25         5.19 
TCGA-A2-A0CW TCGA-A2-A0D4 TCGA-A2-A0ER TCGA-A2-A0EU TCGA-A2-A0YH TCGA-A2-A0YT 
       64.04        25.22        74.40        34.29        21.67        23.77 
TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A13F TCGA-A8-A06T TCGA-A8-A06X 
       38.30        30.61        37.45        12.72        41.06        31.00 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A082 
       26.01         1.02         9.01        17.03        10.98        18.05 
TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08S TCGA-A8-A091 
       36.95        13.02        18.05        19.96        19.07        19.07 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09R 
        1.02        13.02        31.00        29.98        15.02         8.98 
TCGA-A8-A0A9 TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A0AK TCGA-AN-A0FD 
       13.02         0.33         0.23         0.62         7.36         6.44 
TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XT TCGA-AO-A03P TCGA-AO-A0J3 TCGA-AO-A0JI 
        0.33         0.33         0.33        84.69        21.40        38.53 
TCGA-AQ-A04H TCGA-AR-A0TQ TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0TZ 
       24.79        49.32        29.75        24.30        55.86        76.14 
TCGA-AR-A0U2 TCGA-B6-A0IB TCGA-B6-A0IM TCGA-B6-A0IO TCGA-B6-A0RG TCGA-B6-A0RI 
       83.87       129.57       126.12       110.14        68.45       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0X5 
       81.17        78.02       188.68        79.63        17.98        68.94 
TCGA-BH-A0B4 TCGA-BH-A0B8 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DH TCGA-BH-A0E2 
       39.16        51.58        42.90        45.83        38.01        14.30 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0HB TCGA-BH-A0HW TCGA-BH-A0HX 
       10.78        15.16        37.78        26.50        51.32        27.25 
TCGA-BH-A18L TCGA-BH-A1ES TCGA-C8-A12M TCGA-C8-A12U TCGA-C8-A12X TCGA-C8-A1HL 
       26.66       113.82        11.77        12.66        12.66        10.42 
TCGA-C8-A1HN TCGA-D8-A140 TCGA-E2-A105 TCGA-E2-A109 TCGA-E2-A14O TCGA-E2-A14S 
        3.25        13.25        43.00        46.59        44.68        33.17 
TCGA-E2-A14T TCGA-E2-A14W TCGA-E2-A155 TCGA-E2-A15F TCGA-E2-A15O TCGA-E2-A15R 
       33.30        32.02        21.04        21.63        13.02        17.06 
TCGA-E2-A15S TCGA-E2-A15T 
       14.07        14.99 

$subtype2
TCGA-A1-A0SE TCGA-A1-A0SH TCGA-A1-A0SJ TCGA-A2-A04N TCGA-A2-A0CL TCGA-A2-A0CP 
       43.43        47.24        13.68       104.81        64.57        92.48 
TCGA-A2-A0CV TCGA-A2-A0CZ TCGA-A2-A0D3 TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0ES 
       63.45        53.13        28.77        89.36        80.28        37.05 
TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0SU TCGA-A2-A0SY TCGA-A2-A0T3 
       31.82        29.75        24.72        54.64        44.28        18.71 
TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YD TCGA-A2-A0YK 
       20.52        17.46        18.90        20.75        25.28        19.33 
TCGA-A2-A0YL TCGA-A7-A0CG TCGA-A7-A0DB TCGA-A8-A07E TCGA-A8-A07J TCGA-A8-A08C 
       14.63        34.29        33.11        19.99        12.00        19.99 
TCGA-A8-A08O TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A09A TCGA-A8-A0A1 TCGA-A8-A0A2 
       31.00        93.04        40.01         9.99        12.00        19.04 
TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0AB TCGA-AN-A03X TCGA-AN-A046 TCGA-AN-A04A 
       13.02        21.04        17.03         0.33         0.33         2.96 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FW TCGA-AN-A0XL TCGA-AN-A0XS TCGA-AN-A0XV 
        7.17         6.28         0.36         0.33         0.33         5.33 
TCGA-AO-A03M TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03V TCGA-AO-A0J5 TCGA-AO-A0J9 
       47.84        68.75        47.87        29.13        24.16        53.03 
TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ 
       21.53        50.70        50.86        21.37        26.24        62.04 
TCGA-AO-A126 TCGA-AO-A12A TCGA-AO-A12C TCGA-AO-A12E TCGA-AO-A12G TCGA-AR-A0TT 
       93.70        90.58        65.56        57.30        41.62        56.88 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AU 
       51.25        48.82        43.73        43.56        39.98        46.32 
TCGA-AR-A1AV TCGA-AR-A1AX TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IE TCGA-B6-A0IH 
       42.58        36.26       149.59       220.90        65.72       112.37 
TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0RN TCGA-B6-A0RQ TCGA-B6-A0RV TCGA-B6-A0WS 
       84.59       110.93       172.96       140.48       157.41        97.48 
TCGA-B6-A0WY TCGA-B6-A0X0 TCGA-B6-A0X7 TCGA-BH-A0AU TCGA-BH-A0AY TCGA-BH-A0AZ 
      113.79       129.70        58.88        24.53        25.55        28.50 
TCGA-BH-A0B0 TCGA-BH-A0B5 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       46.95        48.36        37.22        32.02        18.21        25.71 
TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BT 
       21.70        61.68        35.67        48.69        27.19        45.57 
TCGA-BH-A0C3 TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO 
       48.13        31.17        23.44        22.13        13.91        17.26 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DX TCGA-BH-A0E1 
       15.65         3.22         2.56        38.47        47.41        15.68 
TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EI TCGA-BH-A0H5 TCGA-BH-A0HA TCGA-BH-A0HF 
       46.19        32.65        24.43        35.51        52.96        23.90 
TCGA-BH-A0HK TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
        5.85        13.61        36.85        24.95        42.35        44.81 
TCGA-BH-A18F TCGA-BH-A18I TCGA-BH-A18M TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1EU 
        8.81         7.23        72.56        91.99        82.85        42.28 
TCGA-BH-A1EW TCGA-C8-A132 TCGA-C8-A1HG TCGA-C8-A1HI TCGA-D8-A141 TCGA-D8-A145 
       55.69         1.45        11.34        11.34        20.58        13.48 
TCGA-D8-A146 TCGA-E2-A106 TCGA-E2-A108 TCGA-E2-A10F TCGA-E2-A14Q TCGA-E2-A14Z 
       21.14        59.41        27.52        28.87        38.24        17.03 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J 
       22.82        17.29        20.71        12.92        17.42        19.40 
TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A1B1 TCGA-E2-A1B6 TCGA-E2-A1BC 
        7.73        19.56        53.03        28.50        16.47 

$subtype3
TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CX TCGA-A2-A0CY 
       31.79         7.96        64.04        55.43        56.81        55.00 
TCGA-A2-A0D1 TCGA-A2-A0EQ TCGA-A2-A0EY TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0T1 
       34.55        79.76        24.16        27.12        44.88        17.13 
TCGA-A2-A0YG TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06U TCGA-A8-A075 
       21.90        13.02         1.02        17.98        29.03        17.03 
TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07W 
       53.98        33.01        18.97        18.97        14.01         9.99 
TCGA-A8-A084 TCGA-A8-A08B TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08P 
       15.06        23.08        12.00        37.05         9.99        31.00 
TCGA-A8-A08X TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09I TCGA-A8-A09N 
       33.99        16.01        41.98        12.00        33.07         1.02 
TCGA-A8-A09Q TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A7 TCGA-AN-A04C TCGA-AN-A0AJ 
       25.02         0.99        14.01         0.99         1.78         8.02 
TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0XN TCGA-AN-A0XO 
        0.16         0.33         6.02         0.33         0.33        12.33 
TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A0J2 TCGA-AO-A0JD 
        5.59        80.28        66.77        81.63        32.78        72.00 
TCGA-AO-A0JE TCGA-AO-A0JM TCGA-AO-A12D TCGA-AQ-A04L TCGA-AR-A0TX TCGA-AR-A0U3 
       76.77        71.80        64.04       130.09        64.83        76.18 
TCGA-AR-A1AT TCGA-B6-A0I8 TCGA-B6-A0I9 TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0RH 
       41.82        24.62        12.13       146.50        18.77       189.01 
TCGA-B6-A0RO TCGA-B6-A0RS TCGA-BH-A0AW TCGA-BH-A0B1 TCGA-BH-A0B7 TCGA-BH-A0BR 
      162.05       100.70        20.45        37.74        56.98        53.69 
TCGA-BH-A0BS TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0DZ TCGA-BH-A0EE 
       53.95        49.05        41.75        44.02        16.27        31.00 
TCGA-BH-A0GY TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HU TCGA-BH-A0HY TCGA-BH-A18J 
       30.35        23.08        41.00        12.89        50.79        20.12 
TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EV TCGA-C8-A12L 
       30.28        37.55         7.36        51.39        12.00        11.93 
TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12W TCGA-C8-A130 TCGA-C8-A131 
       12.66        11.77         0.07        12.66         3.12         1.78 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HM TCGA-D8-A13Y 
        0.62         3.85         3.75        10.92         2.30        11.90 
TCGA-D8-A13Z TCGA-D8-A143 TCGA-E2-A107 TCGA-E2-A10C TCGA-E2-A14P TCGA-E2-A14V 
       20.88        14.17        34.42        40.11        40.96        34.26 
TCGA-E2-A152 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A1B0 
       27.12        25.05        23.34        53.62 

$subtype4
TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04T TCGA-A2-A04U 
       28.01        19.20        18.02        41.95        73.84        22.06 
TCGA-A2-A0CM TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0ST TCGA-A2-A0SX TCGA-A2-A0T0 
       24.79        21.14        33.76        99.19        50.43        17.52 
TCGA-A2-A0T2 TCGA-A2-A0YE TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A7-A0CE TCGA-A7-A0DA 
        8.38        18.21        18.61        31.73        35.31        35.67 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A8-A07C TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A07U 
       31.73        10.72        19.07         9.99         8.98         9.96 
TCGA-A8-A08R TCGA-AN-A04D TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FJ 
        0.99         1.71         6.51         0.33         0.33         7.96 
TCGA-AN-A0FL TCGA-AN-A0FX TCGA-AN-A0G0 TCGA-AN-A0XU TCGA-AO-A03U TCGA-AO-A0J4 
        7.59         0.33         0.53         0.33        59.05        17.65 
TCGA-AO-A0J6 TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12F 
       37.48        55.33       102.58        94.59        96.10        48.36 
TCGA-AQ-A04J TCGA-AR-A0TP TCGA-AR-A0TS TCGA-AR-A0TU TCGA-AR-A0U0 TCGA-AR-A0U4 
       26.93        82.88        37.41        11.84        65.36        55.36 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AY 
       75.55        61.84        52.77        43.07        17.23        20.22 
TCGA-B6-A0I2 TCGA-B6-A0I6 TCGA-B6-A0IJ TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RT 
      143.38        32.78       176.98       140.88       211.56        89.46 
TCGA-B6-A0RU TCGA-B6-A0WX TCGA-B6-A0X1 TCGA-BH-A0AV TCGA-BH-A0B3 TCGA-BH-A0B9 
      131.21        21.47       186.48        38.79        39.55        51.68 
TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BW TCGA-BH-A0DL TCGA-BH-A0E0 TCGA-BH-A0E6 
       24.85        44.05        11.67        48.23         4.41         9.63 
TCGA-BH-A0RX TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18K TCGA-BH-A18Q TCGA-BH-A18V 
        5.59        23.05         2.01        90.84        55.63        51.16 
TCGA-BH-A1F0 TCGA-C8-A12V TCGA-C8-A134 TCGA-D8-A142 TCGA-D8-A147 TCGA-E2-A14N 
       25.81        12.66         0.69        13.97        19.20        47.15 
TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A158 TCGA-E2-A1AZ 
       38.60        31.96        28.60        25.41        14.79        60.53 
TCGA-E2-A1B5 
       32.35 

$subtype5
TCGA-A2-A0CQ TCGA-A2-A0CS TCGA-A2-A0EM TCGA-A2-A0ET TCGA-A2-A0YC TCGA-A2-A0YF 
       88.60        75.55       101.72        35.05        32.55        15.42 
TCGA-A2-A0YI TCGA-A7-A0CH TCGA-A8-A06P TCGA-A8-A07S TCGA-A8-A07Z TCGA-A8-A08A 
       14.50        35.47        13.02         7.99        28.04         0.99 
TCGA-A8-A093 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A0AD 
       17.95         9.99        12.00        19.04        15.02        38.04 
TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AO-A0J7 TCGA-AO-A0J8 
        4.64         7.00         0.30         0.33        20.32        22.36 
TCGA-AO-A125 TCGA-AO-A12B TCGA-AO-A12H TCGA-AR-A0TR TCGA-AR-A1AS TCGA-AR-A1AW 
       99.25        77.56        28.37         5.26        40.83        35.24 
TCGA-B6-A0IC TCGA-B6-A0RP TCGA-B6-A0WZ TCGA-B6-A0X4 TCGA-BH-A0BV TCGA-BH-A0E7 
       50.70       102.77       129.57        28.27        49.94        44.81 
TCGA-BH-A0EB TCGA-BH-A0H6 TCGA-BH-A0HI TCGA-BH-A0HO TCGA-BH-A0W3 TCGA-BH-A18N 
       24.49        24.56        20.38         2.50        23.93        37.74 
TCGA-BH-A18S TCGA-C8-A12N TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A153 
       66.05        11.77        40.41        37.51        28.44        23.24 
TCGA-E2-A154 TCGA-E2-A156 TCGA-E2-A15G TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A1B4 
       19.43        23.87        18.21         9.04        20.58        29.95 
TCGA-E2-A1BD 
       17.10 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.23     0.33     0.07     0.33     0.30 
subtype1 subtype2 subtype3 subtype4 subtype5 
  234.28   220.90   189.01   211.56   129.57 
subtype1 subtype2 subtype3 subtype4 subtype5 
  26.255   31.170   24.390   28.600   23.930 
[1] "0.2 - 234.3 (26.3)" "0.3 - 220.9 (31.2)" "0.1 - 189.0 (24.4)"
[4] "0.3 - 211.6 (28.6)" "0.3 - 129.6 (23.9)"
D2V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1       6        5        2        33        29         16          5
  subtype2      20       12        4        56        24         23          1
  subtype3       6        4        0        36        27         24          5
  subtype4       8        9        0        40        18          8          1
  subtype5       6        7        0        20        12          6          3
          vv
clus       STAGE IIIC STAGE IV STAGE TIS STAGE X
  subtype1          2        1         0       3
  subtype2          6        3         1       6
  subtype3          8        6         0       2
  subtype4          3        3         0       2
  subtype5          0        1         0       3
D2V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           6       20        6        8        6
  STAGE IA          5       12        4        9        7
  STAGE IB          2        4        0        0        0
  STAGE IIA        33       56       36       40       20
  STAGE IIB        29       24       27       18       12
  STAGE IIIA       16       23       24        8        6
  STAGE IIIB        5        1        5        1        3
  STAGE IIIC        2        6        8        3        0
  STAGE IV          1        3        6        3        1
  STAGE TIS         0        1        0        0        0
  STAGE X           3        6        2        2        3
[1] 11  5
[1] 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
  subtype1 19 63 14  5
  subtype2 54 79 19  3
  subtype3 18 78 15  7
  subtype4 22 60  8  1
  subtype5 20 31  3  4
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       19       54       18       22       20
  T2       63       79       78       60       31
  T3       14       19       15        8        3
  T4        5        3        7        1        4
[1] 4 5
[1] 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
  subtype1 44 43  9  4
  subtype2 81 47 15  9
  subtype3 41 39 25 10
  subtype4 58 23  7  4
  subtype5 31 18  5  2
D2V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       44       81       41       58       31
  N1       43       47       39       23       18
  N2        9       15       25        7        5
  N3        4        9       10        4        2
[1] 4 5
[1] 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
  subtype1        0  97   1   4
  subtype2        2 146   3   5
  subtype3        0 111   6   1
  subtype4        0  88   3   1
  subtype5        0  54   1   3
D2V6, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4 subtype5
  CM0 (I+)        0        2        0        0        0
  M0             97      146      111       88       54
  M1              1        3        6        3        1
  MX              4        5        1        1        3
[1] 4 5
[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
  subtype1  98   4
  subtype2 155   1
  subtype3 117   1
  subtype4  92   0
  subtype5  58   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   98    4
  subtype2  155    1
  subtype3  117    1
  subtype4   92    0
  subtype5   58    0
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       98      155      117       92       58
  MALE          4        1        1        0        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA
  subtype1                            97                              1
  subtype2                           113                             29
  subtype3                           110                              6
  subtype4                            84                              1
  subtype5                            44                              4
          vv
clus       MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  subtype1                   0                                0
  subtype2                   0                                7
  subtype3                   0                                0
  subtype4                   1                                0
  subtype5                   0                                5
          vv
clus       MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                  1              3
  subtype2                  0              7
  subtype3                  0              2
  subtype4                  0              5
  subtype5                  1              4
D2V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  INFILTRATING DUCTAL CARCINOMA          97      113      110       84       44
  INFILTRATING LOBULAR CARCINOMA          1       29        6        1        4
  MEDULLARY CARCINOMA                     0        0        0        1        0
  MIXED HISTOLOGY (PLEASE SPECIFY)        0        7        0        0        5
  MUCINOUS CARCINOMA                      1        0        0        0        1
  OTHER  SPECIFY                          3        7        2        5        4
[1] 6 5
[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
  subtype1  28  74
  subtype2  46 110
  subtype3  29  89
  subtype4  40  52
  subtype5  25  33
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28   74
  subtype2   46  110
  subtype3   29   89
  subtype4   40   52
  subtype5   25   33
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        28       46       29       40       25
  YES       74      110       89       52       33
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     7                        10
  subtype2                                0     6                         8
  subtype3                                1    16                         4
  subtype4                                0     3                        12
  subtype5                                0     2                         6
          vv
clus       WHITE
  subtype1    60
  subtype2   128
  subtype3    65
  subtype4    70
  subtype5    38
D2V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1        0        0
  ASIAN                                   7        6       16        3        2
  BLACK OR AFRICAN AMERICAN              10        8        4       12        6
  WHITE                                  60      128       65       70       38
[1] 4 5
[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
  subtype1   0  66
  subtype2   3 119
  subtype3   2  74
  subtype4   1  75
  subtype5   1  38
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   66
  subtype2    3  119
  subtype3    2   74
  subtype4    1   75
  subtype5    1   38
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            0        3        2        1        1
  NOT HISPANIC OR LATINO       66      119       74       75       38
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = CN_CNMF
D3V1, survival
          sevent
clus2        0   1
  subtype1 328  38
  subtype2 197  29
  subtype3  82   8
  subtype4 220  31
  subtype5  33   8
subtype1 subtype2 subtype3 subtype4 subtype5 
     366      226       90      251       41 
subtype1 subtype2 subtype3 subtype4 subtype5 
      38       29        8       31        8 
$subtype1
TCGA-A1-A0SB TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04Q 
        8.52        14.27        47.24        18.21       104.81        41.95 
TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO 
       63.12        64.04        36.13       125.59        64.57       112.08 
TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN 
       92.48        88.60       107.93        28.77       101.72        89.36 
TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST 
      107.61        74.40        37.05        29.75        24.72        99.19 
TCGA-A2-A0SU TCGA-A2-A0SY TCGA-A2-A0T1 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC 
       54.64        44.28        17.13        17.46        18.90        32.55 
TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A1FZ 
       25.28        15.42        14.50        19.33        14.63        22.45 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A25F 
       19.56        16.47        52.47       107.70        17.19        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XZ TCGA-A2-A4RX 
       20.88        39.65        14.07        49.48        31.99         9.01 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A13G 
        8.81         8.91        12.00        34.29        35.47        23.61 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A3IY TCGA-A7-A3IZ 
       29.56        31.36        24.26        23.80        11.34        10.59 
TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A426 TCGA-A7-A5ZW TCGA-A7-A5ZX 
       10.29        11.28        13.41        11.97        10.72        11.05 
TCGA-A8-A06P TCGA-A8-A07E TCGA-A8-A07J TCGA-A8-A07S TCGA-A8-A082 TCGA-A8-A08A 
       13.02        19.99        12.00         7.99        18.05         0.99 
TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09K TCGA-A8-A09T 
       93.04        40.01        41.98         9.99        29.98        19.04 
TCGA-A8-A09V TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A7 TCGA-A8-A0AD TCGA-AC-A23G 
       15.02        14.01        12.00         0.99        38.04        10.85 
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-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
        0.92         2.27         0.99         0.69        14.83         9.40 
TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A6IV TCGA-AC-A6IX 
        1.12         1.68         1.55         1.32         1.18         0.43 
TCGA-AN-A046 TCGA-AN-A0FF TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0XR TCGA-AN-A0XS 
        0.33         4.64         7.17         6.28         0.33         0.33 
TCGA-AN-A0XV TCGA-AO-A03U TCGA-AO-A0J5 TCGA-AO-A0J8 TCGA-AO-A0JA TCGA-AO-A0JC 
        5.33        59.05        24.16        22.36        21.53        50.86 
TCGA-AO-A0JF TCGA-AO-A0JJ TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12B 
       21.37        62.04        99.25        93.70        94.59        77.56 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AQ-A1H3 TCGA-AQ-A7U7 TCGA-AR-A0TX TCGA-AR-A1AJ 
       28.37        14.73        13.22         9.99        64.83        52.77 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AS TCGA-AR-A1AU 
       48.82        62.56        43.73        43.56        40.83        46.32 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24T 
       35.24        36.26        65.46        68.19        65.69        53.26 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A252 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LM 
       50.96        48.16        40.64       128.65        20.25        40.04 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       17.10        20.81        16.96        16.04        20.45        10.59 
TCGA-B6-A0I5 TCGA-B6-A0IC TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0RI 
      149.59        50.70       126.12        84.59       110.93       234.28 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS 
       78.02       172.96       140.48        89.46       157.41        97.48 
TCGA-B6-A0WT TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      188.68       129.57       129.70        28.27        68.94        58.88 
TCGA-B6-A1KI TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B7 TCGA-BH-A0BD TCGA-BH-A0BM 
       73.51        28.50        46.95        56.98        18.21        61.68 
TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BZ TCGA-BH-A0C3 TCGA-BH-A0DE 
       35.67        27.19        53.95        49.05        48.13        31.17 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DT TCGA-BH-A0DV 
       23.44        38.01        13.91        17.26        38.47        45.17 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0EA 
       47.41        16.27        15.68        14.30        44.81        32.65 
TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0HA 
       24.49        31.00        37.78        35.51        24.56        52.96 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0RX TCGA-BH-A0W4 
       20.38         5.85         2.50        13.61         5.59        24.95 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18G TCGA-BH-A18J TCGA-BH-A18M TCGA-BH-A18P 
       42.35        44.81         2.01        20.12        72.56        30.28 
TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1F5 TCGA-BH-A1FB 
       82.85        42.28        49.58        25.81        89.16       120.62 
TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FR 
       74.73       122.89        36.92        63.35        55.00       144.59 
TCGA-BH-A1FU TCGA-BH-A28O TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12N 
       72.07        10.65        20.12       109.28         8.94        11.77 
TCGA-C8-A12V TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A26V TCGA-C8-A26X TCGA-C8-A26Y 
       12.66         3.85        12.33         0.30         0.36         0.43 
TCGA-C8-A275 TCGA-C8-A3M7 TCGA-D8-A141 TCGA-D8-A145 TCGA-D8-A1JB TCGA-D8-A1JE 
        0.03         0.03        20.58        13.48        18.71        18.90 
TCGA-D8-A1JH TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X7 TCGA-D8-A1X8 
       14.01        20.38        12.20        14.70        16.73        25.74 
TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XM TCGA-D8-A1XV TCGA-D8-A27E TCGA-D8-A27I 
       18.15         2.66        17.69        15.16        17.42        14.43 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A3Z5 TCGA-D8-A3Z6 
        9.44        16.41         0.76        13.08        14.50        18.51 
TCGA-D8-A4Z1 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N 
        7.33        27.52        40.41        28.44        28.87        47.15 
TCGA-E2-A14Q TCGA-E2-A14U TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15C TCGA-E2-A15D 
       38.24        43.33        21.04        23.87        22.82        17.29 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15P TCGA-E2-A15T 
       17.42        19.40         9.04        20.58        19.56        14.99 
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-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L9 
       28.44        22.65         3.88        11.08        54.18        19.66 
TCGA-E2-A1LB TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E9-A1N4 TCGA-E9-A1N5 
       40.47         5.52        15.72        18.05        19.20        36.82 
TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1R0 TCGA-E9-A1R4 TCGA-E9-A1RA TCGA-E9-A1RI 
       35.77        21.57        14.30         6.12        32.09        35.64 
TCGA-E9-A227 TCGA-E9-A229 TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A245 TCGA-E9-A248 
        0.79        13.32        24.10        17.06         0.85         1.94 
TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A5FK TCGA-EW-A1IW 
       12.56         0.76        18.41        15.72         0.39        12.20 
TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1OX TCGA-EW-A1P1 
       39.72         8.48        18.21        13.25        29.95        39.78 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PE TCGA-EW-A1PG TCGA-EW-A2FR TCGA-EW-A3E8 
       18.48        30.08        10.52        34.55        55.00        21.27 
TCGA-EW-A424 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DI 
       10.59        59.57       194.27        53.13        43.04        61.91 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NY 
       62.33        90.84        76.64        77.33        53.36        38.20 
TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW 
       32.28        53.95        57.63        13.55        18.12        11.84 
TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL 
        6.67         4.60         0.66         3.58         6.90         5.56 
TCGA-LL-A5YO TCGA-LL-A73Z TCGA-LL-A740 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
        3.19         4.50         4.50         2.79         2.10        12.66 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY 
        7.53        44.61        27.65        24.10        16.87        14.10 
TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P TCGA-W8-A86G 
       14.76        54.51        31.07         7.23         4.44         5.29 

$subtype2
TCGA-A1-A0SD TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A2-A04R TCGA-A2-A04X 
       14.37        13.68         7.96        39.32        82.16        55.43 
TCGA-A2-A0CT TCGA-A2-A0D4 TCGA-A2-A0EO TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV 
       75.25        25.22        80.28        35.05        34.29        31.82 
TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T7 TCGA-A2-A0YG 
       27.12        44.88        18.71        20.52        20.75        21.90 
TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A25E TCGA-A7-A0CD TCGA-A7-A0CJ 
       23.77        17.36        36.79        91.92        38.30        30.61 
TCGA-A7-A13F TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A4SB TCGA-A7-A4SF TCGA-A8-A06O 
       12.72        20.61        22.32        13.74        17.92        13.02 
TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Z TCGA-A8-A076 
        1.02        17.98        41.06        29.03         1.02        53.98 
TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07L TCGA-A8-A07P 
        9.01        33.01        18.97        14.01        17.03        10.98 
TCGA-A8-A07W TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I 
        9.99        36.95        13.02        18.05        19.96        12.00 
TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A092 TCGA-A8-A097 
       37.05        31.00        31.00        19.07        16.01        12.00 
TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09R 
        9.99         1.02        31.00        33.07        15.02         8.98 
TCGA-A8-A09W TCGA-A8-A0A4 TCGA-A8-A0A9 TCGA-AC-A23H TCGA-AC-A2BM TCGA-AC-A2FM 
        0.99        13.02        13.02         2.66        38.20        26.04 
TCGA-AC-A62V TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A049 
        0.07         1.74         0.33         0.33         0.23         0.62 
TCGA-AN-A04A TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0XL TCGA-AN-A0XW TCGA-AO-A03L 
        2.96         0.33         0.36         0.33         5.59        80.28 
TCGA-AO-A03P TCGA-AO-A03T TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0JD TCGA-AO-A0JE 
       84.69        47.87        32.78        21.40        72.00        76.77 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JM TCGA-AO-A12E TCGA-AO-A1KQ TCGA-AO-A1KS 
       26.24        38.53        71.80        57.30        61.87         0.53 
TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A54O TCGA-AR-A0TQ 
       17.79        24.79         5.65        15.62        21.86        49.32 
TCGA-AR-A0TZ TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AK TCGA-AR-A1AP TCGA-AR-A24L 
       76.14        83.87        76.18        51.25        39.98        73.02 
TCGA-AR-A24R TCGA-AR-A24V TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A254 TCGA-AR-A255 
       57.40        54.18        51.75        56.15        39.85        34.82 
TCGA-AR-A2LK TCGA-AR-A2LL TCGA-B6-A0I9 TCGA-B6-A0IG TCGA-B6-A0RG TCGA-B6-A0RL 
       42.87         7.36        12.13       146.50        68.45        81.17 
TCGA-B6-A0RO TCGA-B6-A0WV TCGA-B6-A0WY TCGA-B6-A1KN TCGA-B6-A408 TCGA-BH-A0AU 
      162.05        79.63       113.79       139.17        49.94        24.53 
TCGA-BH-A0B4 TCGA-BH-A0BC TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DI TCGA-BH-A0DQ 
       39.16        32.02        42.90        45.83        22.13         3.22 
TCGA-BH-A0EI TCGA-BH-A0H7 TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0W3 
       24.43        23.08        51.32        27.25        50.79        23.93 
TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A1EN 
       26.66        37.74        37.55        66.05        51.39        69.93 
TCGA-BH-A1ES TCGA-BH-A1EW TCGA-BH-A1F2 TCGA-BH-A1F8 TCGA-BH-A1FM TCGA-BH-A201 
      113.82        55.69        31.53        24.66        45.63         6.90 
TCGA-BH-A42T TCGA-C8-A12M TCGA-C8-A12O TCGA-C8-A12Q TCGA-C8-A12W TCGA-C8-A132 
        0.99        11.77        12.66         0.07        12.66         1.45 
TCGA-C8-A138 TCGA-C8-A1HG TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26Z 
        3.75        11.34        12.03        10.42         3.25         8.28 
TCGA-C8-A273 TCGA-C8-A27A TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A1J9 
        9.67        12.20         0.23        11.90        13.25        17.49 
TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JI TCGA-D8-A1JT TCGA-D8-A1X9 TCGA-D8-A1XA 
       15.78        18.15        18.97        13.32        23.90        27.58 
TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y3 TCGA-D8-A27G 
       16.31         6.35        16.54        15.52        14.14        13.45 
TCGA-D8-A27N TCGA-D8-A27R TCGA-D8-A27W TCGA-E2-A105 TCGA-E2-A109 TCGA-E2-A14O 
        4.80        10.09        12.26        43.00        46.59        44.68 
TCGA-E2-A14P TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A152 
       40.96        33.17        33.30        34.26        32.02        27.12 
TCGA-E2-A15A TCGA-E2-A15E TCGA-E2-A15H TCGA-E2-A15O TCGA-E2-A15S TCGA-E2-A1IE 
       23.34        20.71        12.92        13.02        14.07        38.30 
TCGA-E2-A1IG TCGA-E2-A1LA TCGA-E2-A56Z TCGA-E9-A1NA TCGA-E9-A1NF TCGA-E9-A1NI 
       32.78        24.59         7.20        36.56        20.05         9.86 
TCGA-E9-A1QZ TCGA-E9-A1R2 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RE TCGA-E9-A1RF 
       11.90         0.62         2.76        21.21        34.65         6.58 
TCGA-E9-A1RG TCGA-E9-A228 TCGA-E9-A22A TCGA-E9-A247 TCGA-E9-A295 TCGA-E9-A2JS 
       21.27        12.53        39.09        27.22         0.72        17.75 
TCGA-E9-A54Y TCGA-E9-A5UO TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OY 
        0.23         0.23        16.57        15.68        28.77        29.85 
TCGA-EW-A1P5 TCGA-EW-A1PD TCGA-EW-A2FS TCGA-EW-A2FW TCGA-GI-A2C8 TCGA-LL-A5YM 
       23.11        13.94        52.73        22.09         7.40         4.70 
TCGA-LL-A6FQ TCGA-LL-A7T0 TCGA-OL-A5RZ TCGA-S3-A6ZG 
        2.63         3.22        10.29         6.81 

$subtype3
TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SI TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A3XU 
       43.43        48.10        20.88        75.55        63.45        29.98 
TCGA-A2-A4S2 TCGA-A7-A0DB TCGA-A7-A425 TCGA-A8-A06Y TCGA-A8-A07F TCGA-A8-A07Z 
        6.74        33.11        14.70        26.01        18.97        28.04 
TCGA-A8-A084 TCGA-A8-A08C TCGA-A8-A093 TCGA-A8-A09B TCGA-A8-A0A2 TCGA-A8-A0A6 
       15.06        19.99        17.95        12.00        19.04        21.04 
TCGA-A8-A0AB TCGA-AC-A23E TCGA-AC-A5XS TCGA-AC-A62Y TCGA-AN-A0FK TCGA-AN-A0XO 
       17.03         2.37         1.55         1.81         7.00        12.33 
TCGA-AN-A0XP TCGA-AO-A03N TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A12A TCGA-AR-A0TR 
        0.30        66.77        20.32        53.03        90.58         5.26 
TCGA-AR-A1AV TCGA-AR-A24K TCGA-AR-A24P TCGA-AR-A5QM TCGA-B6-A0IB TCGA-B6-A0IH 
       42.58        50.89         0.85        54.74       129.57       112.37 
TCGA-B6-A0RH TCGA-B6-A0RP TCGA-B6-A401 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0B5 
      189.01       102.77        85.35        82.88        55.00        48.36 
TCGA-BH-A0BA TCGA-BH-A0BJ TCGA-BH-A0BV TCGA-BH-A0C1 TCGA-BH-A0DP TCGA-BH-A0E9 
       37.22        21.70        49.94        44.02        15.65        46.19 
TCGA-BH-A0GZ TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A18F TCGA-BH-A18K TCGA-BH-A1EV 
       10.78        36.85        12.89         8.81        90.84        12.00 
TCGA-BH-A202 TCGA-BH-A28Q TCGA-C8-A1HI TCGA-C8-A274 TCGA-D8-A146 TCGA-D8-A1J8 
        0.72         6.44        11.34         0.03        21.14        14.17 
TCGA-D8-A1JA TCGA-D8-A1XG TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1Y1 TCGA-D8-A27V 
       16.50        14.73         7.96        15.85         3.81        12.53 
TCGA-E2-A107 TCGA-E2-A10B TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A15G TCGA-E2-A1BD 
       34.42        37.51        23.24        19.43        18.21        17.10 
TCGA-E2-A1IH TCGA-E2-A1L8 TCGA-E2-A2P5 TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1RC 
       33.73        39.62        16.93         2.10         1.38        40.24 
TCGA-E9-A1RD TCGA-E9-A249 TCGA-E9-A3HO TCGA-E9-A6HE TCGA-EW-A1P3 TCGA-EW-A1PC 
        0.66         0.95        26.07        15.39        52.96         6.15 
TCGA-EW-A423 TCGA-GM-A3NW TCGA-LD-A66U TCGA-LQ-A4E4 TCGA-OL-A66K TCGA-OL-A66N 
       10.16       110.50         8.28        15.91        33.90        18.21 

$subtype4
TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A04P TCGA-A2-A04T TCGA-A2-A04U 
       31.79        28.01        19.20        18.02        73.84        22.06 
TCGA-A2-A0CM TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 
       24.79        64.04        56.81        21.14        34.55        33.76 
TCGA-A2-A0EQ TCGA-A2-A0EY TCGA-A2-A0SX TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0YE 
       79.76        24.16        50.43        17.52         8.38        18.21 
TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A1G1 TCGA-A2-A25B TCGA-A2-A3XS TCGA-A2-A3XT 
       18.61        31.73        19.20        16.31        33.93        83.01 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4S3 TCGA-A7-A0CE 
       38.40        34.98        38.37         7.30         3.42        35.31 
TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A26G TCGA-A7-A26I 
       37.45        35.67        31.73        10.72        23.74        21.73 
TCGA-A7-A4SA TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A6VV 
       14.93        14.50        21.17        14.73        12.10        10.29 
TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A07O 
        9.37        10.42         8.75        31.00        17.03         9.99 
TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A08B TCGA-A8-A08L TCGA-A8-A08R TCGA-A8-A08X 
        8.98         9.96        23.08         9.99         0.99        33.99 
TCGA-A8-A09D TCGA-A8-A09N TCGA-A8-A09Q TCGA-AC-A23C TCGA-AC-A2BK TCGA-AC-A2QH 
       13.02         1.02        25.02         0.95        38.53         1.02 
TCGA-AC-A3W5 TCGA-AC-A62X TCGA-AC-A6IW TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ 
        1.81         1.12         0.69         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-A0FL TCGA-AN-A0FT TCGA-AN-A0FX TCGA-AN-A0FY 
        6.44         7.96         7.59         6.02         0.33         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XN TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AO-A03M TCGA-AO-A03O 
        0.33         0.33         0.33         0.33        47.84        81.63 
TCGA-AO-A03V TCGA-AO-A0J4 TCGA-AO-A0J6 TCGA-AO-A0JB TCGA-AO-A0JL TCGA-AO-A124 
       29.13        17.65        37.48        50.70        55.33       102.58 
TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A1KR TCGA-AQ-A04J 
       96.10        64.04        48.36        41.62        70.39        26.93 
TCGA-AQ-A04L TCGA-AQ-A54N TCGA-AR-A0TP TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV 
      130.09         2.56        82.88        37.41        56.88        29.75 
TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U4 TCGA-AR-A1AH 
       24.30        55.86        65.36        70.16        55.36        75.55 
TCGA-AR-A1AI TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24Q 
       61.84        43.07        17.23        20.22       109.58        66.05 
TCGA-AR-A24S TCGA-AR-A24U TCGA-AR-A251 TCGA-AR-A256 TCGA-AR-A2LR TCGA-B6-A0I1 
       62.07        53.36        45.17        93.83        20.38        77.62 
TCGA-B6-A0I2 TCGA-B6-A0IE TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IO TCGA-B6-A0IQ 
      143.38        65.72       176.98        18.77       110.14       140.88 
TCGA-B6-A0RE TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WX TCGA-B6-A0X1 TCGA-B6-A1KF 
      211.56       100.70       131.21        21.47       186.48       101.52 
TCGA-B6-A402 TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0B3 TCGA-BH-A0B6 TCGA-BH-A0B9 
       54.28        38.79        20.45        39.55        56.94        51.68 
TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0BR TCGA-BH-A0BW 
       25.71        24.85        44.05        48.69        53.69        11.67 
TCGA-BH-A0C0 TCGA-BH-A0DL TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0GY TCGA-BH-A0H9 
       41.75        48.23         4.41         9.63        30.35        41.00 
TCGA-BH-A0WA TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EY TCGA-BH-A1F6 
       23.05        55.63         7.36        51.16        17.69        97.48 
TCGA-BH-A1FN 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-A12U TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A1HF 
       12.66         3.12         1.78         0.69         0.62        10.92 
TCGA-C8-A1HJ TCGA-C8-A1HM TCGA-C8-A26W TCGA-C8-A278 TCGA-C8-A27B TCGA-D8-A13Z 
        0.16         2.30         0.23         0.03         0.99        20.88 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A147 TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JJ 
       13.97        14.17        19.20        12.03        12.03        20.09 
TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JP TCGA-D8-A1X5 TCGA-D8-A1XJ 
       20.12        20.09        19.40        21.01        18.58        21.83 
TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XQ TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XZ 
       14.50        19.92        16.41        12.99        12.66        15.32 
TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27M TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Y 
       16.04        13.05        13.48        38.60        31.96        28.60 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15M TCGA-E2-A1AZ 
       17.03        25.41        14.79        25.05         7.73        60.53 
TCGA-E2-A1II TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI 
       33.70        20.98        27.42        28.90       106.75       102.61 
TCGA-E2-A1LL TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NC 
       43.04        22.26        19.89        12.00        13.12        39.55 
TCGA-E9-A1ND TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G 
       12.59        34.59        34.13        22.75        12.89        23.51 
TCGA-E9-A244 TCGA-E9-A3QA TCGA-E9-A5FL TCGA-EW-A1J1 TCGA-EW-A1OV TCGA-EW-A1OW 
        0.69         0.62         0.26        18.90        25.94        22.82 
TCGA-EW-A1OZ TCGA-EW-A1P4 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PF 
       40.41        29.82         7.86        18.90        19.99        14.43 
TCGA-EW-A1PH TCGA-EW-A2FV TCGA-EW-A3U0 TCGA-GI-A2C9 TCGA-GM-A2DF TCGA-GM-A2DH 
       19.96        25.91        17.49       109.87        42.71        42.28 
TCGA-GM-A3XL TCGA-LL-A441 TCGA-LL-A5YN TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y 
       69.30         2.99         3.65         3.25         3.88         4.14 
TCGA-LL-A8F5 TCGA-OL-A5D7 TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-OL-A66I 
        6.21        46.55        26.20         9.80        23.70 

$subtype5
TCGA-A2-A0CU TCGA-A2-A0YH TCGA-A2-A1FV TCGA-A2-A1G0 TCGA-A2-A25D TCGA-A8-A091 
        5.19        21.67        23.47        20.25        18.15        19.07 
TCGA-AO-A03R TCGA-AO-A1KP TCGA-B6-A0IA TCGA-B6-A0WW TCGA-B6-A1KC TCGA-B6-A2IU 
       68.75        82.62       220.90        17.98        43.59       170.17 
TCGA-BH-A0AY TCGA-BH-A0B2 TCGA-BH-A0BT TCGA-BH-A0DS TCGA-BH-A0H0 TCGA-BH-A0HB 
       25.55        40.83        45.57         2.56        15.16        26.50 
TCGA-BH-A18I TCGA-BH-A1EO TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A204 TCGA-C8-A12X 
        7.23        91.99       114.15        33.17        83.31        12.66 
TCGA-D8-A1X6 TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1Y2 TCGA-E2-A10C TCGA-E2-A15F 
       17.79        17.16        15.22        14.24        40.11        21.63 
TCGA-E2-A15R TCGA-E2-A1B0 TCGA-E2-A1IN TCGA-E2-A1LG TCGA-E2-A1LK TCGA-E9-A1N6 
       17.06        53.62        22.19        18.87         8.75        13.48 
TCGA-E9-A1RB TCGA-EW-A1P0 TCGA-GM-A2DC TCGA-JL-A3YX TCGA-LL-A7SZ 
       20.81        41.13        53.52        11.57         5.59 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.03     0.07     0.03     0.03     2.56 
subtype1 subtype2 subtype3 subtype4 subtype5 
  234.28   162.05   189.01   211.56   220.90 
subtype1 subtype2 subtype3 subtype4 subtype5 
  23.130   21.335   19.235   21.470   21.630 
[1] "0.0 - 234.3 (23.1)" "0.1 - 162.1 (21.3)" "0.0 - 189.0 (19.2)"
[4] "0.0 - 211.6 (21.5)" "2.6 - 220.9 (21.6)"
D3V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1      40       43        7        7       103        83         1
  subtype2      11       15        1        1        76        47         1
  subtype3       6        2        0        1        30        26         0
  subtype4      19       15        1        0       108        59         0
  subtype5       4        2        0        0        18         9         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
  subtype1         44          6         27        5         0       9
  subtype2         48         14         11        7         0       2
  subtype3         11          4          9        2         0       1
  subtype4         30          3         10        3         1       3
  subtype5          5          0          2        0         0       1
D3V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          40       11        6       19        4
  STAGE IA         43       15        2       15        2
  STAGE IB          7        1        0        1        0
  STAGE II          7        1        1        0        0
  STAGE IIA       103       76       30      108       18
  STAGE IIB        83       47       26       59        9
  STAGE III         1        1        0        0        0
  STAGE IIIA       44       48       11       30        5
  STAGE IIIB        6       14        4        3        0
  STAGE IIIC       27       11        9       10        2
  STAGE IV          5        7        2        3        0
  STAGE TIS         0        0        0        1        0
  STAGE X           9        2        1        3        1
[1] 13  5
[1] 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
  subtype1 139 171  54  10
  subtype2  46 151  23  14
  subtype3  11  60  15   6
  subtype4  48 175  23   5
  subtype5  14  24   2   1
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1      139       46       11       48       14
  T2      171      151       60      175       24
  T3       54       23       15       23        2
  T4       10       14        6        5        1
[1] 4 5
[1] 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
  subtype1 176 131  29  31
  subtype2  90  80  42  15
  subtype3  40  33   7  11
  subtype4 145  69  28  11
  subtype5  17  17   5   2
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0      176       90       40      145       17
  N1      131       80       33       69       17
  N2       29       42        7       28        5
  N3       31       15       11       11        2
[1] 4 5
[1] 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
  subtype1        1 304   5  65
  subtype2        0 208   7  19
  subtype3        0  76   2  14
  subtype4        0 222   3  28
  subtype5        1  35   0   5
D3V6, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4 subtype5
  CM0 (I+)        1        0        0        0        1
  M0            304      208       76      222       35
  M1              5        7        2        3        0
  MX             65       19       14       28        5
[1] 4 5
[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
  subtype1 375   0
  subtype2 224  10
  subtype3  91   1
  subtype4 253   0
  subtype5  41   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  375    0
  subtype2  224   10
  subtype3   91    1
  subtype4  253    0
  subtype5   41    0
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE      375      224       91      253       41
  MALE          0       10        1        0        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  subtype1                          0                           221
  subtype2                          0                           202
  subtype3                          0                            55
  subtype4                          1                           226
  subtype5                          0                            31
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                            107                   0
  subtype2                             18                   0
  subtype3                             31                   0
  subtype4                              5                   4
  subtype5                              5                   1
          vv
clus       MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                               15                 10             22
  subtype2                                4                  3              7
  subtype3                                5                  0              1
  subtype4                                4                  0             12
  subtype5                                1                  1              2
D3V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  INFILTRATING CARCINOMA NOS              0        0        0        1        0
  INFILTRATING DUCTAL CARCINOMA         221      202       55      226       31
  INFILTRATING LOBULAR CARCINOMA        107       18       31        5        5
  MEDULLARY CARCINOMA                     0        0        0        4        1
  MIXED HISTOLOGY (PLEASE SPECIFY)       15        4        5        4        1
  MUCINOUS CARCINOMA                     10        3        0        0        1
  OTHER  SPECIFY                         22        7        1       12        2
[1] 7 5
[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
  subtype1  92 283
  subtype2  72 162
  subtype3  20  72
  subtype4  83 170
  subtype5  15  26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   92  283
  subtype2   72  162
  subtype3   20   72
  subtype4   83  170
  subtype5   15   26
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        92       72       20       83       15
  YES      283      162       72      170       26
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1    16                        44
  subtype2                                0    19                        23
  subtype3                                0     4                         6
  subtype4                                0    15                        59
  subtype5                                0     2                         5
          vv
clus       WHITE
  subtype1   286
  subtype2   153
  subtype3    72
  subtype4   164
  subtype5    33
D3V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0        0        0
  ASIAN                                  16       19        4       15        2
  BLACK OR AFRICAN AMERICAN              44       23        6       59        5
  WHITE                                 286      153       72      164       33
[1] 4 5
[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
  subtype1  17 301
  subtype2   7 179
  subtype3   2  70
  subtype4   9 211
  subtype5   1  35
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17  301
  subtype2    7  179
  subtype3    2   70
  subtype4    9  211
  subtype5    1   35
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO           17        7        2        9        1
  NOT HISPANIC OR LATINO      301      179       70      211       35
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = METHLYATION_CNMF
D4V1, survival
          sevent
clus2        0   1
  subtype1 109  18
  subtype2 171  18
  subtype3 142  26
  subtype4  81   4
  subtype5 105  10
subtype1 subtype2 subtype3 subtype4 subtype5 
     127      189      168       85      115 
subtype1 subtype2 subtype3 subtype4 subtype5 
      18       18       26        4       10 
$subtype1
TCGA-A1-A0SB TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A0SX TCGA-A2-A0T0 
        8.52        31.79        28.01        19.20        50.43        17.52 
TCGA-A2-A0T2 TCGA-A2-A0T7 TCGA-A2-A0YE TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A1G1 
        8.38        20.75        18.21        18.61        31.73        19.20 
TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 
       33.93        83.01        29.98        38.40        34.98        38.37 
TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A26F TCGA-A7-A26G 
        9.01        12.00        31.73        10.72        24.26        23.74 
TCGA-A7-A26I TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A5ZV TCGA-A7-A6VV TCGA-A7-A6VW 
       21.73        14.50        21.17        12.10        10.29         9.37 
TCGA-A7-A6VY TCGA-AC-A2BK TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A3W5 TCGA-AC-A62X 
        8.75        38.53         1.02         2.27         1.81         1.12 
TCGA-AC-A6IW TCGA-AN-A0XU TCGA-AO-A0JB TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A129 
        0.69         0.33        50.70        55.33       102.58        96.10 
TCGA-AO-A1KO TCGA-AO-A1KR TCGA-AQ-A54N TCGA-AR-A0TP TCGA-AR-A0TU TCGA-AR-A0U0 
       14.73        70.39         2.56        82.88        11.84        65.36 
TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AN TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AY 
       55.36        61.84        43.73        43.07        17.23        20.22 
TCGA-AR-A24Q TCGA-AR-A251 TCGA-AR-A256 TCGA-AR-A2LR TCGA-B6-A0I1 TCGA-B6-A0RE 
       66.05        45.17        93.83        20.38        77.62       211.56 
TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WX TCGA-B6-A0X1 TCGA-B6-A1KF TCGA-B6-A402 
      100.70       131.21        21.47       186.48       101.52        54.28 
TCGA-BH-A0B3 TCGA-BH-A0B9 TCGA-BH-A0E0 TCGA-BH-A0GY TCGA-BH-A0H9 TCGA-BH-A0WA 
       39.55        51.68         4.41        30.35        41.00        23.05 
TCGA-BH-A1F6 TCGA-BH-A1FC TCGA-BH-A1FN TCGA-BH-A208 TCGA-C8-A1HJ TCGA-C8-A26Y 
       97.48       114.15        72.07        57.83         0.16         0.43 
TCGA-C8-A27B TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1XK TCGA-D8-A1XQ 
        0.99        20.12        20.09        19.40        14.50        16.41 
TCGA-D8-A1XT TCGA-D8-A1XW TCGA-D8-A27F TCGA-D8-A27H TCGA-E2-A14N TCGA-E2-A1AZ 
        6.35        12.66        16.04        13.05        47.15        60.53 
TCGA-E2-A1B0 TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL 
       53.62        18.87       106.75       102.61         8.75        43.04 
TCGA-E2-A1LS TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 
       15.45        22.26        19.89        13.48        12.00        13.12 
TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1RB TCGA-E9-A1RH TCGA-E9-A22E TCGA-E9-A22G 
       39.55        12.59        20.81        34.59        12.89        23.51 
TCGA-E9-A244 TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A1PH 
        0.69        22.82        29.82         7.86        19.99        19.96 
TCGA-GI-A2C9 TCGA-GM-A2DB TCGA-GM-A3XL TCGA-JL-A3YW TCGA-LL-A5YP TCGA-LL-A6FR 
      109.87        53.13        69.30        11.84         3.25         3.88 
TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A8F5 TCGA-OL-A5RW TCGA-OL-A5RZ TCGA-OL-A5S0 
        4.14         4.50         6.21        26.20        10.29         9.80 
TCGA-OL-A66I 
       23.70 

$subtype2
TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SQ TCGA-A2-A04R 
       43.43        14.27        47.24        20.88        18.21        82.16 
TCGA-A2-A0CK TCGA-A2-A0CO TCGA-A2-A0EU TCGA-A2-A0YC TCGA-A2-A0YF TCGA-A2-A1FX 
      125.59       112.08        34.29        32.55        15.42        36.79 
TCGA-A2-A1G0 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25E TCGA-A2-A3KD TCGA-A2-A4S2 
       20.25        16.31        17.19        91.92        39.65         6.74 
TCGA-A7-A0D9 TCGA-A7-A26E TCGA-A7-A26J TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       37.45        31.36        20.61        10.59        10.29        11.28 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SB TCGA-A7-A6VX TCGA-A8-A08O 
       13.41        14.70        11.97        13.74        10.42        31.00 
TCGA-A8-A0AD TCGA-AC-A23E TCGA-AC-A2BM TCGA-AC-A2FG TCGA-AC-A2QI TCGA-AC-A3TN 
       38.04         2.37        38.20        36.99         0.92         1.12 
TCGA-AC-A3YJ TCGA-AN-A0XL TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT 
        1.32         0.33         0.30         0.33         0.33         0.33 
TCGA-AO-A03N TCGA-AO-A0JD TCGA-AO-A0JJ TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A12B 
       66.77        72.00        62.04        99.25        93.70        77.56 
TCGA-AO-A12C TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AQ-A54O TCGA-AR-A0TR TCGA-AR-A1AK 
       65.56        82.62        61.87        21.86         5.26        51.25 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AS TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24V 
       48.82        62.56        40.83        73.02        65.46        54.18 
TCGA-AR-A2LE TCGA-AR-A2LM TCGA-AR-A2LN TCGA-B6-A0RG TCGA-B6-A0RI TCGA-B6-A0RM 
      128.65        40.04        17.10        68.45       234.28        78.02 
TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WZ TCGA-B6-A0X4 
      162.05       102.77       188.68        79.63       129.57        28.27 
TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A408 TCGA-BH-A0AU 
       58.88        43.59        73.51       170.17        49.94        24.53 
TCGA-BH-A0AZ TCGA-BH-A0B5 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BM TCGA-BH-A0BS 
       28.50        48.36        37.22        32.02        61.68        53.95 
TCGA-BH-A0BT TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0H0 TCGA-BH-A0H6 TCGA-BH-A0HA 
       45.57        15.65         3.22        15.16        24.56        52.96 
TCGA-BH-A0HB TCGA-BH-A0HF TCGA-BH-A0HI TCGA-BH-A0HN TCGA-BH-A0W3 TCGA-BH-A0W4 
       26.50        23.90        20.38        16.96        23.93        24.95 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EX TCGA-BH-A1F5 TCGA-BH-A1FG TCGA-BH-A1FJ 
      113.82        82.85        49.58        89.16       122.89        63.35 
TCGA-BH-A1FL TCGA-BH-A1FR TCGA-BH-A28Q TCGA-C8-A26W TCGA-C8-A26Z TCGA-C8-A273 
       55.00       144.59         6.44         0.23         8.28         9.67 
TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JI TCGA-D8-A1JS TCGA-D8-A1JT 
       15.78        18.15        18.90        18.97        12.20        13.32 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XO 
       17.79        16.73        25.74        18.15         2.66         7.96 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A27T 
       15.85        16.31        15.16        16.54        15.52        13.08 
TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-E2-A106 TCGA-E2-A107 TCGA-E2-A10B 
       12.53        14.50        18.51        59.41        34.42        37.51 
TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A1B4 
       28.44        28.87        17.42        19.40         9.04        29.95 
TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       16.47        38.30         3.88        22.19        20.98        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A572 
       54.18        39.62        19.66         7.20        18.05        27.32 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1NI TCGA-E9-A1R0 TCGA-E9-A1R3 TCGA-E9-A1RD 
       19.20        36.82         9.86        14.30         2.10         0.66 
TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A229 TCGA-E9-A22H 
       21.27        35.64        34.13         0.79        13.32        24.10 
TCGA-E9-A245 TCGA-E9-A249 TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A6HE TCGA-EW-A1IX 
        0.85         0.95        26.07        18.41        15.39        39.72 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1OY TCGA-EW-A1P0 
       18.90        13.25        16.57        28.77        29.85        41.13 
TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1PE TCGA-EW-A2FW TCGA-GM-A5PV 
       52.96        23.11        18.48        10.52        22.09        13.55 
TCGA-GM-A5PX TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A7W6 TCGA-LL-A442 TCGA-LL-A50Y 
       18.12        11.57         8.28         4.60         3.58         6.90 
TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66O 
       14.76        54.51         7.23 

$subtype3
TCGA-A1-A0SF TCGA-A1-A0SJ TCGA-A1-A0SN TCGA-A2-A0CT TCGA-A2-A0SV TCGA-A2-A0SW 
       48.10        13.68        39.32        75.25        27.12        44.88 
TCGA-A2-A0SY TCGA-A2-A0T4 TCGA-A2-A0T6 TCGA-A2-A0YG TCGA-A2-A0YT TCGA-A2-A1FV 
       44.28        20.52        18.90        21.90        23.77        23.47 
TCGA-A2-A1FW TCGA-A2-A1G4 TCGA-A2-A25D TCGA-A2-A3XV TCGA-A7-A13F TCGA-A7-A26H 
       17.36        19.56        18.15        14.07        12.72        23.80 
TCGA-A7-A2KD TCGA-A7-A4SF TCGA-A8-A075 TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A2B8 
       22.32        17.92        17.03         0.95         2.66         1.48 
TCGA-AC-A2FM TCGA-AC-A62V TCGA-AC-A8OP TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XV 
       26.04         0.07         1.74         0.33        12.33         5.33 
TCGA-AO-A03L TCGA-AO-A0JA TCGA-AO-A0JE TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JM 
       80.28        21.53        76.77        26.24        38.53        71.80 
TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04L TCGA-AQ-A0Y5 
       57.30        41.62        17.79        24.79       130.09         5.65 
TCGA-AQ-A1H2 TCGA-AR-A0TQ TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TZ TCGA-AR-A0U2 
       15.62        49.32        29.75        24.30        76.14        83.87 
TCGA-AR-A0U3 TCGA-AR-A1AP TCGA-AR-A1AT TCGA-AR-A1AV TCGA-AR-A24H TCGA-AR-A24N 
       76.18        39.98        41.82        42.58       109.58        68.19 
TCGA-AR-A24R TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A255 TCGA-AR-A2LK TCGA-AR-A2LL 
       57.40        51.75        56.15        34.82        42.87         7.36 
TCGA-AR-A5QN TCGA-B6-A0IK TCGA-B6-A0RL TCGA-B6-A0RN TCGA-B6-A0WW TCGA-B6-A0X5 
       16.04        18.77        81.17       172.96        17.98        68.94 
TCGA-B6-A1KN TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AW TCGA-BH-A0B8 TCGA-BH-A0BZ 
      139.17        82.88        55.00        20.45        51.58        49.05 
TCGA-BH-A0DD TCGA-BH-A0DH TCGA-BH-A0DK TCGA-BH-A0DS TCGA-BH-A0E2 TCGA-BH-A0H7 
       45.83        38.01        13.91         2.56        14.30        23.08 
TCGA-BH-A0HK TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1EY 
        5.85        27.25        50.79        69.93        91.99        17.69 
TCGA-BH-A1F2 TCGA-BH-A1F8 TCGA-BH-A1FD TCGA-BH-A1FM TCGA-BH-A203 TCGA-BH-A204 
       31.53        24.66        33.17        45.63        38.60        83.31 
TCGA-BH-A42T TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V 
        0.99        12.03        10.42         2.30         3.25         0.30 
TCGA-C8-A26X TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A3M8 TCGA-D8-A1J8 
        0.36         0.03         0.03        12.20         0.23        14.17 
TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JJ TCGA-D8-A1JN 
       17.49        16.50        12.03        12.03        20.09        20.38 
TCGA-D8-A1X5 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XF TCGA-D8-A1XJ TCGA-D8-A1XU 
       18.58        23.90        27.58        15.22        21.83        12.99 
TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27G TCGA-D8-A27N TCGA-D8-A27W 
       15.32         3.81        14.14        13.45         4.80        12.26 
TCGA-E2-A105 TCGA-E2-A109 TCGA-E2-A10C TCGA-E2-A1BD TCGA-E2-A1IG TCGA-E2-A1LE 
       43.00        46.59        40.11        17.10        32.78        28.90 
TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E9-A1NA TCGA-E9-A1NF TCGA-E9-A1R5 TCGA-E9-A1R6 
       16.93         5.52        36.56        20.05         1.38         2.76 
TCGA-E9-A1R7 TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A228 TCGA-E9-A247 
       21.21        40.24        34.65         6.58        12.53        27.22 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A54Y TCGA-E9-A5UO TCGA-EW-A1IW TCGA-EW-A1J5 
        0.72        17.75         0.23         0.23        12.20        15.68 
TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1PA TCGA-EW-A1PC TCGA-EW-A2FS 
       25.94        29.95        40.41        18.90         6.15        52.73 
TCGA-EW-A3E8 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DC 
       21.27        10.16        10.59         7.40        59.57        53.52 
TCGA-GM-A2DL TCGA-GM-A3NW TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A6FQ TCGA-LL-A740 
       90.84       110.50         5.56         4.70         2.63         4.50 
TCGA-LL-A7T0 TCGA-LQ-A4E4 TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-S3-A6ZG 
        3.22        15.91        33.90        31.07        18.21         6.81 

$subtype4
TCGA-A1-A0SM TCGA-A2-A0SU TCGA-A2-A0T5 TCGA-A2-A0YD TCGA-A2-A0YL TCGA-A2-A1FZ 
        7.96        54.64        17.46        25.28        14.63        22.45 
TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A3KC TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 
       16.47        52.47        20.88         7.30         8.81         8.91 
TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A4SC TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A8-A0A6 
       23.61        29.56        14.66        10.72        11.05        21.04 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A62Y TCGA-AC-A6IX TCGA-AO-A1KS 
        0.69        14.83         9.40         1.81         0.43         0.53 
TCGA-AQ-A1H3 TCGA-AR-A1AU TCGA-AR-A24K TCGA-AR-A24P TCGA-AR-A24T TCGA-AR-A24W 
       13.22        46.32        50.89         0.85        53.26        50.96 
TCGA-AR-A24X TCGA-AR-A254 TCGA-AR-A5QP TCGA-B6-A0RV TCGA-B6-A0WY TCGA-BH-A0B2 
       48.16        39.85        20.45       157.41       113.79        40.83 
TCGA-BH-A0BJ TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0E1 TCGA-BH-A0GZ TCGA-BH-A0H3 
       21.70        23.44        22.13        15.68        10.78        37.78 
TCGA-BH-A0HP TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1FH TCGA-BH-A201 TCGA-BH-A202 
       13.61        12.00        55.69        36.92         6.90         0.72 
TCGA-BH-A28O TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HI TCGA-D8-A1JH TCGA-D8-A1JP 
       10.65        12.33        10.92        11.34        14.01        21.01 
TCGA-D8-A1JU TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A27E 
       14.70        17.16        14.73        19.92        17.69        17.42 
TCGA-D8-A27K TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A4Z1 TCGA-E2-A14U TCGA-E2-A1IH 
        9.44         0.76        10.09         7.33        43.33        33.73 
TCGA-E2-A1L7 TCGA-E2-A1LB TCGA-E9-A1R2 TCGA-E9-A1RA TCGA-E9-A22B TCGA-E9-A24A 
       27.42        40.47         0.62        32.09        22.75        12.56 
TCGA-E9-A3X8 TCGA-EW-A1IY TCGA-EW-A1PD TCGA-EW-A2FR TCGA-GM-A2DM TCGA-GM-A3NY 
       15.72         8.48        13.94        55.00        76.64        38.20 
TCGA-GM-A3XG TCGA-GM-A3XN TCGA-LD-A74U TCGA-MS-A51U TCGA-OL-A5RV TCGA-OL-A5RX 
       32.28        53.95         6.67         2.79        24.10        16.87 
TCGA-W8-A86G 
        5.29 

$subtype5
TCGA-A2-A0CR TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0ST TCGA-A2-A0T1 TCGA-A2-A0YH 
      107.93        89.36       107.61        99.19        17.13        21.67 
TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A25A TCGA-A2-A25F TCGA-A2-A3XW TCGA-A2-A3XZ 
       14.50        19.33       107.70        10.59        49.48        31.99 
TCGA-A2-A4S3 TCGA-A7-A3IY TCGA-A7-A4SA TCGA-AC-A23G TCGA-AC-A2FB TCGA-AC-A2FF 
        3.42        11.34        14.93        10.85        40.57        55.43 
TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A3BB TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A5XS 
       38.79        50.70         0.99         1.68         1.55         1.55 
TCGA-AC-A6IV TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03U TCGA-AO-A0JC TCGA-AO-A0JF 
        1.18         5.59        47.84        59.05        50.86        21.37 
TCGA-AO-A128 TCGA-AQ-A7U7 TCGA-AR-A0TT TCGA-AR-A0TX TCGA-AR-A1AJ TCGA-AR-A1AO 
       94.59         9.99        56.88        64.83        52.77        43.56 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24O TCGA-AR-A24S TCGA-AR-A24U TCGA-AR-A252 
       35.24        36.26        65.69        62.07        53.36        40.64 
TCGA-AR-A2LH TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QQ TCGA-B6-A0RT TCGA-B6-A401 
       20.25        20.81        16.96        10.59        89.46        85.35 
TCGA-BH-A0B6 TCGA-BH-A0BF TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0DV TCGA-BH-A0RX 
       56.94        25.71        41.75        48.13        45.17         5.59 
TCGA-BH-A0W5 TCGA-BH-A1EU TCGA-BH-A1F0 TCGA-BH-A1FB TCGA-BH-A1FE TCGA-BH-A1FU 
       42.35        42.28        25.81       120.62        74.73        72.07 
TCGA-BH-A209 TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A1HG TCGA-C8-A278 
      130.16        20.12       109.28         8.94        11.34         0.03 
TCGA-C8-A3M7 TCGA-D8-A1JB TCGA-D8-A1Y2 TCGA-D8-A27I TCGA-D8-A27L TCGA-D8-A27M 
        0.03        18.71        14.24        14.43        16.41        13.48 
TCGA-E2-A108 TCGA-E2-A1B1 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1IF TCGA-E2-A1II 
       27.52        53.03        32.35        28.50        37.41        33.70 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1LA TCGA-E2-A3DX TCGA-E9-A1NE TCGA-E9-A1NG 
       28.44        22.65        24.59        15.72        35.77        21.57 
TCGA-E9-A1QZ TCGA-E9-A1R4 TCGA-E9-A22A TCGA-E9-A243 TCGA-E9-A248 TCGA-E9-A2JT 
       11.90         6.12        39.09        17.06         1.94         0.76 
TCGA-E9-A3QA TCGA-EW-A1IZ TCGA-EW-A1P1 TCGA-EW-A1P7 TCGA-EW-A1PF TCGA-EW-A1PG 
        0.62        18.21        39.78        30.08        14.43        34.55 
TCGA-EW-A2FV TCGA-EW-A3U0 TCGA-GM-A2DA TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH 
       25.91        17.49       194.27        43.04        42.71        42.28 
TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A4E0 TCGA-LL-A440 
       61.91        62.33        77.33        53.36        57.63         0.66 
TCGA-LL-A441 TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A7SZ TCGA-OL-A5RU TCGA-OL-A5RY 
        2.99         3.65         3.19         5.59        27.65        14.10 
TCGA-OL-A66P 
        4.44 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.16     0.23     0.03     0.43     0.03 
subtype1 subtype2 subtype3 subtype4 subtype5 
  211.56   234.28   172.96   157.41   194.27 
subtype1 subtype2 subtype3 subtype4 subtype5 
  21.170   22.090   20.485   16.870   28.440 
[1] "0.2 - 211.6 (21.2)" "0.2 - 234.3 (22.1)" "0.0 - 173.0 (20.5)"
[4] "0.4 - 157.4 (16.9)" "0.0 - 194.3 (28.4)"
D4V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       6        8        0        0        61        31         0
  subtype2      13       16        3        3        51        55         0
  subtype3       9       10        0        1        48        38         1
  subtype4       6       12        0        2        19        18         0
  subtype5      18       12        2        2        41        16         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  subtype1         12          1          3        3       1
  subtype2         31          6         12        1       2
  subtype3         38          8         11        3       2
  subtype4         13          1         13        1       0
  subtype5         16          1          7        0       0
D4V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           6       13        9        6       18
  STAGE IA          8       16       10       12       12
  STAGE IB          0        3        0        0        2
  STAGE II          0        3        1        2        2
  STAGE IIA        61       51       48       19       41
  STAGE IIB        31       55       38       18       16
  STAGE III         0        0        1        0        1
  STAGE IIIA       12       31       38       13       16
  STAGE IIIB        1        6        8        1        1
  STAGE IIIC        3       12       11       13        7
  STAGE IV          3        1        3        1        0
  STAGE X           1        2        2        0        0
[1] 12  5
[1] 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
  subtype1  22  89  12   3
  subtype2  55 108  24   5
  subtype3  32  99  28  10
  subtype4  25  47  12   1
  subtype5  49  54  12   1
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       22       55       32       25       49
  T2       89      108       99       47       54
  T3       12       24       28       12       12
  T4        3        5       10        1        1
[1] 4 5
[1] 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
  subtype1 76 35 11  4
  subtype2 67 87 22 13
  subtype3 67 55 32 11
  subtype4 35 27 10 13
  subtype5 60 36 12  8
D4V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       76       67       67       35       60
  N1       35       87       55       27       36
  N2       11       22       32       10       12
  N3        4       13       11       13        8
[1] 4 5
[1] 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
  subtype1        0 105   3  19
  subtype2        1 160   1  31
  subtype3        0 135   3  31
  subtype4        0  68   1  16
  subtype5        0  94   0  22
D4V6, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4 subtype5
  CM0 (I+)        0        1        0        0        0
  M0            105      160      135       68       94
  M1              3        1        3        1        0
  MX             19       31       31       16       22
[1] 4 5
[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
  subtype1 127   0
  subtype2 190   3
  subtype3 166   3
  subtype4  83   2
  subtype5 116   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  127    0
  subtype2  190    3
  subtype3  166    3
  subtype4   83    2
  subtype5  116    0
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE      127      190      166       83      116
  MALE          0        3        3        2        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  subtype1                          1                           104
  subtype2                          0                           117
  subtype3                          0                           124
  subtype4                          0                            51
  subtype5                          0                            77
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                              4                   3
  subtype2                             44                   0
  subtype3                             34                   0
  subtype4                             29                   0
  subtype5                             31                   2
          vv
clus       MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                                2                  0             12
  subtype2                               14                  7             11
  subtype3                                3                  3              5
  subtype4                                3                  1              1
  subtype5                                2                  1              3
D4V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  INFILTRATING CARCINOMA NOS              1        0        0        0        0
  INFILTRATING DUCTAL CARCINOMA         104      117      124       51       77
  INFILTRATING LOBULAR CARCINOMA          4       44       34       29       31
  MEDULLARY CARCINOMA                     3        0        0        0        2
  MIXED HISTOLOGY (PLEASE SPECIFY)        2       14        3        3        2
  MUCINOUS CARCINOMA                      0        7        3        1        1
  OTHER  SPECIFY                         12       11        5        1        3
[1] 7 5
[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
  subtype1  44  83
  subtype2  60 133
  subtype3  54 115
  subtype4  23  62
  subtype5  34  82
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   44   83
  subtype2   60  133
  subtype3   54  115
  subtype4   23   62
  subtype5   34   82
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        44       60       54       23       34
  YES       83      133      115       62       82
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     5                        43
  subtype2                                0     8                        19
  subtype3                                0    12                        23
  subtype4                                0     4                         8
  subtype5                                1     5                        19
          vv
clus       WHITE
  subtype1    76
  subtype2   163
  subtype3   130
  subtype4    72
  subtype5    88
D4V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        0        1
  ASIAN                                   5        8       12        4        5
  BLACK OR AFRICAN AMERICAN              43       19       23        8       19
  WHITE                                  76      163      130       72       88
[1] 4 5
[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
  subtype1   6 107
  subtype2  10 165
  subtype3  11 144
  subtype4   2  73
  subtype5   6 101
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6  107
  subtype2   10  165
  subtype3   11  144
  subtype4    2   73
  subtype5    6  101
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            6       10       11        2        6
  NOT HISPANIC OR LATINO      107      165      144       73      101
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = RPPA_CNMF
D5V1, survival
          sevent
clus2        0   1
  subtype1 122  25
  subtype2 120  13
  subtype3 103  13
subtype1 subtype2 subtype3 
     147      133      116 
subtype1 subtype2 subtype3 
      25       13       13 
$subtype1
TCGA-A1-A0SH TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A04T TCGA-A2-A04U 
       47.24        31.79        28.01        18.02        73.84        22.06 
TCGA-A2-A04W TCGA-A2-A04Y TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CX TCGA-A2-A0CY 
       64.04        36.13        64.57        24.79        56.81        55.00 
TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0EQ TCGA-A2-A0EY TCGA-A2-A0SV 
       21.14        34.55        33.76        79.76        24.16        27.12 
TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0YE 
       44.88        50.43        17.52        17.13         8.38        18.21 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A7-A0CE TCGA-A7-A0CJ 
       21.90        21.67        18.61        31.73        35.31        30.61 
TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A8-A06R TCGA-A8-A06U TCGA-A8-A06X 
       35.67        31.73        10.72        17.98        29.03        31.00 
TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A07I TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A07W 
       26.01        17.03        14.01         9.99         8.98         9.99 
TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08X TCGA-A8-A09A TCGA-A8-A09I 
       37.05         9.99        31.00        33.99         9.99        33.07 
TCGA-A8-A09M TCGA-A8-A09R TCGA-A8-A09X TCGA-A8-A0A7 TCGA-AN-A04D TCGA-AN-A0AK 
       15.02         8.98        14.01         0.99         1.71         7.36 
TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FJ 
        6.51         0.16         0.33         0.33         0.33         7.96 
TCGA-AN-A0FL TCGA-AN-A0FV TCGA-AN-A0FY TCGA-AN-A0G0 TCGA-AN-A0XU TCGA-AN-A0XW 
        7.59         0.33         0.33         0.53         0.33         5.59 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03O TCGA-AO-A03U TCGA-AO-A0J2 TCGA-AO-A0J6 
       80.28        47.84        81.63        59.05        32.78        37.48 
TCGA-AO-A0JB TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A129 
       50.70        72.00        76.77        55.33       102.58        96.10 
TCGA-AO-A12D TCGA-AO-A12F TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT 
       64.04        48.36        82.88        49.32        37.41        56.88 
TCGA-AR-A0TU TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0U0 TCGA-AR-A0U1 
       11.84        29.75        24.30        55.86        65.36        70.16 
TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AO TCGA-AR-A1AQ TCGA-AR-A1AT 
       76.18        75.55        61.84        43.56        43.07        41.82 
TCGA-AR-A1AY TCGA-B6-A0I6 TCGA-B6-A0I9 TCGA-B6-A0IJ TCGA-B6-A0IQ TCGA-B6-A0RU 
       20.22        32.78        12.13       176.98       140.88       131.21 
TCGA-B6-A0X1 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B9 TCGA-BH-A0BF TCGA-BH-A0BW 
      186.48        40.83        39.55        51.68        25.71        11.67 
TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0DL TCGA-BH-A0E0 TCGA-BH-A0E2 
       49.05        41.75        48.13        48.23         4.41        14.30 
TCGA-BH-A0EE TCGA-BH-A18G TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18T 
       31.00         2.01        30.28        55.63        37.55         7.36 
TCGA-BH-A18V TCGA-C8-A12L TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U 
       51.16        11.93        12.66        11.77         0.07        12.66 
TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A130 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 
       12.66        12.66         3.12         1.45         0.69         3.85 
TCGA-C8-A138 TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A147 
        3.75        11.90        20.88        13.97        14.17        19.20 
TCGA-E2-A14P TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 
       40.96        31.96        28.60        17.03        25.41        27.12 
TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A1AZ 
       14.79        25.05        60.53 

$subtype2
TCGA-A1-A0SJ TCGA-A2-A04V TCGA-A2-A0CQ TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU 
       13.68        63.12        88.60        75.55        75.25         5.19 
TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EO TCGA-A2-A0EV 
       63.45        64.04        28.77        25.22        80.28        31.82 
TCGA-A2-A0SU TCGA-A2-A0T5 TCGA-A2-A0YD TCGA-A2-A0YI TCGA-A7-A0CD TCGA-A7-A0CH 
       54.64        17.46        25.28        14.50        38.30        35.47 
TCGA-A7-A0DB TCGA-A7-A13F TCGA-A8-A06Z TCGA-A8-A07S TCGA-A8-A07Z TCGA-A8-A082 
       33.11        12.72         1.02         7.99        28.04        18.05 
TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08G TCGA-A8-A08T TCGA-A8-A08Z 
       36.95        13.02         0.99        19.96        93.04        40.01 
TCGA-A8-A091 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09W 
       19.07         9.99        12.00         1.02        31.00         0.99 
TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A0AJ TCGA-AN-A0FD TCGA-AN-A0FF 
        0.23         0.62         2.96         8.02         6.44         4.64 
TCGA-AN-A0FK TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XO TCGA-AN-A0XP 
        7.00         6.02         0.36         0.33        12.33         0.30 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A0J3 TCGA-AO-A0J7 
        0.33         0.33        66.77        84.69        21.40        20.32 
TCGA-AO-A0JC TCGA-AO-A0JG TCGA-AO-A126 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12C 
       50.86        26.24        93.70        90.58        77.56        65.56 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AR-A0TR TCGA-AR-A1AK TCGA-AR-A1AS TCGA-AR-A1AV 
       41.62        28.37         5.26        51.25        40.83        42.58 
TCGA-B6-A0IB TCGA-B6-A0IG TCGA-B6-A0IO TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RP 
      129.57       146.50       110.14        81.17        78.02       102.77 
TCGA-B6-A0X0 TCGA-BH-A0B1 TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BQ TCGA-BH-A0BS 
      129.70        37.74        21.70        61.68        27.19        53.95 
TCGA-BH-A0BV TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DH TCGA-BH-A0DK TCGA-BH-A0DT 
       49.94        42.90        45.83        38.01        13.91        38.47 
TCGA-BH-A0E7 TCGA-BH-A0EB TCGA-BH-A0H5 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HK 
       44.81        24.49        35.51        41.00        52.96         5.85 
TCGA-BH-A0HL TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0W4 TCGA-BH-A0W5 
        2.37        12.89        51.32        27.25        24.95        42.35 
TCGA-BH-A18F TCGA-BH-A18N TCGA-BH-A18S TCGA-C8-A12M TCGA-C8-A12X TCGA-D8-A140 
        8.81        37.74        66.05        11.77        12.66        13.25 
TCGA-D8-A145 TCGA-D8-A146 TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B 
       13.48        21.14        34.42        46.59        40.41        37.51 
TCGA-E2-A10E TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14W TCGA-E2-A153 
       28.44        44.68        38.24        33.17        32.02        23.24 
TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15A TCGA-E2-A15D TCGA-E2-A15E 
       19.43        21.04        23.87        23.34        17.29        20.71 
TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15O 
       18.21        12.92        19.40         9.04        20.58        13.02 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B4 TCGA-E2-A1BC 
       19.56        17.06        14.07        14.99        29.95        16.47 
TCGA-E2-A1BD 
       17.10 

$subtype3
TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A0CP TCGA-A2-A0CZ TCGA-A2-A0ER TCGA-A2-A0ES 
      104.81        41.95        92.48        53.13        74.40        37.05 
TCGA-A2-A0EU TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0T3 TCGA-A2-A0T4 
       34.29        29.75        24.72        99.19        18.71        20.52 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YF TCGA-A2-A0YK TCGA-A2-A0YL 
       18.90        20.75        32.55        15.42        19.33        14.63 
TCGA-A2-A0YT TCGA-A7-A0CG TCGA-A7-A0D9 TCGA-A8-A06P TCGA-A8-A076 TCGA-A8-A079 
       23.77        34.29        37.45        13.02        53.98         9.01 
TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07P TCGA-A8-A084 TCGA-A8-A08O TCGA-A8-A095 
       19.99        18.97        10.98        15.06        31.00        41.98 
TCGA-A8-A09K TCGA-A8-A0A4 TCGA-AN-A0FS TCGA-AN-A0FX TCGA-AN-A0XN TCGA-AO-A0J5 
       29.98        13.02         6.28         0.33         0.33        24.16 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JF TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JM 
       22.36        53.03        21.37        38.53        62.04        71.80 
TCGA-AO-A128 TCGA-AO-A12E TCGA-AQ-A04L TCGA-AR-A0TX TCGA-AR-A0TZ TCGA-AR-A0U2 
       94.59        57.30       130.09        64.83        76.14        83.87 
TCGA-AR-A0U4 TCGA-AR-A1AJ TCGA-AR-A1AL TCGA-AR-A1AP TCGA-AR-A1AU TCGA-AR-A1AW 
       55.36        52.77        48.82        39.98        46.32        35.24 
TCGA-AR-A1AX TCGA-B6-A0I2 TCGA-B6-A0I8 TCGA-B6-A0IK TCGA-B6-A0RG TCGA-B6-A0RH 
       36.26       143.38        24.62        18.77        68.45       189.01 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WX 
      172.96       162.05       140.48        89.46       157.41        21.47 
TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B4 
       24.53        38.79        25.55        28.50        46.95        39.16 
TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BO TCGA-BH-A0BP 
       48.36        56.98        37.22        32.02        35.67        48.69 
TCGA-BH-A0BR TCGA-BH-A0BT TCGA-BH-A0C1 TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DP 
       53.69        45.57        44.02        23.44        22.13        15.65 
TCGA-BH-A0DS TCGA-BH-A0DV TCGA-BH-A0E1 TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EA 
        2.56        45.17        15.68         9.63        46.19        32.65 
TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0HN TCGA-BH-A0HP 
       24.43        30.35        24.56        23.08        16.96        13.61 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A18J TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18U 
       50.79         5.59        20.12        26.66        72.56        51.39 
TCGA-C8-A12N TCGA-C8-A131 TCGA-C8-A135 TCGA-E2-A108 TCGA-E2-A10C TCGA-E2-A14T 
       11.77         1.78         0.62        27.52        40.11        33.30 
TCGA-E2-A14V TCGA-E2-A15C TCGA-E2-A15F TCGA-E2-A15M TCGA-E2-A1B0 TCGA-E2-A1B1 
       34.26        22.82        21.63         7.73        53.62        53.03 
TCGA-E2-A1B5 TCGA-E2-A1B6 
       32.35        28.50 

subtype1 subtype2 subtype3 
    0.07     0.23     0.33 
subtype1 subtype2 subtype3 
  186.48   146.50   189.01 
subtype1 subtype2 subtype3 
  28.010   25.280   32.975 
[1] "0.1 - 186.5 (28.0)" "0.2 - 146.5 (25.3)" "0.3 - 189.0 (33.0)"
D5V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1       7        8        1        55        36         24          2
  subtype2      12       12        0        46        38         14          6
  subtype3      13       10        3        36        20         24          5
          vv
clus       STAGE IIIC STAGE IV STAGE X
  subtype1         10        8       3
  subtype2          1        3       3
  subtype3          4        3       2
D5V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           7       12       13
  STAGE IA          8       12       10
  STAGE IB          1        0        3
  STAGE IIA        55       46       36
  STAGE IIB        36       38       20
  STAGE IIIA       24       14       24
  STAGE IIIB        2        6        5
  STAGE IIIC       10        1        4
  STAGE IV          8        3        3
  STAGE X           3        3        2
[1] 10  3
[1] 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
  subtype1  22 106  22   4
  subtype2  34  83  11   6
  subtype3  38  57  17   8
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       22       34       38
  T2      106       83       57
  T3       22       11       17
  T4        4        6        8
[1] 4 3
[1] 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
  subtype1 72 45 22 12
  subtype2 64 53 10  6
  subtype3 57 34 20  7
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       72       64       57
  N1       45       53       34
  N2       22       10       20
  N3       12        6        7
[1] 4 3
[1] 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
  subtype1        0 145   8   1
  subtype2        0 128   3   4
  subtype3        1 114   3   2
D5V6, multiclass
          clus
vv         subtype1 subtype2 subtype3
  CM0 (I+)        0        0        1
  M0            145      128      114
  M1              8        3        3
  MX              1        4        2
[1] 4 3
[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
  subtype1 154   0
  subtype2 131   4
  subtype3 119   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  154    0
  subtype2  131    4
  subtype3  119    1
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      154      131      119
  MALE          0        4        1
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA
  subtype1                           141                              4
  subtype2                           119                              5
  subtype3                            94                             21
          vv
clus       MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  subtype1                   1                                1
  subtype2                   0                                4
  subtype3                   0                                3
          vv
clus       MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                  0              7
  subtype2                  2              5
  subtype3                  0              2
D5V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  INFILTRATING DUCTAL CARCINOMA         141      119       94
  INFILTRATING LOBULAR CARCINOMA          4        5       21
  MEDULLARY CARCINOMA                     1        0        0
  MIXED HISTOLOGY (PLEASE SPECIFY)        1        4        3
  MUCINOUS CARCINOMA                      0        2        0
  OTHER  SPECIFY                          7        5        2
[1] 6 3
[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
  subtype1 57 97
  subtype2 44 91
  subtype3 43 77
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   57   97
  subtype2   44   91
  subtype3   43   77
     clus
vv    subtype1 subtype2 subtype3
  NO        57       44       43
  YES       97       91       77
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1    16                        14
  subtype2                                0     7                         9
  subtype3                                0     4                         6
          vv
clus       WHITE
  subtype1    98
  subtype2   101
  subtype3    95
D5V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0
  ASIAN                                  16        7        4
  BLACK OR AFRICAN AMERICAN              14        9        6
  WHITE                                  98      101       95
[1] 4 3
[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
  subtype1   2 114
  subtype2   2  98
  subtype3   2  85
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  114
  subtype2    2   98
  subtype3    2   85
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        2        2
  NOT HISPANIC OR LATINO      114       98       85
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = RPPA_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 54  8
  subtype2 99 10
  subtype3 78 13
  subtype4 89 15
  subtype5 25  5
subtype1 subtype2 subtype3 subtype4 subtype5 
      62      109       91      104       30 
subtype1 subtype2 subtype3 subtype4 subtype5 
       8       10       13       15        5 
$subtype1
TCGA-A1-A0SH TCGA-A2-A0CQ TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0D3 TCGA-A2-A0EO 
       47.24        88.60        75.55        63.45        28.77        80.28 
TCGA-A2-A0SU TCGA-A2-A0T5 TCGA-A2-A0YD TCGA-A7-A0CD TCGA-A7-A0CH TCGA-A7-A0CJ 
       54.64        17.46        25.28        38.30        35.47        30.61 
TCGA-A7-A0DB TCGA-A8-A07S TCGA-A8-A07Z TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08T 
       33.11         7.99        28.04        13.02         0.99        93.04 
TCGA-A8-A08Z TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09E TCGA-AN-A0FF 
       40.01         9.99        12.00         1.02        31.00         4.64 
TCGA-AN-A0FK TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XS 
        7.00         0.36         0.33        12.33         0.30         0.33 
TCGA-AO-A12A TCGA-AR-A0TR TCGA-AR-A1AS TCGA-AR-A1AV TCGA-B6-A0RL TCGA-B6-A0RM 
       90.58         5.26        40.83        42.58        81.17        78.02 
TCGA-B6-A0RP TCGA-B6-A0X0 TCGA-BH-A0B2 TCGA-BH-A0DH TCGA-BH-A0DT TCGA-BH-A0E7 
      102.77       129.70        40.83        38.01        38.47        44.81 
TCGA-BH-A0EB TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A18N TCGA-D8-A146 TCGA-E2-A10A 
       24.49        24.95        42.35        37.74        21.14        40.41 
TCGA-E2-A10B TCGA-E2-A14Q TCGA-E2-A14Z TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A156 
       37.51        38.24        17.03        23.24        19.43        23.87 
TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15J TCGA-E2-A15O 
       17.29        20.71        21.63        18.21        19.40        13.02 
TCGA-E2-A1B4 TCGA-E2-A1BD 
       29.95        17.10 

$subtype2
TCGA-A1-A0SJ TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A0CP TCGA-A2-A0CZ TCGA-A2-A0ER 
       13.68       104.81        41.95        92.48        53.13        74.40 
TCGA-A2-A0ES TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0T3 
       37.05        34.29        31.82        29.75        24.72        18.71 
TCGA-A2-A0T4 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YF TCGA-A2-A0YI 
       20.52        18.90        20.75        32.55        15.42        14.50 
TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A7-A0CG TCGA-A7-A0D9 TCGA-A8-A06P 
       19.33        14.63        23.77        34.29        37.45        13.02 
TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07P TCGA-A8-A084 TCGA-A8-A08O TCGA-A8-A095 
       19.99        18.97        10.98        15.06        31.00        41.98 
TCGA-A8-A09K TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A0FS TCGA-AN-A0XN TCGA-AO-A0J5 
       29.98         0.23         0.62         6.28         0.33        24.16 
TCGA-AO-A0J8 TCGA-AO-A0JF TCGA-AO-A0JM TCGA-AO-A12C TCGA-AQ-A04L TCGA-AR-A0TZ 
       22.36        21.37        71.80        65.56       130.09        76.14 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX TCGA-B6-A0I2 
       51.25        48.82        46.32        35.24        36.26       143.38 
TCGA-B6-A0I8 TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IO TCGA-B6-A0RN TCGA-B6-A0RO 
       24.62       146.50        18.77       110.14       172.96       162.05 
TCGA-B6-A0RQ TCGA-B6-A0RV TCGA-BH-A0AU TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 
      140.48       157.41        24.53        25.55        28.50        46.95 
TCGA-BH-A0B1 TCGA-BH-A0B5 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BJ TCGA-BH-A0BM 
       37.74        48.36        37.22        32.02        21.70        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BR TCGA-BH-A0BT TCGA-BH-A0C1 TCGA-BH-A0DG 
       35.67        48.69        53.69        45.57        44.02        23.44 
TCGA-BH-A0DI TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DV TCGA-BH-A0E1 TCGA-BH-A0E6 
       22.13        15.65         2.56        45.17        15.68         9.63 
TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0H5 TCGA-BH-A0H6 
       46.19        32.65        24.43        30.35        35.51        24.56 
TCGA-BH-A0H7 TCGA-BH-A0HK TCGA-BH-A0HN TCGA-BH-A0HP TCGA-BH-A0HY TCGA-BH-A0RX 
       23.08         5.85        16.96        13.61        50.79         5.59 
TCGA-BH-A18F TCGA-BH-A18J TCGA-BH-A18M TCGA-BH-A18U TCGA-C8-A12N TCGA-D8-A145 
        8.81        20.12        72.56        51.39        11.77        13.48 
TCGA-E2-A108 TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A14O TCGA-E2-A14T TCGA-E2-A14V 
       27.52        40.11        28.44        44.68        33.30        34.26 
TCGA-E2-A15C TCGA-E2-A15K TCGA-E2-A15P TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B5 
       22.82         9.04        19.56        53.62        53.03        32.35 
TCGA-E2-A1BC 
       16.47 

$subtype3
TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A0CL 
       31.79        28.01        18.02        73.84        22.06        64.57 
TCGA-A2-A0CM TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0EQ TCGA-A2-A0ST 
       24.79        21.14        34.55        33.76        79.76        99.19 
TCGA-A2-A0SX TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0YE TCGA-A2-A0YJ TCGA-A2-A0YM 
       50.43        17.52         8.38        18.21        18.61        31.73 
TCGA-A7-A0CE TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A8-A075 TCGA-A8-A076 
       35.31        35.67        31.73        10.72        17.03        53.98 
TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A08L TCGA-A8-A08P TCGA-AN-A04D TCGA-AN-A0AL 
        9.99         8.98         9.99        31.00         1.71         6.51 
TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FX TCGA-AN-A0G0 
        0.33         0.33         7.96         7.59         0.33         0.53 
TCGA-AN-A0XU TCGA-AO-A03U TCGA-AO-A0J2 TCGA-AO-A0J6 TCGA-AO-A0JL TCGA-AO-A124 
        0.33        59.05        32.78        37.48        55.33       102.58 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12F TCGA-AR-A0TP TCGA-AR-A0TS TCGA-AR-A0TU 
       94.59        96.10        48.36        82.88        37.41        11.84 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
       65.36        70.16        83.87        55.36        75.55        61.84 
TCGA-AR-A1AJ TCGA-AR-A1AO TCGA-AR-A1AQ TCGA-AR-A1AY TCGA-B6-A0I6 TCGA-B6-A0IJ 
       52.77        43.56        43.07        20.22        32.78       176.98 
TCGA-B6-A0IQ TCGA-B6-A0RH TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0WX TCGA-B6-A0X1 
      140.88       189.01        89.46       131.21        21.47       186.48 
TCGA-BH-A0AV TCGA-BH-A0B3 TCGA-BH-A0B9 TCGA-BH-A0BW TCGA-BH-A0DL TCGA-BH-A0E0 
       38.79        39.55        51.68        11.67        48.23         4.41 
TCGA-BH-A18G TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A18V TCGA-C8-A12P TCGA-C8-A12U 
        2.01        55.63         7.36        51.16        11.77        12.66 
TCGA-C8-A12V TCGA-C8-A131 TCGA-C8-A134 TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A143 
       12.66         1.78         0.69        20.88        13.97        14.17 
TCGA-D8-A147 TCGA-E2-A14X TCGA-E2-A150 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A1AZ 
       19.20        31.96        25.41        14.79        25.05        60.53 
TCGA-E2-A1B6 
       28.50 

$subtype4
TCGA-A2-A04V TCGA-A2-A04Y TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0CY 
       63.12        36.13        75.25         5.19        64.04        55.00 
TCGA-A2-A0D4 TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0YH TCGA-A7-A13F TCGA-A8-A06R 
       25.22        27.12        44.88        21.67        12.72        17.98 
TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07W 
       29.03        31.00        26.01         1.02         9.01         9.99 
TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A08G TCGA-A8-A091 TCGA-A8-A09A TCGA-A8-A09M 
       18.05        36.95        19.96        19.07         9.99        15.02 
TCGA-A8-A09R TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A4 TCGA-AN-A04A TCGA-AN-A0AJ 
        8.98         0.99        14.01        13.02         2.96         8.02 
TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FD TCGA-AN-A0FZ TCGA-AN-A0XT 
        7.36         0.16         0.33         6.44         0.33         0.33 
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-A0J3 TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD 
       21.40        20.32        53.03        50.70        50.86        72.00 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A126 TCGA-AO-A12B TCGA-AO-A12E 
       26.24        38.53        62.04        93.70        77.56        57.30 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TY 
       41.62        28.37        56.88        29.75        24.30        55.86 
TCGA-AR-A0U3 TCGA-AR-A1AP TCGA-B6-A0IB TCGA-B6-A0RG TCGA-BH-A0B4 TCGA-BH-A0BF 
       76.18        39.98       129.57        68.45        39.16        25.71 
TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C3 
       27.19        53.95        49.94        49.05        41.75        48.13 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DK TCGA-BH-A0E2 TCGA-BH-A0H9 TCGA-BH-A0HA 
       42.90        45.83        13.91        14.30        41.00        52.96 
TCGA-BH-A0HL TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A18L TCGA-BH-A18P 
        2.37        12.89        51.32        27.25        26.66        30.28 
TCGA-BH-A18S TCGA-C8-A12M TCGA-C8-A12O TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 
       66.05        11.77        12.66        12.66        12.66         3.12 
TCGA-C8-A138 TCGA-D8-A13Y TCGA-D8-A140 TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A14S 
        3.75        11.90        13.25        34.42        46.59        33.17 
TCGA-E2-A14W TCGA-E2-A155 TCGA-E2-A15A TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15R 
       32.02        21.04        23.34        20.58         7.73        17.06 
TCGA-E2-A15S TCGA-E2-A15T 
       14.07        14.99 

$subtype5
TCGA-A2-A04W TCGA-A2-A0CX TCGA-A2-A0EY TCGA-A2-A0T1 TCGA-A2-A0YG TCGA-A8-A07I 
       64.04        56.81        24.16        17.13        21.90        14.01 
TCGA-A8-A08J TCGA-A8-A08X TCGA-A8-A09I TCGA-A8-A0A7 TCGA-AN-A0FT TCGA-AN-A0FV 
       37.05        33.99        33.07         0.99         6.02         0.33 
TCGA-AO-A0JE TCGA-AO-A12D TCGA-AR-A0TQ TCGA-AR-A0TX TCGA-AR-A1AT TCGA-B6-A0I9 
       76.77        64.04        49.32        64.83        41.82        12.13 
TCGA-BH-A0B7 TCGA-BH-A0EE TCGA-BH-A18R TCGA-C8-A12L TCGA-C8-A12Q TCGA-C8-A132 
       56.98        31.00        37.55        11.93         0.07         1.45 
TCGA-C8-A135 TCGA-C8-A137 TCGA-E2-A14P TCGA-E2-A14Y TCGA-E2-A152 TCGA-E2-A15H 
        0.62         3.85        40.96        28.60        27.12        12.92 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.30     0.23     0.33     0.16     0.07 
subtype1 subtype2 subtype3 subtype4 subtype5 
  129.70   172.96   189.01   129.57    76.77 
subtype1 subtype2 subtype3 subtype4 subtype5 
  28.405   30.350   31.730   26.890   27.860 
[1] "0.3 - 129.7 (28.4)" "0.2 - 173.0 (30.4)" "0.3 - 189.0 (31.7)"
[4] "0.2 - 129.6 (26.9)" "0.1 - 76.8 (27.9)" 
D6V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1       9        6        1        21        12          5          5
  subtype2      11       13        3        31        22         20          3
  subtype3       4        6        0        43        20         11          1
  subtype4       7        5        0        32        30         22          4
  subtype5       1        0        0        10        10          4          0
          vv
clus       STAGE IIIC STAGE IV STAGE X
  subtype1          0        2       3
  subtype2          3        3       2
  subtype3          3        3       2
  subtype4          4        4       1
  subtype5          5        2       0
D6V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           9       11        4        7        1
  STAGE IA          6       13        6        5        0
  STAGE IB          1        3        0        0        0
  STAGE IIA        21       31       43       32       10
  STAGE IIB        12       22       20       30       10
  STAGE IIIA        5       20       11       22        4
  STAGE IIIB        5        3        1        4        0
  STAGE IIIC        0        3        3        4        5
  STAGE IV          2        3        3        4        2
  STAGE X           3        2        2        1        0
[1] 10  5
[1] 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
  subtype1 22 32  3  6
  subtype2 38 53 14  6
  subtype3 14 68 10  1
  subtype4 15 73 18  3
  subtype5  5 20  5  2
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       22       38       14       15        5
  T2       32       53       68       73       20
  T3        3       14       10       18        5
  T4        6        6        1        3        2
[1] 4 5
[1] 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
  subtype1 35 19  5  3
  subtype2 50 37 17  5
  subtype3 53 25 11  4
  subtype4 47 37 16  7
  subtype5  8 14  3  6
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       35       50       53       47        8
  N1       19       37       25       37       14
  N2        5       17       11       16        3
  N3        3        5        4        7        6
[1] 4 5
[1] 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
  subtype1        0  58   2   4
  subtype2        1 105   3   2
  subtype3        0  89   3   1
  subtype4        0 105   4   0
  subtype5        0  30   2   0
D6V6, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4 subtype5
  CM0 (I+)        0        1        0        0        0
  M0             58      105       89      105       30
  M1              2        3        3        4        2
  MX              4        2        1        0        0
[1] 4 5
[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
  subtype1  63   1
  subtype2 111   0
  subtype3  93   0
  subtype4 105   4
  subtype5  32   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   63    1
  subtype2  111    0
  subtype3   93    0
  subtype4  105    4
  subtype5   32    0
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       63      111       93      105       32
  MALE          1        0        0        4        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA
  subtype1                            59                              1
  subtype2                            90                             17
  subtype3                            86                              0
  subtype4                            90                             10
  subtype5                            29                              2
          vv
clus       MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  subtype1                   0                                3
  subtype2                   0                                3
  subtype3                   1                                0
  subtype4                   0                                2
  subtype5                   0                                0
          vv
clus       MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                  0              1
  subtype2                  0              1
  subtype3                  0              6
  subtype4                  2              5
  subtype5                  0              1
D6V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  INFILTRATING DUCTAL CARCINOMA          59       90       86       90       29
  INFILTRATING LOBULAR CARCINOMA          1       17        0       10        2
  MEDULLARY CARCINOMA                     0        0        1        0        0
  MIXED HISTOLOGY (PLEASE SPECIFY)        3        3        0        2        0
  MUCINOUS CARCINOMA                      0        0        0        2        0
  OTHER  SPECIFY                          1        1        6        5        1
[1] 6 5
[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
  subtype1 24 40
  subtype2 42 69
  subtype3 41 52
  subtype4 29 80
  subtype5  8 24
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24   40
  subtype2   42   69
  subtype3   41   52
  subtype4   29   80
  subtype5    8   24
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        24       42       41       29        8
  YES       40       69       52       80       24
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     3                         4
  subtype2                                0     2                         4
  subtype3                                0     7                        13
  subtype4                                0     9                         7
  subtype5                                1     6                         1
          vv
clus       WHITE
  subtype1    46
  subtype2    94
  subtype3    65
  subtype4    72
  subtype5    17
D6V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        0        1
  ASIAN                                   3        2        7        9        6
  BLACK OR AFRICAN AMERICAN               4        4       13        7        1
  WHITE                                  46       94       65       72       17
[1] 4 5
[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
  subtype1  1 47
  subtype2  2 78
  subtype3  1 77
  subtype4  2 71
  subtype5  0 24
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   47
  subtype2    2   78
  subtype3    1   77
  subtype4    2   71
  subtype5    0   24
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            1        2        1        2        0
  NOT HISPANIC OR LATINO       47       78       77       71       24
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MRNASEQ_CNMF
D7V1, survival
          sevent
clus2        0   1
  subtype1 161  24
  subtype2 131  10
  subtype3 202  18
  subtype4 123  30
  subtype5 198  30
  subtype6  44   3
  subtype7  13   2
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
     185      141      220      153      228       47       15 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      24       10       18       30       30        3        2 
$subtype1
TCGA-A1-A0SB TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A04P TCGA-A2-A04Q 
        8.52        31.79        28.01        19.20        18.02        41.95 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A0CM TCGA-A2-A0CY TCGA-A2-A0D0 TCGA-A2-A0D2 
       73.84        22.06        24.79        55.00        21.14        33.76 
TCGA-A2-A0ST TCGA-A2-A0SX TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0YE TCGA-A2-A0YJ 
       99.19        50.43        17.52         8.38        18.21        18.61 
TCGA-A2-A0YM TCGA-A2-A1G1 TCGA-A2-A25F TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU 
       31.73        19.20        10.59        33.93        83.01        29.98 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RX TCGA-A2-A4S1 
       49.48        38.40        34.98        38.37         9.01        12.00 
TCGA-A7-A0CE TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A26G TCGA-A7-A26I 
       35.31        35.67        31.73        10.72        23.74        21.73 
TCGA-A7-A3IY TCGA-A7-A3J0 TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A5ZV TCGA-A7-A6VV 
       11.34        10.29        14.50        21.17        12.10        10.29 
TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A07C TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A07U 
        9.37         8.75        19.07         9.99         8.98         9.96 
TCGA-A8-A08R TCGA-A8-A08X TCGA-AC-A2BK TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A62X 
        0.99        33.99        38.53         1.02         2.27         1.12 
TCGA-AC-A6IW TCGA-AN-A04D TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AT 
        0.69         1.71         6.51         0.16         0.33         0.33 
TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FX TCGA-AN-A0G0 TCGA-AN-A0XN TCGA-AN-A0XU 
        7.96         7.59         0.33         0.53         0.33         0.33 
TCGA-AO-A03U TCGA-AO-A0J4 TCGA-AO-A0J6 TCGA-AO-A0JB TCGA-AO-A0JL TCGA-AO-A124 
       59.05        17.65        37.48        50.70        55.33       102.58 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12F TCGA-AO-A1KR TCGA-AQ-A04J TCGA-AQ-A54N 
       94.59        96.10        48.36        70.39        26.93         2.56 
TCGA-AR-A0TP TCGA-AR-A0TS TCGA-AR-A0TU TCGA-AR-A0U0 TCGA-AR-A0U4 TCGA-AR-A1AH 
       82.88        37.41        11.84        65.36        55.36        75.55 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AY TCGA-AR-A24Q 
       61.84        52.77        43.07        17.23        20.22        66.05 
TCGA-AR-A251 TCGA-AR-A256 TCGA-AR-A2LR TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 
       45.17        93.83        20.38        10.59        77.62       143.38 
TCGA-B6-A0I6 TCGA-B6-A0IJ TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RT TCGA-B6-A0RU 
       32.78       176.98       140.88       211.56        89.46       131.21 
TCGA-B6-A0WX TCGA-B6-A0X1 TCGA-B6-A1KF TCGA-B6-A402 TCGA-BH-A0AV TCGA-BH-A0B3 
       21.47       186.48       101.52        54.28        38.79        39.55 
TCGA-BH-A0B9 TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BW TCGA-BH-A0DL TCGA-BH-A0E0 
       51.68        24.85        44.05        11.67        48.23         4.41 
TCGA-BH-A0E6 TCGA-BH-A0RX TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18Q TCGA-BH-A18T 
        9.63         5.59        23.05         2.01        55.63         7.36 
TCGA-BH-A18V TCGA-BH-A1F0 TCGA-BH-A1F6 TCGA-BH-A1FC TCGA-BH-A1FN TCGA-C8-A12V 
       51.16        25.81        97.48       114.15        72.07        12.66 
TCGA-C8-A134 TCGA-C8-A1HJ TCGA-C8-A27B TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A147 
        0.69         0.16         0.99        13.97        14.17        19.20 
TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1XK TCGA-D8-A1XQ TCGA-D8-A1XW TCGA-D8-A27F 
       20.09        19.40        14.50        16.41        12.66        16.04 
TCGA-D8-A27H TCGA-D8-A27M TCGA-E2-A14N TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Y 
       13.05        13.48        47.15        38.60        31.96        28.60 
TCGA-E2-A150 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A1AZ TCGA-E2-A1B6 TCGA-E2-A1II 
       25.41        14.79        25.05        60.53        28.50        33.70 
TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A1LS 
       18.87       106.75       102.61         8.75        43.04        15.45 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N8 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A22G 
       22.26        19.89        12.00        39.55        12.59        23.51 
TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A3QA TCGA-E9-A5FL TCGA-EW-A1OW TCGA-EW-A1P4 
       17.06         0.69         0.62         0.26        22.82        29.82 
TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A1PH TCGA-EW-A3U0 TCGA-GI-A2C9 
       30.08         7.86        19.99        19.96        17.49       109.87 
TCGA-GM-A2DF TCGA-GM-A3XL TCGA-LL-A441 TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y 
       42.71        69.30         2.99         3.25         3.88         4.14 
TCGA-LL-A8F5 TCGA-OL-A5D7 TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-OL-A66I 
        6.21        46.55        26.20         9.80        23.70 

$subtype2
TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SH TCGA-A2-A0CP TCGA-A2-A0CR 
       14.37        43.43        48.10        47.24        92.48       107.93 
TCGA-A2-A0CV TCGA-A2-A0CZ TCGA-A2-A0EO TCGA-A2-A0ES TCGA-A2-A0EW TCGA-A2-A0EX 
       63.45        53.13        80.28        37.05        29.75        24.72 
TCGA-A2-A0SU TCGA-A2-A0T7 TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A1G0 TCGA-A2-A1G6 
       54.64        20.75        19.33        14.63        20.25        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A4RY TCGA-A7-A0CG 
       52.47       107.70        20.88        39.65         8.81        34.29 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A426 TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A8-A08O 
       29.56        31.36        11.97        10.72        11.05        31.00 
TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-AC-A23G TCGA-AC-A2FB 
       12.00         9.99        13.02        21.04        10.85        40.57 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3YI 
       55.43        36.99        38.79        14.83         9.40         1.55 
TCGA-AN-A0FS TCGA-AO-A03R TCGA-AO-A0JG TCGA-AO-A12A TCGA-AO-A12C TCGA-AO-A12E 
        6.28        68.75        26.24        90.58        65.56        57.30 
TCGA-AO-A12G TCGA-AO-A1KO TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AO 
       41.62        14.73        51.25        48.82        62.56        43.56 
TCGA-AR-A24M TCGA-AR-A24O TCGA-AR-A24T TCGA-AR-A24W TCGA-AR-A255 TCGA-AR-A2LH 
       65.46        65.69        53.26        50.96        34.82        20.25 
TCGA-AR-A2LM TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QP TCGA-B6-A0IE TCGA-B6-A0IH 
       40.04        20.81        16.96        20.45        65.72       112.37 
TCGA-B6-A0RQ TCGA-B6-A0RV TCGA-B6-A0WY TCGA-B6-A0X7 TCGA-BH-A0AZ TCGA-BH-A0B1 
      140.48       157.41       113.79        58.88        28.50        37.74 
TCGA-BH-A0BC TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0DE TCGA-BH-A0DG 
       32.02        21.70        61.68        35.67        31.17        23.44 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0E9 TCGA-BH-A0H3 TCGA-BH-A0HF 
       22.13        13.91        17.26        46.19        37.78        23.90 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A18M TCGA-BH-A1FB 
       13.61        36.85        24.95        42.35        72.56       120.62 
TCGA-BH-A1FE TCGA-BH-A1FH TCGA-BH-A201 TCGA-BH-A28O TCGA-BH-A42U TCGA-BH-A42V 
       74.73        36.92         6.90        10.65       109.28         8.94 
TCGA-C8-A132 TCGA-C8-A1HI TCGA-D8-A145 TCGA-D8-A1JB TCGA-D8-A1JH TCGA-D8-A1X8 
        1.45        11.34        13.48        18.71        14.01        25.74 
TCGA-D8-A1XB TCGA-D8-A1XM TCGA-D8-A1XY TCGA-D8-A27I TCGA-D8-A27L TCGA-D8-A27P 
       18.15        17.69        16.54        14.43        16.41         0.76 
TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A4Z1 TCGA-E2-A14Q TCGA-E2-A14U TCGA-E2-A15C 
       12.53        14.50         7.33        38.24        43.33        22.82 
TCGA-E2-A15E TCGA-E2-A15H TCGA-E2-A15P TCGA-E2-A1B1 TCGA-E2-A1IJ TCGA-E2-A1IO 
       20.71        12.92        19.56        53.03        28.44        20.98 
TCGA-E9-A1N9 TCGA-E9-A1NE TCGA-E9-A1RI TCGA-EW-A1IW TCGA-EW-A1J2 TCGA-EW-A1P1 
       13.12        35.77        35.64        12.20        13.25        39.78 
TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FV TCGA-EW-A424 TCGA-GM-A2DI TCGA-GM-A3XG 
       14.43        34.55        25.91        10.59        61.91        32.28 
TCGA-GM-A5PV TCGA-LD-A74U TCGA-LL-A440 TCGA-LL-A73Z TCGA-MS-A51U TCGA-OL-A5DA 
       13.55         6.67         0.66         4.50         2.79        44.61 
TCGA-OL-A5RV TCGA-OL-A5RX TCGA-W8-A86G 
       24.10        16.87         5.29 

$subtype3
TCGA-A1-A0SG TCGA-A2-A04N TCGA-A2-A0CQ TCGA-A2-A0CS TCGA-A2-A0D3 TCGA-A2-A0EM 
       14.27       104.81        88.60        75.55        28.77       101.72 
TCGA-A2-A0EN TCGA-A2-A0EV TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD 
       89.36        31.82        17.46        18.90        32.55        25.28 
TCGA-A2-A0YF TCGA-A2-A0YI TCGA-A2-A1FZ TCGA-A2-A4S2 TCGA-A7-A0CH TCGA-A7-A0DB 
       15.42        14.50        22.45         6.74        35.47        33.11 
TCGA-A7-A13G TCGA-A7-A26H TCGA-A7-A3J1 TCGA-A7-A6VX TCGA-A8-A06P TCGA-A8-A06T 
       23.61        23.80        11.28        10.42        13.02        41.06 
TCGA-A8-A06Y TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07S TCGA-A8-A08A TCGA-A8-A08C 
       26.01        18.97        18.97         7.99         0.99        19.99 
TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 
       19.07        93.04        40.01        17.95        41.98         9.99 
TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A0A1 TCGA-A8-A0A2 
       12.00         1.02        19.04        15.02        12.00        19.04 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23E TCGA-AC-A2B8 TCGA-AC-A2QI 
       13.02        17.03        38.04         2.37         1.48         0.92 
TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3TN TCGA-AC-A3YJ TCGA-AC-A62Y TCGA-AN-A03Y 
        0.99         0.69         1.12         1.32         1.81         0.33 
TCGA-AN-A046 TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0XO TCGA-AN-A0XP 
        0.33         4.64         7.00         7.17        12.33         0.30 
TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XV TCGA-AO-A0J8 TCGA-AO-A0JF TCGA-AO-A125 
        0.33         0.33         5.33        22.36        21.37        99.25 
TCGA-AO-A12B TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A7U7 TCGA-AR-A0TR TCGA-AR-A1AP 
       77.56        15.62        13.22         9.99         5.26        39.98 
TCGA-AR-A1AS TCGA-AR-A1AV TCGA-AR-A24K TCGA-AR-A24N TCGA-AR-A24P TCGA-AR-A24S 
       40.83        42.58        50.89        68.19         0.85        62.07 
TCGA-AR-A24X TCGA-AR-A2LE TCGA-AR-A2LL TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IB 
       48.16       128.65         7.36       149.59       220.90       129.57 
TCGA-B6-A0IC TCGA-B6-A0IP TCGA-B6-A0RI TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP 
       50.70       110.93       234.28       172.96       162.05       102.77 
TCGA-B6-A0WS TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A401 
       97.48       129.57       129.70        73.51       170.17        85.35 
TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0B0 TCGA-BH-A0B5 TCGA-BH-A0BD 
       49.94        82.88        55.00        46.95        48.36        18.21 
TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0DH TCGA-BH-A0DP 
       27.19        53.95        45.57        49.94        38.01        15.65 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0E1 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0HI 
        2.56        38.47        15.68        32.65        24.49        20.38 
TCGA-BH-A0HN TCGA-BH-A0HO TCGA-BH-A0HU TCGA-BH-A0W3 TCGA-BH-A0W7 TCGA-BH-A18I 
       16.96         2.50        12.89        23.93        44.81         7.23 
TCGA-BH-A18S TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1FD TCGA-BH-A1FJ TCGA-BH-A1FL 
       66.05        82.85        42.28        33.17        63.35        55.00 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-C8-A12N TCGA-C8-A1HE TCGA-C8-A26V TCGA-C8-A26W 
        6.44        20.12        11.77        12.33         0.30         0.23 
TCGA-D8-A141 TCGA-D8-A146 TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JP TCGA-D8-A1JS 
       20.58        21.14        18.15        18.90        21.01        12.20 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1XC TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS 
       17.79        16.73         2.66         7.96        15.85        16.31 
TCGA-D8-A1XV TCGA-D8-A27E TCGA-D8-A27K TCGA-D8-A27T TCGA-D8-A3Z6 TCGA-E2-A107 
       15.16        17.42         9.44        13.08        18.51        34.42 
TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14Z TCGA-E2-A153 TCGA-E2-A154 
       37.51        28.44        28.87        17.03        23.24        19.43 
TCGA-E2-A156 TCGA-E2-A15D TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       23.87        17.29        18.21        17.42        19.40         9.04 
TCGA-E2-A15L TCGA-E2-A1B4 TCGA-E2-A1BD TCGA-E2-A1IF TCGA-E2-A1IK TCGA-E2-A1IL 
       20.58        29.95        17.10        37.41        22.65         3.88 
TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A2P5 
       22.19        11.08        54.18        39.62        19.66        16.93 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A572 TCGA-E9-A1N4 TCGA-E9-A1NI 
        5.52        15.72        18.05        27.32        19.20         9.86 
TCGA-E9-A1R3 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A227 
        2.10        32.09        20.81        40.24         0.66         0.79 
TCGA-E9-A229 TCGA-E9-A22H TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A3HO TCGA-E9-A3X8 
       13.32        24.10         0.95        12.56        26.07        15.72 
TCGA-E9-A6HE TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1P3 
       15.39        39.72         8.48        16.57        15.68        52.96 
TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1PE TCGA-EW-A423 TCGA-GM-A2D9 TCGA-GM-A2DM 
       23.11        18.48        10.52        10.16        59.57        76.64 
TCGA-GM-A2DN TCGA-GM-A3NY TCGA-GM-A3XN TCGA-GM-A5PX TCGA-JL-A3YX TCGA-LD-A66U 
       77.33        38.20        53.95        18.12        11.57         8.28 
TCGA-LD-A7W6 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YN TCGA-LL-A6FQ TCGA-OL-A5RU 
        4.60         3.58         6.90         3.65         2.63        27.65 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-S3-A6ZG 
       33.90        31.07        18.21         6.81 

$subtype4
TCGA-A1-A0SI TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
       20.88         7.96        39.32        64.04        55.43        36.13 
TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0EY TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0T1 
       56.81        34.55        24.16        27.12        44.88        17.13 
TCGA-A2-A0YG TCGA-A2-A3XV TCGA-A2-A3XZ TCGA-A7-A26F TCGA-A7-A2KD TCGA-A7-A56D 
       21.90        14.07        31.99        24.26        22.32        14.73 
TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06U TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07B 
        1.02        17.98        29.03        17.03        53.98        33.01 
TCGA-A8-A07E TCGA-A8-A07I TCGA-A8-A084 TCGA-A8-A08B TCGA-A8-A08J TCGA-A8-A08L 
       19.99        14.01        15.06        23.08        37.05         9.99 
TCGA-A8-A08P TCGA-A8-A092 TCGA-A8-A09I TCGA-A8-A09N TCGA-A8-A09W TCGA-A8-A09X 
       31.00        16.01        33.07         1.02         0.99        14.01 
TCGA-A8-A0A7 TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A3W5 TCGA-AN-A04C TCGA-AN-A0AJ 
        0.99         0.95         2.66         1.81         1.78         8.02 
TCGA-AN-A0AS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N 
        0.33         6.02         0.33        80.28        47.84        66.77 
TCGA-AO-A0J2 TCGA-AO-A0JA TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JM TCGA-AO-A12D 
       32.78        21.53        72.00        76.77        71.80        64.04 
TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AR-A0TX TCGA-AR-A1AT TCGA-AR-A1AX TCGA-AR-A24U 
      130.09         5.65        64.83        41.82        36.26        53.36 
TCGA-AR-A250 TCGA-AR-A254 TCGA-B6-A0I8 TCGA-B6-A0I9 TCGA-B6-A0IG TCGA-B6-A0IK 
       56.15        39.85        24.62        12.13       146.50        18.77 
TCGA-B6-A0RH TCGA-B6-A0RS TCGA-B6-A1KN TCGA-BH-A0AW TCGA-BH-A0B7 TCGA-BH-A0BA 
      189.01       100.70       139.17        20.45        56.98        37.22 
TCGA-BH-A0BR TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0EE 
       53.69        41.75        44.02        47.41        16.27        31.00 
TCGA-BH-A0GY TCGA-BH-A0HY TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18P TCGA-BH-A18R 
       30.35        50.79        20.12        90.84        30.28        37.55 
TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EV TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F2 
       51.39        69.93        12.00        49.58        17.69        31.53 
TCGA-BH-A1FU TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 TCGA-C8-A12L TCGA-C8-A12O 
       72.07         0.72        38.60        57.83        11.93        12.66 
TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A135 TCGA-C8-A137 
       11.77         0.07         3.12         1.78         0.62         3.85 
TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A26X TCGA-C8-A26Y 
        3.75        10.92        12.03        10.42         0.36         0.43 
TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A3M7 TCGA-D8-A13Z TCGA-D8-A1J8 
        0.03         0.03         0.03         0.03        20.88        14.17 
TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JJ TCGA-D8-A1JK 
       17.49        16.50        12.03        12.03        20.09        20.12 
TCGA-D8-A1JN TCGA-D8-A1XJ TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A27N TCGA-E2-A10C 
       20.38        21.83         6.35        12.99         4.80        40.11 
TCGA-E2-A14P TCGA-E2-A14V TCGA-E2-A152 TCGA-E2-A1B0 TCGA-E2-A1LB TCGA-E2-A1LE 
       40.96        34.26        27.12        53.62        40.47        28.90 
TCGA-E9-A1N6 TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1R5 TCGA-E9-A1RH TCGA-E9-A226 
       13.48        20.05        21.57         1.38        34.59        34.13 
TCGA-E9-A22E TCGA-E9-A248 TCGA-EW-A1PC TCGA-EW-A2FR TCGA-GM-A2DB TCGA-GM-A2DD 
       12.89         1.94         6.15        55.00        53.13        43.04 
TCGA-GM-A2DH TCGA-JL-A3YW TCGA-LL-A5YL TCGA-LL-A5YO TCGA-LL-A740 TCGA-OL-A5D6 
       42.28        11.84         5.56         3.19         4.50        12.66 
TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66P 
       14.10        10.29         4.44 

$subtype5
TCGA-A1-A0SJ TCGA-A1-A0SQ TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A0CT TCGA-A2-A0CU 
       13.68        18.21        82.16        63.12        75.25         5.19 
TCGA-A2-A0CW TCGA-A2-A0D4 TCGA-A2-A0ER TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0T3 
       64.04        25.22        74.40        35.05        34.29        18.71 
TCGA-A2-A0T4 TCGA-A2-A0YH TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX 
       20.52        21.67        23.77        23.47        17.36        36.79 
TCGA-A2-A1G4 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25E TCGA-A2-A4RW TCGA-A2-A4S0 
       19.56        16.31        17.19        91.92         7.30         8.91 
TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A13F TCGA-A7-A26J 
        3.42        38.30        30.61        37.45        12.72        20.61 
TCGA-A7-A3IZ TCGA-A7-A3RF TCGA-A7-A4SB TCGA-A7-A4SF TCGA-A8-A06O TCGA-A8-A06X 
       10.59        13.41        13.74        17.92        13.02        31.00 
TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A07W TCGA-A8-A07Z 
        1.02         9.01        17.03        10.98         9.99        28.04 
TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I 
       18.05        36.95        13.02        18.05        19.96        12.00 
TCGA-A8-A091 TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09Q 
       19.07        13.02        31.00        29.98        15.02        25.02 
TCGA-A8-A09R TCGA-AC-A2BM TCGA-AC-A2FM TCGA-AC-A62V TCGA-AC-A6IV TCGA-AN-A03X 
        8.98        38.20        26.04         0.07         1.18         0.33 
TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A0AK TCGA-AN-A0FD TCGA-AN-A0FW 
        0.23         0.62         2.96         7.36         6.44         0.36 
TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XT TCGA-AN-A0XW TCGA-AO-A03P TCGA-AO-A03T 
        0.33         0.33         0.33         5.59        84.69        47.87 
TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J7 TCGA-AO-A0JI TCGA-AO-A126 TCGA-AO-A12H 
       29.13        21.40        20.32        38.53        93.70        28.37 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A54O 
       82.62        61.87         0.53        17.79        24.79        21.86 
TCGA-AR-A0TQ TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0TZ 
       49.32        56.88        29.75        24.30        55.86        76.14 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AU TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24R 
       83.87        76.18        46.32       109.58        73.02        57.40 
TCGA-AR-A24V TCGA-AR-A24Z TCGA-AR-A252 TCGA-AR-A2LK TCGA-B6-A0IM TCGA-B6-A0IN 
       54.18        51.75        40.64        42.87       126.12        84.59 
TCGA-B6-A0IO TCGA-B6-A0RG TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0WT TCGA-B6-A0WV 
      110.14        68.45        81.17        78.02       188.68        79.63 
TCGA-B6-A0WW TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A1KC TCGA-BH-A0AU TCGA-BH-A0B4 
       17.98        28.27        68.94        43.59        24.53        39.16 
TCGA-BH-A0B8 TCGA-BH-A0BZ TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0E2 TCGA-BH-A0E7 
       51.58        49.05        42.90        45.83        14.30        44.81 
TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0HA 
       24.43        10.78        15.16        24.56        23.08        52.96 
TCGA-BH-A0HB TCGA-BH-A0HL TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A18L TCGA-BH-A18N 
       26.50         2.37        51.32        27.25        26.66        37.74 
TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1EW TCGA-BH-A1F5 TCGA-BH-A1F8 TCGA-BH-A1FG 
       91.99       113.82        55.69        89.16        24.66       122.89 
TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A204 TCGA-BH-A42T TCGA-C8-A12M TCGA-C8-A12U 
       45.63       144.59        83.31         0.99        11.77        12.66 
TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A1HG TCGA-C8-A1HN TCGA-C8-A26Z TCGA-C8-A273 
       12.66        12.66        11.34         3.25         8.28         9.67 
TCGA-C8-A27A TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A1JC TCGA-D8-A1JI 
       12.20         0.23        11.90        13.25        15.78        18.97 
TCGA-D8-A1JT TCGA-D8-A1X5 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XD TCGA-D8-A1XF 
       13.32        18.58        23.90        27.58        17.16        15.22 
TCGA-D8-A1XG TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27G 
       14.73        15.32        15.52         3.81        14.14        13.45 
TCGA-D8-A27R TCGA-D8-A27W TCGA-E2-A105 TCGA-E2-A106 TCGA-E2-A109 TCGA-E2-A10A 
       10.09        12.26        43.00        59.41        46.59        40.41 
TCGA-E2-A14O TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14W TCGA-E2-A155 TCGA-E2-A15A 
       44.68        33.17        33.30        32.02        21.04        23.34 
TCGA-E2-A15F TCGA-E2-A15O TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1IE 
       21.63        13.02        17.06        14.07        14.99        38.30 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1L7 TCGA-E2-A1LA TCGA-E2-A56Z TCGA-E9-A1N5 
       32.78        33.73        27.42        24.59         7.20        36.82 
TCGA-E9-A1NA TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RE 
       36.56         0.62         6.12         2.76        21.21        34.65 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A228 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A245 
        6.58        21.27        12.53        39.09        22.75         0.85 
TCGA-E9-A247 TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A5UO TCGA-EW-A1IZ TCGA-EW-A1J1 
       27.22         0.72        17.75         0.23        18.21        18.90 
TCGA-EW-A1J6 TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1PA 
       28.77        29.95        29.85        40.41        41.13        18.90 
TCGA-EW-A1PD TCGA-EW-A2FS TCGA-EW-A2FW TCGA-GI-A2C8 TCGA-GM-A2DC TCGA-GM-A2DK 
       13.94        52.73        22.09         7.40        53.52        62.33 
TCGA-GM-A2DO TCGA-LL-A5YM TCGA-LL-A7T0 TCGA-OL-A5D8 TCGA-OL-A66H TCGA-OL-A66O 
       53.36         4.70         3.22         7.53        14.76         7.23 

$subtype6
TCGA-A2-A0CK TCGA-A2-A0CO TCGA-A2-A0EP TCGA-A2-A0SY TCGA-A7-A425 TCGA-A7-A4SA 
      125.59       112.08       107.61        44.28        14.70        14.93 
TCGA-A7-A4SC TCGA-A8-A07J TCGA-AC-A2FO TCGA-AC-A3W6 TCGA-AC-A5XS TCGA-AC-A6IX 
       14.66        12.00        50.70         1.68         1.55         0.43 
TCGA-AC-A8OP TCGA-AN-A0XL TCGA-AO-A0J5 TCGA-AO-A0J9 TCGA-AO-A0JJ TCGA-AR-A1AN 
        1.74         0.33        24.16        53.03        62.04        43.73 
TCGA-AR-A2LN TCGA-AR-A5QM TCGA-AR-A5QN TCGA-BH-A0AY TCGA-BH-A0BP TCGA-BH-A0C3 
       17.10        54.74        16.04        25.55        48.69        48.13 
TCGA-BH-A0DQ TCGA-BH-A0DV TCGA-BH-A0H9 TCGA-BH-A0HK TCGA-BH-A18F TCGA-D8-A1JU 
        3.22        45.17        41.00         5.85         8.81        14.70 
TCGA-E2-A108 TCGA-E2-A15M TCGA-E2-A1B5 TCGA-E2-A1BC TCGA-E9-A1QZ TCGA-E9-A1R0 
       27.52         7.73        32.35        16.47        11.90        14.30 
TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A5FK TCGA-EW-A3E8 TCGA-GM-A2DA TCGA-GM-A2DL 
        0.76        18.41         0.39        21.27       194.27        90.84 
TCGA-GM-A3NW TCGA-GM-A4E0 TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A66J 
      110.50        57.63        15.91         2.10        54.51 

$subtype7
TCGA-A2-A0CL TCGA-A2-A0EQ TCGA-A2-A25D TCGA-AO-A03O TCGA-AO-A0JC TCGA-AR-A1AW 
       64.57        79.76        18.15        81.63        50.86        35.24 
TCGA-BH-A0B6 TCGA-BH-A0BF TCGA-BH-A0H5 TCGA-BH-A209 TCGA-C8-A1HM TCGA-D8-A1XL 
       56.94        25.71        35.51       130.16         2.30        19.92 
TCGA-D8-A1Y2 TCGA-EW-A1OV TCGA-LL-A7SZ 
       14.24        25.94         5.59 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    0.16     0.66     0.23     0.03     0.07     0.33     2.30 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  211.56   157.41   234.28   189.01   188.68   194.27   130.16 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  22.060   25.910   19.040   20.880   22.915   18.410   35.240 
[1] "0.2 - 211.6 (22.1)" "0.7 - 157.4 (25.9)" "0.2 - 234.3 (19.0)"
[4] "0.0 - 189.0 (20.9)" "0.1 - 188.7 (22.9)" "0.3 - 194.3 (18.4)"
[7] "2.3 - 130.2 (35.2)"
D7V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1      13       14        0        0        89        39         0
  subtype2      11       14        2        5        32        35         1
  subtype3      25       24        2        1        78        43         0
  subtype4       9       11        1        1        49        35         0
  subtype5      15       12        5        0        73        62         1
  subtype6       4        4        0        2        14        10         0
  subtype7       3        1        0        0         6         4         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
  subtype1         17          2          6        3         0       2
  subtype2         20          0         15        3         1       2
  subtype3         24          7         11        3         0       6
  subtype4         27          5         11        5         0       4
  subtype5         43         13          8        2         0       3
  subtype6          6          0          7        1         0       0
  subtype7          1          0          1        0         0       0
D7V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I          13       11       25        9       15        4        3
  STAGE IA         14       14       24       11       12        4        1
  STAGE IB          0        2        2        1        5        0        0
  STAGE II          0        5        1        1        0        2        0
  STAGE IIA        89       32       78       49       73       14        6
  STAGE IIB        39       35       43       35       62       10        4
  STAGE III         0        1        0        0        1        0        0
  STAGE IIIA       17       20       24       27       43        6        1
  STAGE IIIB        2        0        7        5       13        0        0
  STAGE IIIC        6       15       11       11        8        7        1
  STAGE IV          3        3        3        5        2        1        0
  STAGE TIS         0        1        0        0        0        0        0
  STAGE X           2        2        6        4        3        0        0
[1] 13  7
[1] 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
  subtype1  38 124  18   5
  subtype2  45  69  26   0
  subtype3  80 113  22   9
  subtype4  34  99  17   8
  subtype5  54 145  24  13
  subtype6   9  28  10   1
  subtype7   4  11   1   0
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  T1       38       45       80       34       54        9        4
  T2      124       69      113       99      145       28       11
  T3       18       26       22       17       24       10        1
  T4        5        0        9        8       13        1        0
[1] 4 7
[1] 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
  subtype1 118  48  13   7
  subtype2  56  53  12  17
  subtype3 116  71  20  15
  subtype4  61  51  27  14
  subtype5  91  95  35   9
  subtype6  25  13   3   7
  subtype7  10   4   1   1
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  N0      118       56      116       61       91       25       10
  N1       48       53       71       51       95       13        4
  N2       13       12       20       27       35        3        1
  N3        7       17       15       14        9        7        1
[1] 4 7
[1] 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
  subtype1        0 164   3  19
  subtype2        1 113   3  24
  subtype3        1 188   3  32
  subtype4        0 135   5  18
  subtype5        0 211   2  24
  subtype6        0  36   1  11
  subtype7        0  12   0   4
D7V6, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  CM0 (I+)        0        1        1        0        0        0        0
  M0            164      113      188      135      211       36       12
  M1              3        3        3        5        2        1        0
  MX             19       24       32       18       24       11        4
[1] 4 7
[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
  subtype1 186   0
  subtype2 141   0
  subtype3 222   2
  subtype4 157   1
  subtype5 229   8
  subtype6  48   0
  subtype7  16   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  186    0
  subtype2  141    0
  subtype3  222    2
  subtype4  157    1
  subtype5  229    8
  subtype6   48    0
  subtype7   16    0
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE      186      141      222      157      229       48       16
  MALE          0        0        2        1        8        0        0
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  subtype1                          1                           161
  subtype2                          0                            71
  subtype3                          0                           146
  subtype4                          0                           142
  subtype5                          0                           196
  subtype6                          0                            19
  subtype7                          0                            14
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                              1                   4
  subtype2                             56                   0
  subtype3                             54                   0
  subtype4                             10                   0
  subtype5                             18                   0
  subtype6                             27                   0
  subtype7                              1                   1
          vv
clus       MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                                1                  2             15
  subtype2                               10                  1              3
  subtype3                                9                  3             12
  subtype4                                2                  0              4
  subtype5                                6                  8              9
  subtype6                                1                  0              1
  subtype7                                0                  0              0
D7V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  INFILTRATING CARCINOMA NOS              1        0        0        0        0
  INFILTRATING DUCTAL CARCINOMA         161       71      146      142      196
  INFILTRATING LOBULAR CARCINOMA          1       56       54       10       18
  MEDULLARY CARCINOMA                     4        0        0        0        0
  MIXED HISTOLOGY (PLEASE SPECIFY)        1       10        9        2        6
  MUCINOUS CARCINOMA                      2        1        3        0        8
  OTHER  SPECIFY                         15        3       12        4        9
                                  clus
vv                                 subtype6 subtype7
  INFILTRATING CARCINOMA NOS              0        0
  INFILTRATING DUCTAL CARCINOMA          19       14
  INFILTRATING LOBULAR CARCINOMA         27        1
  MEDULLARY CARCINOMA                     0        1
  MIXED HISTOLOGY (PLEASE SPECIFY)        1        0
  MUCINOUS CARCINOMA                      0        0
  OTHER  SPECIFY                          1        0
[1] 7 7
[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
  subtype1  59 127
  subtype2  43  98
  subtype3  53 171
  subtype4  37 121
  subtype5  78 159
  subtype6   9  39
  subtype7   6  10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   59  127
  subtype2   43   98
  subtype3   53  171
  subtype4   37  121
  subtype5   78  159
  subtype6    9   39
  subtype7    6   10
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO        59       43       53       37       78        9        6
  YES      127       98      171      121      159       39       10
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     6                        54
  subtype2                                0     5                        11
  subtype3                                0     8                        21
  subtype4                                1    22                        17
  subtype5                                0    15                        30
  subtype6                                0     0                         1
  subtype7                                0     1                         5
          vv
clus       WHITE
  subtype1   117
  subtype2   119
  subtype3   169
  subtype4    94
  subtype5   166
  subtype6    43
  subtype7    10
D7V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        1        0
  ASIAN                                   6        5        8       22       15
  BLACK OR AFRICAN AMERICAN              54       11       21       17       30
  WHITE                                 117      119      169       94      166
                                  clus
vv                                 subtype6 subtype7
  AMERICAN INDIAN OR ALASKA NATIVE        0        0
  ASIAN                                   0        1
  BLACK OR AFRICAN AMERICAN               1        5
  WHITE                                  43       10
[1] 4 7
[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
  subtype1   6 157
  subtype2   7 115
  subtype3  11 170
  subtype4   1 122
  subtype5   8 188
  subtype6   2  36
  subtype7   1  15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6  157
  subtype2    7  115
  subtype3   11  170
  subtype4    1  122
  subtype5    8  188
  subtype6    2   36
  subtype7    1   15
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            6        7       11        1        8        2
  NOT HISPANIC OR LATINO      157      115      170      122      188       36
                        clus
vv                       subtype7
  HISPANIC OR LATINO            1
  NOT HISPANIC OR LATINO       15
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MRNASEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2        0   1
  subtype1 151  22
  subtype2 212  16
  subtype3 169  19
  subtype4 139  31
  subtype5 156  20
  subtype6  45   9
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
     173      228      188      170      176       54 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      22       16       19       31       20        9 
$subtype1
TCGA-A1-A0SB TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04T 
        8.52        28.01        19.20        18.02        41.95        73.84 
TCGA-A2-A04U TCGA-A2-A0CM TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0ST TCGA-A2-A0SX 
       22.06        24.79        21.14        33.76        99.19        50.43 
TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0YE TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A1G1 
       17.52         8.38        18.21        18.61        31.73        19.20 
TCGA-A2-A25F TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XX TCGA-A2-A3XY 
       10.59        33.93        83.01        29.98        38.40        34.98 
TCGA-A2-A3Y0 TCGA-A2-A4RX TCGA-A7-A0CE TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E 
       38.37         9.01        35.31        35.67        31.73        10.72 
TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26I TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A5ZV 
       24.26        23.74        21.73        14.50        21.17        12.10 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A07C TCGA-A8-A07O TCGA-A8-A07R 
       10.29         9.37         8.75        19.07         9.99         8.98 
TCGA-A8-A07U TCGA-A8-A08R TCGA-AC-A2BK TCGA-AC-A2QJ TCGA-AC-A62X TCGA-AC-A6IW 
        9.96         0.99        38.53         2.27         1.12         0.69 
TCGA-AN-A04D TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FJ TCGA-AN-A0FL 
        1.71         6.51         0.33         0.33         7.96         7.59 
TCGA-AN-A0FX TCGA-AN-A0G0 TCGA-AN-A0XU TCGA-AO-A03U TCGA-AO-A0J4 TCGA-AO-A0J6 
        0.33         0.53         0.33        59.05        17.65        37.48 
TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12F TCGA-AO-A1KR 
       55.33       102.58        94.59        96.10        48.36        70.39 
TCGA-AQ-A04J TCGA-AQ-A54N TCGA-AR-A0TP TCGA-AR-A0TS TCGA-AR-A0TU TCGA-AR-A0U0 
       26.93         2.56        82.88        37.41        11.84        65.36 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AQ TCGA-AR-A1AR 
       55.36        75.55        61.84        52.77        43.07        17.23 
TCGA-AR-A1AY TCGA-AR-A24Q TCGA-AR-A251 TCGA-AR-A256 TCGA-AR-A2LR TCGA-AR-A5QQ 
       20.22        66.05        45.17        93.83        20.38        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I6 TCGA-B6-A0IJ TCGA-B6-A0IQ TCGA-B6-A0RE 
       77.62       143.38        32.78       176.98       140.88       211.56 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0WX TCGA-B6-A0X1 TCGA-B6-A1KF TCGA-B6-A402 
       89.46       131.21        21.47       186.48       101.52        54.28 
TCGA-BH-A0AV TCGA-BH-A0B3 TCGA-BH-A0B9 TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BW 
       38.79        39.55        51.68        24.85        44.05        11.67 
TCGA-BH-A0DL TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0RX TCGA-BH-A0WA TCGA-BH-A18G 
       48.23         4.41         9.63         5.59        23.05         2.01 
TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1F0 TCGA-BH-A1F6 TCGA-BH-A1FC 
       55.63         7.36        51.16        25.81        97.48       114.15 
TCGA-C8-A12V TCGA-C8-A134 TCGA-C8-A1HJ TCGA-C8-A27B TCGA-D8-A142 TCGA-D8-A147 
       12.66         0.69         0.16         0.99        13.97        19.20 
TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1XK TCGA-D8-A1XQ TCGA-D8-A1XW TCGA-D8-A27F 
       20.09        19.40        14.50        16.41        12.66        16.04 
TCGA-D8-A27H TCGA-D8-A27M TCGA-E2-A14N TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Y 
       13.05        13.48        47.15        38.60        31.96        28.60 
TCGA-E2-A150 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A1AZ TCGA-E2-A1B6 TCGA-E2-A1II 
       25.41        14.79        25.05        60.53        28.50        33.70 
TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A1LS 
       18.87       106.75       102.61         8.75        43.04        15.45 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N8 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A22G 
       22.26        19.89        12.00        39.55        12.59        23.51 
TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A3QA TCGA-E9-A5FL TCGA-EW-A1OW TCGA-EW-A1P4 
       17.06         0.69         0.62         0.26        22.82        29.82 
TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A1PH TCGA-EW-A3U0 TCGA-GI-A2C9 
       30.08         7.86        19.99        19.96        17.49       109.87 
TCGA-GM-A2DF TCGA-GM-A3XL TCGA-LL-A441 TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y 
       42.71        69.30         2.99         3.25         3.88         4.14 
TCGA-LL-A8F5 TCGA-OL-A5D7 TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-OL-A66I 
        6.21        46.55        26.20         9.80        23.70 

$subtype2
TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A2-A0CK TCGA-A2-A0CO TCGA-A2-A0CP 
       14.37        43.43        48.10       125.59       112.08        92.48 
TCGA-A2-A0CR TCGA-A2-A0CT TCGA-A2-A0CZ TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP 
      107.93        75.25        53.13        89.36        80.28       107.61 
TCGA-A2-A0ES TCGA-A2-A0EU TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0SY TCGA-A2-A0T4 
       37.05        34.29        29.75        24.72        44.28        20.52 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YD TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A1FZ 
       18.90        20.75        25.28        19.33        14.63        22.45 
TCGA-A2-A1G0 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25D TCGA-A2-A3KC 
       20.25        16.47        52.47       107.70        18.15        20.88 
TCGA-A2-A3KD TCGA-A2-A3XW TCGA-A2-A3XZ TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S2 
       39.65        49.48        31.99         7.30         8.81         6.74 
TCGA-A7-A0CG TCGA-A7-A0DB TCGA-A7-A13H TCGA-A7-A3J1 TCGA-A7-A425 TCGA-A7-A426 
       34.29        33.11        29.56        11.28        14.70        11.97 
TCGA-A7-A4SA TCGA-A7-A4SC TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A8-A07E TCGA-A8-A07J 
       14.93        14.66        10.72        11.05        19.99        12.00 
TCGA-A8-A08O TCGA-A8-A09A TCGA-A8-A09D TCGA-A8-A0A1 TCGA-A8-A0A4 TCGA-A8-A0A6 
       31.00         9.99        13.02        12.00        13.02        21.04 
TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
       10.85         1.48        40.57        55.43        36.99        38.79 
TCGA-AC-A2FO TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3W6 
       50.70         0.99         0.69        14.83         9.40         1.68 
TCGA-AC-A3YI TCGA-AC-A5XS TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AN-A0FN 
        1.55         1.55         1.18         0.43         1.74         7.17 
TCGA-AN-A0FS TCGA-AN-A0FW TCGA-AN-A0XL TCGA-AN-A0XS TCGA-AO-A03L TCGA-AO-A03M 
        6.28         0.36         0.33         0.33        80.28        47.84 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A0J5 TCGA-AO-A0J9 TCGA-AO-A0JB TCGA-AO-A0JC 
       68.75        47.87        24.16        53.03        50.70        50.86 
TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A12E TCGA-AO-A1KO 
       72.00        21.37        26.24        62.04        57.30        14.73 
TCGA-AQ-A7U7 TCGA-AR-A0TQ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
        9.99        49.32        51.25        48.82        62.56        43.73 
TCGA-AR-A1AU TCGA-AR-A1AX TCGA-AR-A24O TCGA-AR-A24W TCGA-AR-A252 TCGA-AR-A255 
       46.32        36.26        65.69        50.96        40.64        34.82 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN 
       40.04        17.10        20.81        16.96        54.74        16.04 
TCGA-AR-A5QP TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IN TCGA-B6-A0RG TCGA-B6-A0RQ 
       20.45        65.72       112.37        84.59        68.45       140.48 
TCGA-B6-A0RV TCGA-B6-A0WY TCGA-B6-A0X7 TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 
      157.41       113.79        58.88        25.55        28.50        46.95 
TCGA-BH-A0B1 TCGA-BH-A0B6 TCGA-BH-A0B8 TCGA-BH-A0BA TCGA-BH-A0BJ TCGA-BH-A0BM 
       37.74        56.94        51.58        37.22        21.70        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0DE TCGA-BH-A0DG 
       35.67        48.69        41.75        48.13        31.17        23.44 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DV TCGA-BH-A0DX 
       22.13        13.91        17.26        15.65        45.17        47.41 
TCGA-BH-A0E2 TCGA-BH-A0E9 TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H5 TCGA-BH-A0HB 
       14.30        46.19        30.35        10.78        35.51        26.50 
TCGA-BH-A0HF TCGA-BH-A0HK TCGA-BH-A0HP TCGA-BH-A0HX TCGA-BH-A0W4 TCGA-BH-A0W5 
       23.90         5.85        13.61        27.25        24.95        42.35 
TCGA-BH-A18F TCGA-BH-A18I TCGA-BH-A18M TCGA-BH-A18R TCGA-BH-A1EU TCGA-BH-A1FB 
        8.81         7.23        72.56        37.55        42.28       120.62 
TCGA-BH-A1FE TCGA-BH-A1FH TCGA-BH-A201 TCGA-BH-A28O TCGA-BH-A42U TCGA-BH-A42V 
       74.73        36.92         6.90        10.65       109.28         8.94 
TCGA-C8-A132 TCGA-C8-A3M7 TCGA-D8-A145 TCGA-D8-A1JB TCGA-D8-A1JH TCGA-D8-A1JU 
        1.45         0.03        13.48        18.71        14.01        14.70 
TCGA-D8-A1XM TCGA-D8-A1Y0 TCGA-D8-A27I TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 
       17.69        15.52        14.43        13.08        12.53        14.50 
TCGA-D8-A4Z1 TCGA-E2-A108 TCGA-E2-A10F TCGA-E2-A14Q TCGA-E2-A14U TCGA-E2-A14Z 
        7.33        27.52        28.87        38.24        43.33        17.03 
TCGA-E2-A15C TCGA-E2-A15E TCGA-E2-A15M TCGA-E2-A1B1 TCGA-E2-A1B5 TCGA-E2-A1BC 
       22.82        20.71         7.73        53.03        32.35        16.47 
TCGA-E2-A1IF TCGA-E2-A1IJ TCGA-E2-A1IO TCGA-E2-A1L6 TCGA-E2-A3DX TCGA-E9-A1NE 
       37.41        28.44        20.98        54.18        15.72        35.77 
TCGA-E9-A1QZ TCGA-E9-A295 TCGA-E9-A2JT TCGA-E9-A3X8 TCGA-E9-A5FK TCGA-E9-A6HE 
       11.90         0.72         0.76        15.72         0.39        15.39 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1J2 TCGA-EW-A1J5 TCGA-EW-A1P1 TCGA-EW-A1PF 
       12.20        39.72        13.25        15.68        39.78        14.43 
TCGA-EW-A1PG TCGA-EW-A2FV TCGA-EW-A3E8 TCGA-GM-A2DA TCGA-GM-A2DI TCGA-GM-A2DL 
       34.55        25.91        21.27       194.27        61.91        90.84 
TCGA-GM-A3NW TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX 
      110.50        32.28        53.95        57.63        13.55        18.12 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A5YL TCGA-LL-A5YN 
        8.28         6.67         4.60         0.66         5.56         3.65 
TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66N TCGA-W8-A86G 
        2.79         2.10        54.51        31.07        18.21         5.29 

$subtype3
TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A2-A04N TCGA-A2-A0CQ TCGA-A2-A0CS TCGA-A2-A0CV 
       14.27        47.24       104.81        88.60        75.55        63.45 
TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0ET TCGA-A2-A0T5 TCGA-A2-A0YI TCGA-A2-A4S0 
       28.77       101.72        35.05        17.46        14.50         8.91 
TCGA-A7-A0CH TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3J0 
       35.47        23.61        31.36        22.32        11.34        10.29 
TCGA-A7-A3RF TCGA-A7-A4SB TCGA-A8-A06P TCGA-A8-A07G TCGA-A8-A07S TCGA-A8-A08A 
       13.41        13.74        13.02        18.97         7.99         0.99 
TCGA-A8-A08C TCGA-A8-A08Z TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09T TCGA-A8-A09V 
       19.99        40.01        41.98         9.99        19.04        15.02 
TCGA-A8-A0A2 TCGA-A8-A0AB TCGA-AC-A23E TCGA-AC-A2QI TCGA-AC-A3TN TCGA-AC-A3YJ 
       19.04        17.03         2.37         0.92         1.12         1.32 
TCGA-AC-A62Y TCGA-AN-A049 TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0XP TCGA-AN-A0XR 
        1.81         0.62         4.64         7.00         0.30         0.33 
TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A125 TCGA-AO-A12A 
        0.33         5.33        20.32        22.36        99.25        90.58 
TCGA-AO-A12B TCGA-AO-A12G TCGA-AO-A12H TCGA-AQ-A1H3 TCGA-AR-A0TR TCGA-AR-A1AP 
       77.56        41.62        28.37        13.22         5.26        39.98 
TCGA-AR-A1AS TCGA-AR-A24K TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24P TCGA-AR-A24T 
       40.83        50.89        65.46        68.19         0.85        53.26 
TCGA-AR-A24X TCGA-AR-A2LE TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IP 
       48.16       128.65       149.59       220.90        50.70       110.93 
TCGA-B6-A0RI TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0WS TCGA-B6-A0WZ TCGA-B6-A0X0 
      234.28       172.96       102.77        97.48       129.57       129.70 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A40C 
       28.27        68.94        73.51       170.17        85.35        55.00 
TCGA-BH-A0B5 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BV 
       48.36        32.02        18.21        27.19        53.95        49.94 
TCGA-BH-A0DH TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0E1 TCGA-BH-A0E7 
       38.01         3.22         2.56        38.47        15.68        44.81 
TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0H3 TCGA-BH-A0H6 TCGA-BH-A0HI TCGA-BH-A0HN 
       32.65        24.49        37.78        24.56        20.38        16.96 
TCGA-BH-A0HO TCGA-BH-A0HQ TCGA-BH-A0W3 TCGA-BH-A0W7 TCGA-BH-A18S TCGA-BH-A1ET 
        2.50        36.85        23.93        44.81        66.05        82.85 
TCGA-BH-A1EW TCGA-BH-A1F5 TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FR TCGA-BH-A28Q 
       55.69        89.16        63.35        55.00       144.59         6.44 
TCGA-BH-A2L8 TCGA-C8-A12N TCGA-C8-A1HE TCGA-C8-A26V TCGA-C8-A26W TCGA-D8-A141 
       20.12        11.77        12.33         0.30         0.23        20.58 
TCGA-D8-A146 TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JI TCGA-D8-A1JS TCGA-D8-A1X7 
       21.14        18.15        18.90        18.97        12.20        16.73 
TCGA-D8-A1X8 TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XG TCGA-D8-A1XO TCGA-D8-A1XR 
       25.74        18.15         2.66        14.73         7.96        15.85 
TCGA-D8-A1XS TCGA-D8-A1XV TCGA-D8-A27E TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27P 
       16.31        15.16        17.42         9.44        16.41         0.76 
TCGA-D8-A3Z6 TCGA-E2-A10B TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A156 TCGA-E2-A15D 
       18.51        37.51        23.24        19.43        23.87        17.29 
TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15P 
       18.21        17.42        19.40         9.04        20.58        19.56 
TCGA-E2-A1B4 TCGA-E2-A1BD TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IU 
       29.95        17.10        22.65         3.88        22.19        11.08 
TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A2P6 TCGA-E2-A570 TCGA-E2-A572 TCGA-E9-A1N4 
       39.62        19.66         5.52        18.05        27.32        19.20 
TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1R0 TCGA-E9-A1R3 TCGA-E9-A1RA TCGA-E9-A1RC 
       21.57         9.86        14.30         2.10        32.09        40.24 
TCGA-E9-A1RD TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A22H TCGA-E9-A245 TCGA-E9-A249 
        0.66        34.13         0.79        24.10         0.85         0.95 
TCGA-E9-A24A TCGA-E9-A3Q9 TCGA-EW-A1IY TCGA-EW-A1J3 TCGA-EW-A1P3 TCGA-EW-A1P5 
       12.56        18.41         8.48        16.57        52.96        23.11 
TCGA-EW-A1P6 TCGA-EW-A1PE TCGA-EW-A424 TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NY 
       18.48        10.52        10.59        76.64        77.33        38.20 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX 
        3.58         6.90        44.61        27.65        24.10        16.87 
TCGA-OL-A66K TCGA-S3-A6ZG 
       33.90         6.81 

$subtype4
TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A2-A04W TCGA-A2-A04X 
       20.88        31.79         7.96        39.32        64.04        55.43 
TCGA-A2-A04Y TCGA-A2-A0CL TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0CY TCGA-A2-A0D1 
       36.13        64.57        64.04        56.81        55.00        34.55 
TCGA-A2-A0EQ TCGA-A2-A0EV TCGA-A2-A0EY TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0YG 
       79.76        31.82        24.16        27.12        44.88        21.90 
TCGA-A2-A0YH TCGA-A2-A0YT TCGA-A2-A25B TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A26H 
       21.67        23.77        16.31        12.00         3.42        23.80 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A6VX TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X 
       17.92        14.73        10.42         1.02        17.98        31.00 
TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07W 
       17.03        53.98        33.01        18.97        14.01         9.99 
TCGA-A8-A084 TCGA-A8-A08B TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L 
       15.06        23.08        18.05        12.00        37.05         9.99 
TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A092 TCGA-A8-A097 TCGA-A8-A09I 
       31.00        19.07        93.04        16.01        12.00        33.07 
TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09W TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A2QH 
        1.02         8.98         0.99         0.95         2.66         1.02 
TCGA-AN-A046 TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FT 
        0.33         8.02         7.36         0.16         0.33         6.02 
TCGA-AN-A0FV TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XW TCGA-AO-A03N TCGA-AO-A03O 
        0.33         0.33        12.33         5.59        66.77        81.63 
TCGA-AO-A0JA TCGA-AO-A0JM TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AR-A0TT TCGA-AR-A0TW 
       21.53        71.80       130.09         5.65        56.88        24.30 
TCGA-AR-A1AT TCGA-AR-A1AW TCGA-AR-A24H TCGA-AR-A24S TCGA-AR-A250 TCGA-AR-A254 
       41.82        35.24       109.58        62.07        56.15        39.85 
TCGA-B6-A0I8 TCGA-B6-A0I9 TCGA-B6-A0IG TCGA-B6-A0RH TCGA-B6-A0RO TCGA-B6-A0WW 
       24.62        12.13       146.50       189.01       162.05        17.98 
TCGA-B6-A1KN TCGA-B6-A408 TCGA-B6-A40B TCGA-BH-A0B4 TCGA-BH-A0BF TCGA-BH-A0BT 
      139.17        49.94        82.88        39.16        25.71        45.57 
TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0DZ TCGA-BH-A0H7 TCGA-BH-A0HU TCGA-BH-A0HY 
       49.05        44.02        16.27        23.08        12.89        50.79 
TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18P TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO 
       20.12        90.84        30.28        51.39        69.93        91.99 
TCGA-BH-A1EV TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F2 TCGA-BH-A1F8 TCGA-BH-A1FM 
       12.00        49.58        17.69        31.53        24.66        45.63 
TCGA-BH-A1FN TCGA-BH-A202 TCGA-BH-A209 TCGA-C8-A12O TCGA-C8-A12U TCGA-C8-A12W 
       72.07         0.72       130.16        12.66        12.66        12.66 
TCGA-C8-A130 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HM TCGA-C8-A274 
        3.12         3.85         3.75        10.92         2.30         0.03 
TCGA-D8-A13Y TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JC TCGA-D8-A1JJ 
       11.90        14.17        17.49        16.50        15.78        20.09 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1X9 TCGA-D8-A1XJ TCGA-D8-A1XL TCGA-D8-A1XY 
       20.38        21.01        23.90        21.83        19.92        16.54 
TCGA-D8-A1XZ TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27G TCGA-D8-A27N TCGA-D8-A27R 
       15.32        14.24        14.14        13.45         4.80        10.09 
TCGA-E2-A107 TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A14V TCGA-E2-A152 TCGA-E2-A15A 
       34.42        40.11        28.44        34.26        27.12        23.34 
TCGA-E2-A1IH TCGA-E2-A2P5 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NF 
       33.73        16.93        13.48        13.12        36.56        20.05 
TCGA-E9-A1R4 TCGA-E9-A1RB TCGA-E9-A1RF TCGA-E9-A22A TCGA-E9-A22E TCGA-EW-A1IZ 
        6.12        20.81         6.58        39.09        12.89        18.21 
TCGA-EW-A1OV TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1PC TCGA-EW-A2FR TCGA-EW-A423 
       25.94        29.85        40.41         6.15        55.00        10.16 
TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DH TCGA-GM-A2DO TCGA-JL-A3YX TCGA-LL-A7SZ 
        7.40        59.57        42.28        53.36        11.57         5.59 
TCGA-LQ-A4E4 TCGA-OL-A5RZ 
       15.91        10.29 

$subtype5
TCGA-A1-A0SJ TCGA-A1-A0SQ TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A0CU TCGA-A2-A0D4 
       13.68        18.21        82.16        63.12         5.19        25.22 
TCGA-A2-A0ER TCGA-A2-A0SU TCGA-A2-A0T3 TCGA-A2-A0YC TCGA-A2-A0YF TCGA-A2-A1FV 
       74.40        54.64        18.71        32.55        15.42        23.47 
TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1G4 TCGA-A2-A25C TCGA-A2-A25E TCGA-A7-A0CD 
       17.36        36.79        19.56        17.19        91.92        38.30 
TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A13F TCGA-A7-A26J TCGA-A7-A3IZ TCGA-A8-A06O 
       30.61        37.45        12.72        20.61        10.59        13.02 
TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07L 
       41.06        29.03        26.01         1.02         9.01        17.03 
TCGA-A8-A07P TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08G 
       10.98        28.04        18.05        36.95        13.02        19.96 
TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09K 
       19.07        17.95        12.00         1.02        31.00        29.98 
TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A0A9 TCGA-A8-A0AD TCGA-AC-A2BM TCGA-AC-A2FM 
       15.02        25.02        13.02        38.04        38.20        26.04 
TCGA-AC-A62V TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A04A TCGA-AN-A0FD 
        0.07         0.33         0.33         0.23         2.96         6.44 
TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AO-A03P TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0JI 
        0.33         0.33        84.69        29.13        21.40        38.53 
TCGA-AO-A126 TCGA-AO-A12C TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AO-A1KT 
       93.70        65.56        82.62        61.87         0.53        17.79 
TCGA-AQ-A04H TCGA-AQ-A1H2 TCGA-AQ-A54O TCGA-AR-A0TV TCGA-AR-A0TY TCGA-AR-A0TZ 
       24.79        15.62        21.86        29.75        55.86        76.14 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AV TCGA-AR-A24L TCGA-AR-A24R TCGA-AR-A24V 
       83.87        76.18        42.58        73.02        57.40        54.18 
TCGA-AR-A24Z TCGA-AR-A2LK TCGA-AR-A2LL TCGA-B6-A0IB TCGA-B6-A0IM TCGA-B6-A0IO 
       51.75        42.87         7.36       129.57       126.12       110.14 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A1KC TCGA-BH-A0AU 
       81.17        78.02       188.68        79.63        43.59        24.53 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0EI TCGA-BH-A0H0 TCGA-BH-A0H9 TCGA-BH-A0HA 
       42.90        45.83        24.43        15.16        41.00        52.96 
TCGA-BH-A0HL TCGA-BH-A0HW TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A1ES TCGA-BH-A1FD 
        2.37        51.32        26.66        37.74       113.82        33.17 
TCGA-BH-A1FG TCGA-BH-A204 TCGA-BH-A42T TCGA-C8-A12M TCGA-C8-A12X TCGA-C8-A1HG 
      122.89        83.31         0.99        11.77        12.66        11.34 
TCGA-C8-A1HI TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A27A 
       11.34        10.42         3.25         8.28         9.67        12.20 
TCGA-C8-A3M8 TCGA-D8-A140 TCGA-D8-A1JT TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1XA 
        0.23        13.25        13.32        18.58        17.79        27.58 
TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XU TCGA-D8-A1Y1 TCGA-D8-A27W TCGA-E2-A105 
       17.16        15.22        12.99         3.81        12.26        43.00 
TCGA-E2-A106 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A14O TCGA-E2-A14S TCGA-E2-A14T 
       59.41        46.59        40.41        44.68        33.17        33.30 
TCGA-E2-A14W TCGA-E2-A155 TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15O TCGA-E2-A15R 
       32.02        21.04        21.63        12.92        13.02        17.06 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1IE TCGA-E2-A1IG TCGA-E2-A1L7 TCGA-E2-A1LA 
       14.07        14.99        38.30        32.78        27.42        24.59 
TCGA-E2-A56Z TCGA-E9-A1N5 TCGA-E9-A1R2 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 
        7.20        36.82         0.62         1.38         2.76        21.21 
TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22B 
       34.65        21.27        35.64        12.53        13.32        22.75 
TCGA-E9-A247 TCGA-E9-A2JS TCGA-E9-A3HO TCGA-E9-A5UO TCGA-EW-A1J1 TCGA-EW-A1J6 
       27.22        17.75        26.07         0.23        18.90        28.77 
TCGA-EW-A1OX TCGA-EW-A1P0 TCGA-EW-A1PA TCGA-EW-A1PD TCGA-EW-A2FS TCGA-EW-A2FW 
       29.95        41.13        18.90        13.94        52.73        22.09 
TCGA-GM-A2DC TCGA-GM-A2DK TCGA-LL-A5YM TCGA-LL-A6FQ TCGA-LL-A7T0 TCGA-OL-A5D8 
       53.52        62.33         4.70         2.63         3.22         7.53 
TCGA-OL-A66H TCGA-OL-A66O 
       14.76         7.23 

$subtype6
TCGA-A2-A0T1 TCGA-A2-A3XV TCGA-A8-A08X TCGA-A8-A09X TCGA-A8-A0A7 TCGA-AC-A3W5 
       17.13        14.07        33.99        14.01         0.99         1.81 
TCGA-AN-A04C TCGA-AO-A0J2 TCGA-AO-A0JE TCGA-AO-A12D TCGA-AR-A0TX TCGA-AR-A1AO 
        1.78        32.78        76.77        64.04        64.83        43.56 
TCGA-AR-A24U TCGA-AR-A2LH TCGA-B6-A0IK TCGA-B6-A0RS TCGA-BH-A0AW TCGA-BH-A0B7 
       53.36        20.25        18.77       100.70        20.45        56.98 
TCGA-BH-A0BR TCGA-BH-A0EE TCGA-BH-A1FU TCGA-BH-A203 TCGA-BH-A208 TCGA-C8-A12L 
       53.69        31.00        72.07        38.60        57.83        11.93 
TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A131 TCGA-C8-A135 TCGA-C8-A1HK TCGA-C8-A26X 
       11.77         0.07         1.78         0.62        12.03         0.36 
TCGA-C8-A26Y TCGA-C8-A275 TCGA-C8-A278 TCGA-D8-A13Z TCGA-D8-A143 TCGA-D8-A1JF 
        0.43         0.03         0.03        20.88        14.17        12.03 
TCGA-D8-A1JG TCGA-D8-A1JK TCGA-D8-A1XT TCGA-E2-A14P TCGA-E2-A1B0 TCGA-E2-A1LB 
       12.03        20.12         6.35        40.96        53.62        40.47 
TCGA-E2-A1LE TCGA-E9-A1RH TCGA-E9-A248 TCGA-GM-A2DB TCGA-GM-A2DD TCGA-JL-A3YW 
       28.90        34.59         1.94        53.13        43.04        11.84 
TCGA-LL-A5YO TCGA-LL-A73Z TCGA-LL-A740 TCGA-OL-A5D6 TCGA-OL-A5RY TCGA-OL-A66P 
        3.19         4.50         4.50        12.66        14.10         4.44 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.16     0.03     0.23     0.03     0.07     0.03 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  211.56   194.27   234.28   189.01   188.68   100.70 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  22.260   24.835   20.220   20.845   22.420   15.650 
[1] "0.2 - 211.6 (22.3)" "0.0 - 194.3 (24.8)" "0.2 - 234.3 (20.2)"
[4] "0.0 - 189.0 (20.8)" "0.1 - 188.7 (22.4)" "0.0 - 100.7 (15.6)"
D8V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1      12       15        0        0        83        36         0
  subtype2      24       21        3        7        52        56         0
  subtype3      19       21        1        0        68        39         0
  subtype4      11        8        0        1        56        38         0
  subtype5      12       11        5        1        60        48         1
  subtype6       2        4        1        0        22        11         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
  subtype1         15          2          5        3         0       2
  subtype2         32          1         25        3         1       4
  subtype3         24          7          9        1         0       5
  subtype4         34          8         10        7         0       3
  subtype5         27          8          4        2         0       2
  subtype6          6          1          6        1         0       1
D8V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I          12       24       19       11       12        2
  STAGE IA         15       21       21        8       11        4
  STAGE IB          0        3        1        0        5        1
  STAGE II          0        7        0        1        1        0
  STAGE IIA        83       52       68       56       60       22
  STAGE IIB        36       56       39       38       48       11
  STAGE III         0        0        0        0        1        1
  STAGE IIIA       15       32       24       34       27        6
  STAGE IIIB        2        1        7        8        8        1
  STAGE IIIC        5       25        9       10        4        6
  STAGE IV          3        3        1        7        2        1
  STAGE TIS         0        1        0        0        0        0
  STAGE X           2        4        5        3        2        1
[1] 13  6
[1] 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
  subtype1  38 115  16   4
  subtype2  69 111  45   3
  subtype3  67 104  14   9
  subtype4  29 119  18  10
  subtype5  43 108  21   8
  subtype6  18  32   4   2
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1       38       69       67       29       43       18
  T2      115      111      104      119      108       32
  T3       16       45       14       18       21        4
  T4        4        3        9       10        8        2
[1] 4 6
[1] 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
  subtype1 111  45  12   6
  subtype2 102  77  20  27
  subtype3  92  69  18  12
  subtype4  74  50  34  12
  subtype5  77  74  20   6
  subtype6  21  20   7   7
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0      111      102       92       74       77       21
  N1       45       77       69       50       74       20
  N2       12       20       18       34       20        7
  N3        6       27       12       12        6        7
[1] 4 6
[1] 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
  subtype1        0 153   3  18
  subtype2        2 183   3  41
  subtype3        0 167   1  26
  subtype4        0 146   7  23
  subtype5        0 161   2  18
  subtype6        0  49   1   6
D8V6, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  CM0 (I+)        0        2        0        0        0        0
  M0            153      183      167      146      161       49
  M1              3        3        1        7        2        1
  MX             18       41       26       23       18        6
[1] 4 6
[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
  subtype1 174   0
  subtype2 229   0
  subtype3 193   1
  subtype4 174   2
  subtype5 173   8
  subtype6  56   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  174    0
  subtype2  229    0
  subtype3  193    1
  subtype4  174    2
  subtype5  173    8
  subtype6   56    0
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE      174      229      193      174      173       56
  MALE          0        0        1        2        8        0
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  subtype1                          1                           153
  subtype2                          0                           110
  subtype3                          0                           130
  subtype4                          0                           150
  subtype5                          0                           155
  subtype6                          0                            51
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                              1                   4
  subtype2                            104                   0
  subtype3                             32                   0
  subtype4                             15                   1
  subtype5                             10                   0
  subtype6                              5                   0
          vv
clus       MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                                1                  0             13
  subtype2                                9                  1              5
  subtype3                               10                  8             14
  subtype4                                4                  0              6
  subtype5                                5                  5              6
  subtype6                                0                  0              0
D8V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  INFILTRATING CARCINOMA NOS              1        0        0        0        0
  INFILTRATING DUCTAL CARCINOMA         153      110      130      150      155
  INFILTRATING LOBULAR CARCINOMA          1      104       32       15       10
  MEDULLARY CARCINOMA                     4        0        0        1        0
  MIXED HISTOLOGY (PLEASE SPECIFY)        1        9       10        4        5
  MUCINOUS CARCINOMA                      0        1        8        0        5
  OTHER  SPECIFY                         13        5       14        6        6
                                  clus
vv                                 subtype6
  INFILTRATING CARCINOMA NOS              0
  INFILTRATING DUCTAL CARCINOMA          51
  INFILTRATING LOBULAR CARCINOMA          5
  MEDULLARY CARCINOMA                     0
  MIXED HISTOLOGY (PLEASE SPECIFY)        0
  MUCINOUS CARCINOMA                      0
  OTHER  SPECIFY                          0
[1] 7 6
[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
  subtype1  57 117
  subtype2  63 166
  subtype3  55 139
  subtype4  41 135
  subtype5  56 125
  subtype6  13  43
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   57  117
  subtype2   63  166
  subtype3   55  139
  subtype4   41  135
  subtype5   56  125
  subtype6   13   43
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO        57       63       55       41       56       13
  YES      117      166      139      135      125       43
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     5                        53
  subtype2                                0     6                        16
  subtype3                                0     7                        17
  subtype4                                0    13                        21
  subtype5                                0    15                        22
  subtype6                                1    11                        10
          vv
clus       WHITE
  subtype1   108
  subtype2   195
  subtype3   155
  subtype4   115
  subtype5   117
  subtype6    28
D8V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        0        0
  ASIAN                                   5        6        7       13       15
  BLACK OR AFRICAN AMERICAN              53       16       17       21       22
  WHITE                                 108      195      155      115      117
                                  clus
vv                                 subtype6
  AMERICAN INDIAN OR ALASKA NATIVE        1
  ASIAN                                  11
  BLACK OR AFRICAN AMERICAN              10
  WHITE                                  28
[1] 4 6
[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
  subtype1   6 146
  subtype2   9 185
  subtype3   9 149
  subtype4   4 136
  subtype5   8 140
  subtype6   0  47
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6  146
  subtype2    9  185
  subtype3    9  149
  subtype4    4  136
  subtype5    8  140
  subtype6    0   47
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            6        9        9        4        8        0
  NOT HISPANIC OR LATINO      146      185      149      136      140       47
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = MIRSEQ_CNMF
D9V1, survival
          sevent
clus2        0   1
  subtype1 259  20
  subtype2 358  51
  subtype3 241  43
subtype1 subtype2 subtype3 
     279      409      284 
subtype1 subtype2 subtype3 
      20       51       43 
$subtype1
TCGA-A1-A0SB TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A2-A04N TCGA-A2-A0CK TCGA-A2-A0CO 
        8.52        43.43        48.10       104.81       125.59       112.08 
TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CZ TCGA-A2-A0EM 
       92.48       107.93         5.19        63.45        53.13       101.72 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EV 
       89.36        80.28       107.61        74.40        37.05        31.82 
TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0SU TCGA-A2-A0SY TCGA-A2-A0T4 
       29.75        24.72        24.16        54.64        44.28        20.52 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YD TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A1G0 
       18.90        20.75        25.28        19.33        14.63        20.25 
TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25D TCGA-A2-A3KC TCGA-A2-A3KD 
       16.47        52.47       107.70        18.15        20.88        39.65 
TCGA-A2-A3XW TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S2 TCGA-A7-A0CG TCGA-A7-A0DB 
       49.48         7.30         8.81         6.74        34.29        33.11 
TCGA-A7-A13H TCGA-A7-A26H TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J1 TCGA-A7-A425 
       29.56        23.80        11.34        10.59        11.28        14.70 
TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SC TCGA-A7-A5ZW TCGA-A7-A5ZX 
       11.97        14.93        13.74        14.66        10.72        11.05 
TCGA-A8-A07E TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09D TCGA-A8-A0A6 
       19.99        41.98        12.00         9.99        13.02        21.04 
TCGA-A8-A0AB TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF 
       17.03        10.85         1.48        38.20        40.57        55.43 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3BB 
       36.99        38.79        26.04        50.70         0.92         0.99 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3YI 
        0.69        14.83         9.40         1.12         1.68         1.55 
TCGA-AC-A5XS TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AN-A0FF 
        1.55         1.81         1.18         0.43         1.74         4.64 
TCGA-AN-A0FS TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AO-A03T TCGA-AO-A0J9 TCGA-AO-A0JG 
        6.28         0.33         5.33        47.87        53.03        26.24 
TCGA-AO-A0JI TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12E TCGA-AO-A1KO TCGA-AQ-A1H3 
       38.53        94.59        90.58        57.30        14.73        13.22 
TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AU 
       21.86         9.99        51.25        48.82        62.56        46.32 
TCGA-AR-A1AX TCGA-AR-A24K TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24T TCGA-AR-A24W 
       36.26        50.89        65.69         0.85        53.26        50.96 
TCGA-AR-A2LH TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       20.25         7.36        40.04        17.10        20.81        16.96 
TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0IH TCGA-B6-A0IK TCGA-B6-A0RM 
       54.74        16.04        20.45       112.37        18.77        78.02 
TCGA-B6-A0RQ TCGA-B6-A0RU TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A40B 
      140.48       131.21        73.51       170.17        85.35        82.88 
TCGA-B6-A40C TCGA-BH-A0AZ TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0BA TCGA-BH-A0BD 
       55.00        28.50        48.36        56.94        37.22        18.21 
TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0DE 
       35.67        27.19        49.05        44.02        48.13        31.17 
TCGA-BH-A0DI TCGA-BH-A0DO TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0E2 TCGA-BH-A0E9 
       22.13        17.26        38.47        45.17        14.30        46.19 
TCGA-BH-A0EA TCGA-BH-A0H3 TCGA-BH-A0HP TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A18F 
       32.65        37.78        13.61        24.95        42.35         8.81 
TCGA-BH-A18M TCGA-BH-A1EO TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1FB 
       72.56        91.99        42.28        55.69        49.58       120.62 
TCGA-BH-A1FE TCGA-BH-A1FH TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A28O TCGA-BH-A28Q 
       74.73        36.92        72.07         6.90        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A132 TCGA-C8-A137 TCGA-C8-A26W 
       20.12       109.28         8.94         1.45         3.85         0.23 
TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A145 TCGA-D8-A1JB 
        0.36         8.28         0.03         0.23        13.48        18.71 
TCGA-D8-A1JH TCGA-D8-A1JU TCGA-D8-A1X8 TCGA-D8-A1XB TCGA-D8-A1XM TCGA-D8-A1Y2 
       14.01        14.70        25.74        18.15        17.69        14.24 
TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27N 
       17.42        13.45        14.43         9.44        16.41         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-A107 TCGA-E2-A108 TCGA-E2-A10F TCGA-E2-A14Q TCGA-E2-A14U TCGA-E2-A15E 
       34.42        27.52        28.87        38.24        43.33        20.71 
TCGA-E2-A15F TCGA-E2-A15P TCGA-E2-A1B1 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IH 
       21.63        19.56        53.03        16.47        17.10        33.73 
TCGA-E2-A1IK TCGA-E2-A1L6 TCGA-E2-A2P5 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
       22.65        54.18        16.93        15.72         7.20        18.05 
TCGA-E2-A572 TCGA-E9-A1N4 TCGA-E9-A1NE TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R3 
       27.32        19.20        35.77        11.90        14.30         2.10 
TCGA-E9-A1RD TCGA-E9-A226 TCGA-E9-A245 TCGA-E9-A295 TCGA-E9-A2JT TCGA-E9-A3Q9 
        0.66        34.13         0.85         0.72         0.76        18.41 
TCGA-E9-A3X8 TCGA-E9-A5FK TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1J2 TCGA-EW-A1P1 
       15.72         0.39        15.39        12.20        13.25        39.78 
TCGA-EW-A1P3 TCGA-EW-A1PA TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FV TCGA-EW-A3E8 
       52.96        18.90        14.43        34.55        25.91        21.27 
TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DC TCGA-GM-A2DI 
       10.59         7.40        59.57       194.27        53.52        61.91 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3XG 
       62.33        90.84        76.64        77.33       110.50        32.28 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YX TCGA-LD-A66U 
       53.95        57.63        13.55        18.12        11.57         8.28 
TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A50Y TCGA-LL-A5YL 
        6.67         4.60         0.66         2.99         6.90         5.56 
TCGA-LL-A5YM TCGA-LL-A6FQ TCGA-LL-A73Z TCGA-LL-A740 TCGA-LQ-A4E4 TCGA-MS-A51U 
        4.70         2.63         4.50         4.50        15.91         2.79 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX 
        2.10        12.66        44.61        27.65        24.10        16.87 
TCGA-OL-A5RY TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       14.10        14.76        54.51        33.90        31.07        18.21 
TCGA-OL-A66O TCGA-S3-A6ZG TCGA-W8-A86G 
        7.23         6.81         5.29 

$subtype2
TCGA-A1-A0SD TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM 
       14.37        14.27        47.24        20.88        13.68         7.96 
TCGA-A1-A0SN TCGA-A1-A0SQ TCGA-A2-A04R TCGA-A2-A04W TCGA-A2-A04Y TCGA-A2-A0CQ 
       39.32        18.21        82.16        64.04        36.13        88.60 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0D3 TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0SV 
       75.55        75.25        28.77        35.05        34.29        27.12 
TCGA-A2-A0SW TCGA-A2-A0T1 TCGA-A2-A0T3 TCGA-A2-A0T5 TCGA-A2-A0YC TCGA-A2-A0YF 
       44.88        17.13        18.71        17.46        32.55        15.42 
TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX 
       21.67        14.50        23.77        23.47        17.36        36.79 
TCGA-A2-A1FZ TCGA-A2-A1G4 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25E TCGA-A2-A3XV 
       22.45        19.56        16.31        17.19        91.92        14.07 
TCGA-A7-A0CD TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A13F TCGA-A7-A13G 
       38.30        35.47        30.61        37.45        12.72        23.61 
TCGA-A7-A26E TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A06P 
       31.36        20.61        22.32        10.42        13.02        13.02 
TCGA-A8-A06Q TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 
        1.02        41.06        29.03        26.01         1.02        17.03 
TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07P 
       53.98        33.01        18.97        14.01        12.00        10.98 
TCGA-A8-A07S TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A 
        7.99        28.04        15.06        36.95        13.02         0.99 
TCGA-A8-A08B TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08S 
       23.08        19.96        12.00        37.05        31.00        19.07 
TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A099 
       93.04        40.01        19.07        16.01        17.95         9.99 
TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N 
       12.00         1.02        31.00        29.98        15.02         1.02 
TCGA-A8-A09T TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A9 
       19.04        14.01        12.00        19.04        13.02        13.02 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23H TCGA-AC-A3YJ TCGA-AN-A03X 
       38.04         0.95         2.37         2.66         1.32         0.33 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A0AK TCGA-AN-A0AS 
        0.33         0.23         0.33         0.62         7.36         0.33 
TCGA-AN-A0FD TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XP 
        6.44         7.00         7.17         0.33         0.33         0.30 
TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03O 
        0.33         0.33         5.59        80.28        66.77        81.63 
TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J8 TCGA-AO-A0JA TCGA-AO-A0JB 
       29.13        21.40        24.16        22.36        21.53        50.70 
TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JJ TCGA-AO-A0JM 
       50.86        72.00        76.77        21.37        62.04        71.80 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A12B TCGA-AO-A12C TCGA-AO-A12G TCGA-AO-A12H 
       99.25        93.70        77.56        65.56        41.62        28.37 
TCGA-AO-A1KP TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04L TCGA-AQ-A1H2 
       82.62         0.53        17.79        24.79       130.09        15.62 
TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
       49.32         5.26        29.75        64.83        55.86        76.14 
TCGA-AR-A0U3 TCGA-AR-A1AN TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AT TCGA-AR-A1AV 
       76.18        43.73        39.98        40.83        41.82        42.58 
TCGA-AR-A1AW TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24R 
       35.24       109.58        73.02        65.46        68.19        57.40 
TCGA-AR-A24S TCGA-AR-A24V TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 
       62.07        54.18        48.16        51.75        56.15        40.64 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LK TCGA-B6-A0I5 TCGA-B6-A0I8 
       39.85        34.82       128.65        42.87       149.59        24.62 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IG TCGA-B6-A0IM 
       12.13       220.90       129.57        50.70       146.50       126.12 
TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
       84.59       110.14       110.93        68.45       189.01       234.28 
TCGA-B6-A0RL TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RV TCGA-B6-A0WS 
       81.17       172.96       162.05       102.77       157.41        97.48 
TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X5 
      188.68        79.63        17.98       129.57       129.70        68.94 
TCGA-B6-A1KN TCGA-B6-A408 TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0B0 
      139.17        49.94        24.53        20.45        25.55        46.95 
TCGA-BH-A0B1 TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B7 TCGA-BH-A0B8 TCGA-BH-A0BC 
       37.74        40.83        39.16        56.98        51.58        32.02 
TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BP TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT 
       21.70        61.68        48.69        53.69        53.95        45.57 
TCGA-BH-A0BV TCGA-BH-A0C7 TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DK TCGA-BH-A0DP 
       49.94        42.90        23.44        38.01        13.91        15.65 
TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E7 
        3.22         2.56        47.41        16.27        15.68        44.81 
TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 
       24.43        10.78        15.16        35.51        24.56        23.08 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HF TCGA-BH-A0HI TCGA-BH-A0HK 
       41.00        52.96        26.50        23.90        20.38         5.85 
TCGA-BH-A0HL TCGA-BH-A0HN TCGA-BH-A0HO TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW 
        2.37        16.96         2.50        36.85        12.89        51.32 
TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0W3 TCGA-BH-A0W7 TCGA-BH-A18I TCGA-BH-A18J 
       27.25        50.79        23.93        44.81         7.23        20.12 
TCGA-BH-A18K TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18S TCGA-BH-A1EN TCGA-BH-A1ES 
       90.84        37.74        30.28        66.05        69.93       113.82 
TCGA-BH-A1ET TCGA-BH-A1EV TCGA-BH-A1EY TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F8 
       82.85        12.00        17.69        31.53        89.16        24.66 
TCGA-BH-A1FG TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A202 
      122.89        63.35        55.00        45.63       144.59         0.72 
TCGA-BH-A204 TCGA-BH-A208 TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12Q 
       83.31        57.83        11.77        11.77        12.66         0.07 
TCGA-C8-A12U TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A135 TCGA-C8-A138 
       12.66        12.66        12.66         3.12         0.62         3.75 
TCGA-C8-A1HE TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN 
       12.33        11.34        12.03        10.42         2.30         3.25 
TCGA-C8-A26V TCGA-C8-A273 TCGA-C8-A274 TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 
        0.30         9.67         0.03        11.90        13.25        20.58 
TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE 
       21.14        14.17        17.49        15.78        18.15        18.90 
TCGA-D8-A1JF TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS 
       12.03        18.97        20.09        20.38        21.01        12.20 
TCGA-D8-A1JT TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XC 
       13.32        17.79        16.73        23.90        27.58         2.66 
TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XU 
       17.16        14.73         7.96        15.85        16.31        12.99 
TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27V TCGA-D8-A3Z6 
       16.54        15.52         3.81        14.14        12.53        18.51 
TCGA-E2-A105 TCGA-E2-A106 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C 
       43.00        59.41        46.59        40.41        37.51        40.11 
TCGA-E2-A10E TCGA-E2-A14O TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14V TCGA-E2-A152 
       28.44        44.68        33.17        33.30        34.26        27.12 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15C TCGA-E2-A15D 
       23.24        19.43        21.04        23.87        22.82        17.29 
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-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B4 
        7.73        13.02        17.06        14.07        14.99        29.95 
TCGA-E2-A1B5 TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IJ TCGA-E2-A1IL 
       32.35        38.30        37.41        32.78        28.44         3.88 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA 
       22.19        20.98        11.08        39.62        19.66        24.59 
TCGA-E2-A1LB TCGA-E2-A1LS TCGA-E2-A2P6 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1NF 
       40.47        15.45         5.52        36.82        13.48        20.05 
TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 
       21.57         9.86         0.62         6.12         1.38         2.76 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG 
       21.21        32.09        40.24        34.65         6.58        21.27 
TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22B TCGA-E9-A22E 
       35.64         0.79        12.53        13.32        22.75        12.89 
TCGA-E9-A22H TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A54Y TCGA-EW-A1IX 
       24.10        27.22         0.95        12.56         0.23        39.72 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 
        8.48        18.21        18.90        16.57        15.68        28.77 
TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P5 
       25.94        29.95        29.85        40.41        41.13        23.11 
TCGA-EW-A1P6 TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A2FS TCGA-EW-A2FW TCGA-GM-A3NY 
       18.48        13.94        10.52        52.73        22.09        38.20 
TCGA-LL-A442 
        3.58 

$subtype3
TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04T 
       31.79        28.01        19.20        18.02        41.95        73.84 
TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04X TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CW 
       22.06        63.12        55.43        64.57        24.79        64.04 
TCGA-A2-A0CY TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D4 TCGA-A2-A0EQ 
       55.00        21.14        34.55        33.76        25.22        79.76 
TCGA-A2-A0ST TCGA-A2-A0SX TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0YG TCGA-A2-A0YM 
       99.19        50.43        17.52         8.38        21.90        31.73 
TCGA-A2-A1G1 TCGA-A2-A25F TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XX 
       19.20        10.59        33.93        83.01        29.98        38.40 
TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RX TCGA-A2-A4S0 TCGA-A2-A4S1 
       34.98        31.99        38.37         9.01         8.91        12.00 
TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A26F 
        3.42        35.31        35.67        31.73        10.72        24.26 
TCGA-A7-A26G TCGA-A7-A26I TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A4SD TCGA-A7-A4SE 
       23.74        21.73        10.29        13.41        14.50        21.17 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY 
       17.92        14.73        12.10        10.29         9.37         8.75 
TCGA-A8-A06R TCGA-A8-A079 TCGA-A8-A07C TCGA-A8-A07G TCGA-A8-A07L TCGA-A8-A07O 
       17.98         9.01        19.07        18.97        17.03         9.99 
TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A082 TCGA-A8-A08L TCGA-A8-A08R 
        8.98         9.96         9.99        18.05         9.99         0.99 
TCGA-A8-A08X TCGA-A8-A09I TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A0A7 TCGA-AC-A2BK 
       33.99        33.07        25.02         8.98         0.99        38.53 
TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A3W5 TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IW 
        1.02         2.27         1.81         0.07         1.12         0.69 
TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AL TCGA-AN-A0AM 
        2.96         1.78         1.71         8.02         6.51         0.16 
TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FT TCGA-AN-A0FV 
        0.33         0.33         7.96         7.59         6.02         0.33 
TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0G0 TCGA-AN-A0XO 
        0.36         0.33         0.33         0.33         0.53        12.33 
TCGA-AN-A0XU TCGA-AO-A03M TCGA-AO-A03R TCGA-AO-A03U TCGA-AO-A0J2 TCGA-AO-A0J4 
        0.33        47.84        68.75        59.05        32.78        17.65 
TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A129 TCGA-AO-A12D 
       37.48        20.32        55.33       102.58        96.10        64.04 
TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AQ-A04J TCGA-AQ-A0Y5 TCGA-AQ-A54N 
       48.36        61.87        70.39        26.93         5.65         2.56 
TCGA-AR-A0TP TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AH 
       82.88        37.41        56.88        83.87        55.36        75.55 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AO TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AY 
       61.84        52.77        43.56        43.07        17.23        20.22 
TCGA-AR-A24Q TCGA-AR-A24U TCGA-AR-A251 TCGA-AR-A256 TCGA-AR-A2LR TCGA-AR-A5QQ 
       66.05        53.36        45.17        93.83        20.38        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I6 TCGA-B6-A0IE TCGA-B6-A0IJ TCGA-B6-A0IQ 
       77.62       143.38        32.78        65.72       176.98       140.88 
TCGA-B6-A0RE TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0X4 
      211.56       100.70        89.46        21.47       113.79        28.27 
TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A402 TCGA-BH-A0AV TCGA-BH-A0B3 
       58.88        43.59       101.52        54.28        38.79        39.55 
TCGA-BH-A0B9 TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BW TCGA-BH-A0C0 
       51.68        25.71        24.85        44.05        11.67        41.75 
TCGA-BH-A0DD TCGA-BH-A0DL TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0EE TCGA-BH-A0GY 
       45.83        48.23         4.41         9.63        31.00        30.35 
TCGA-BH-A0RX TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18L TCGA-BH-A18Q TCGA-BH-A18R 
        5.59        23.05         2.01        26.66        55.63        37.55 
TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1F0 TCGA-BH-A1F6 TCGA-BH-A1FC 
        7.36        51.39        51.16        25.81        97.48       114.15 
TCGA-BH-A1FN TCGA-BH-A203 TCGA-BH-A209 TCGA-BH-A42T TCGA-C8-A12L TCGA-C8-A12P 
       72.07        38.60       130.16         0.99        11.93        11.77 
TCGA-C8-A12V TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ 
       12.66         1.78         0.69        10.92        11.34         0.16 
TCGA-C8-A26Y TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-D8-A13Z 
        0.43         0.03         0.03        12.20         0.99        20.88 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A147 TCGA-D8-A1JA TCGA-D8-A1JG TCGA-D8-A1JK 
       13.97        14.17        19.20        16.50        12.03        20.12 
TCGA-D8-A1JL TCGA-D8-A1X5 TCGA-D8-A1XF TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL 
       20.09        18.58        15.22        21.83        14.50        19.92 
TCGA-D8-A1XQ TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A27F 
       16.41         6.35        15.16        12.66        15.32        16.04 
TCGA-D8-A27H TCGA-D8-A27M TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14R TCGA-E2-A14W 
       13.05        13.48        47.15        40.96        38.60        32.02 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A158 TCGA-E2-A159 
       31.96        28.60        17.03        25.41        14.79        25.05 
TCGA-E2-A15A TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B6 TCGA-E2-A1II TCGA-E2-A1L7 
       23.34        60.53        53.62        28.50        33.70        27.42 
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-A573 TCGA-E2-A574 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1ND 
       22.26        19.89        12.00        13.12        36.56        12.59 
TCGA-E9-A1RB TCGA-E9-A1RH TCGA-E9-A22A TCGA-E9-A22G TCGA-E9-A243 TCGA-E9-A244 
       20.81        34.59        39.09        23.51        17.06         0.69 
TCGA-E9-A248 TCGA-E9-A2JS TCGA-E9-A3QA TCGA-E9-A5FL TCGA-E9-A5UO TCGA-EW-A1OW 
        1.94        17.75         0.62         0.26         0.23        22.82 
TCGA-EW-A1P4 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PH 
       29.82        30.08         7.86        19.99         6.15        19.96 
TCGA-EW-A2FR TCGA-EW-A3U0 TCGA-EW-A423 TCGA-GI-A2C9 TCGA-GM-A2DB TCGA-GM-A2DD 
       55.00        17.49        10.16       109.87        53.13        43.04 
TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DO TCGA-GM-A3XL TCGA-JL-A3YW TCGA-LL-A5YN 
       42.71        42.28        53.36        69.30        11.84         3.65 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A7SZ TCGA-LL-A7T0 
        3.19         3.25         3.88         4.14         5.59         3.22 
TCGA-LL-A8F5 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5RW TCGA-OL-A5RZ TCGA-OL-A5S0 
        6.21        46.55         7.53        26.20        10.29         9.80 
TCGA-OL-A66I TCGA-OL-A66P 
       23.70         4.44 

subtype1 subtype2 subtype3 
    0.03     0.03     0.03 
subtype1 subtype2 subtype3 
  194.27   234.28   211.56 
subtype1 subtype2 subtype3 
   20.25    23.08    21.01 
[1] "0.0 - 194.3 (20.2)" "0.0 - 234.3 (23.1)" "0.0 - 211.6 (21.0)"
D9V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1      24       29        6        8        66        65         1
  subtype2      40       33        3        1       137        98         1
  subtype3      16       17        1        0       132        60         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
  subtype1         39          6         32        2         0       3
  subtype2         64         15         14       10         0       9
  subtype3         33          5         12        4         1       5
D9V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          24       40       16
  STAGE IA         29       33       17
  STAGE IB          6        3        1
  STAGE II          8        1        0
  STAGE IIA        66      137      132
  STAGE IIB        65       98       60
  STAGE III         1        1        0
  STAGE IIIA       39       64       33
  STAGE IIIB        6       15        5
  STAGE IIIC       32       14       12
  STAGE IV          2       10        4
  STAGE TIS         0        0        1
  STAGE X           3        9        5
[1] 13  3
[1] 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
  subtype1  87 137  49   7
  subtype2 121 244  40  20
  subtype3  55 195  26   9
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       87      121       55
  T2      137      244      195
  T3       49       40       26
  T4        7       20        9
[1] 4 3
[1] 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
  subtype1 120  96  27  34
  subtype2 188 152  55  20
  subtype3 162  81  27  14
D9V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0      120      188      162
  N1       96      152       81
  N2       27       55       27
  N3       34       20       14
[1] 4 3
[1] 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
  subtype1        1 217   2  61
  subtype2        1 376  10  38
  subtype3        0 250   4  33
D9V6, multiclass
          clus
vv         subtype1 subtype2 subtype3
  CM0 (I+)        1        1        0
  M0            217      376      250
  M1              2       10        4
  MX             61       38       33
[1] 4 3
[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
  subtype1 280   1
  subtype2 419   6
  subtype3 283   4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  280    1
  subtype2  419    6
  subtype3  283    4
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      280      419      283
  MALE          1        6        4
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  subtype1                          0                           138
  subtype2                          0                           350
  subtype3                          1                           247
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                            125                   0
  subtype2                             32                   0
  subtype3                              8                   5
          vv
clus       MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                                7                  4              7
  subtype2                               17                  5             21
  subtype3                                4                  5             16
D9V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  INFILTRATING CARCINOMA NOS              0        0        1
  INFILTRATING DUCTAL CARCINOMA         138      350      247
  INFILTRATING LOBULAR CARCINOMA        125       32        8
  MEDULLARY CARCINOMA                     0        0        5
  MIXED HISTOLOGY (PLEASE SPECIFY)        7       17        4
  MUCINOUS CARCINOMA                      4        5        5
  OTHER  SPECIFY                          7       21       16
[1] 7 3
[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
  subtype1  57 224
  subtype2 140 285
  subtype3  81 206
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   57  224
  subtype2  140  285
  subtype3   81  206
     clus
vv    subtype1 subtype2 subtype3
  NO        57      140       81
  YES      224      285      206
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    11                        32
  subtype2                                1    30                        31
  subtype3                                0    16                        75
          vv
clus       WHITE
  subtype1   227
  subtype2   307
  subtype3   175
D9V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0
  ASIAN                                  11       30       16
  BLACK OR AFRICAN AMERICAN              32       31       75
  WHITE                                 227      307      175
[1] 4 3
[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
  subtype1  12 242
  subtype2  17 313
  subtype3   7 240
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12  242
  subtype2   17  313
  subtype3    7  240
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           12       17        7
  NOT HISPANIC OR LATINO      242      313      240
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_CHIERARCHICAL
D10V1, survival
          sevent
clus2        0   1
  subtype1 143  11
  subtype2 161  16
  subtype3 337  51
  subtype4 110  18
  subtype5 107  18
subtype1 subtype2 subtype3 subtype4 subtype5 
     154      177      388      128      125 
subtype1 subtype2 subtype3 subtype4 subtype5 
      11       16       51       18       18 
$subtype1
TCGA-A1-A0SB TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CZ TCGA-A2-A0EP 
        8.52       112.08        92.48       107.93        53.13       107.61 
TCGA-A2-A0ES TCGA-A2-A0EW TCGA-A2-A0YD TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A1G6 
       37.05        29.75        25.28        19.33        14.63        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A4RY TCGA-A2-A4S2 
       52.47       107.70        20.88        39.65         8.81         6.74 
TCGA-A7-A0CG TCGA-A7-A13H TCGA-A7-A3J1 TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SC 
       34.29        29.56        11.28        14.70        11.97        14.66 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2FB TCGA-AC-A2FF 
       10.72        11.05        10.85         1.48        40.57        55.43 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD 
       36.99        38.79         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-A6IV 
        9.40         1.12         1.81         1.68         1.55         1.18 
TCGA-AC-A8OP TCGA-AN-A0FF TCGA-AO-A128 TCGA-AO-A1KO TCGA-AQ-A1H3 TCGA-AQ-A7U7 
        1.74         4.64        94.59        14.73        13.22         9.99 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AU TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24T 
       48.82        62.56        46.32        65.69         0.85        53.26 
TCGA-AR-A24W TCGA-AR-A2LH TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       50.96        20.25        40.04        17.10        20.81        16.96 
TCGA-AR-A5QM TCGA-AR-A5QP TCGA-B6-A0IH TCGA-B6-A0RQ TCGA-B6-A2IU TCGA-B6-A401 
       54.74        20.45       112.37       140.48       170.17        85.35 
TCGA-B6-A40C TCGA-BH-A0BO TCGA-BH-A0BZ TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DO 
       55.00        35.67        49.05        23.44        22.13        17.26 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0E9 TCGA-BH-A0H3 TCGA-BH-A0W4 
       38.47        45.17        47.41        46.19        37.78        24.95 
TCGA-BH-A18M TCGA-BH-A1EU TCGA-BH-A1EX TCGA-BH-A1FB TCGA-BH-A1FE TCGA-BH-A1FH 
       72.56        42.28        49.58       120.62        74.73        36.92 
TCGA-BH-A201 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V 
        6.90        10.65         6.44        20.12       109.28         8.94 
TCGA-C8-A274 TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A145 TCGA-D8-A1JB TCGA-D8-A1JH 
        0.03         0.03         0.23        13.48        18.71        14.01 
TCGA-D8-A1JU TCGA-D8-A1X8 TCGA-D8-A27G TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       14.70        25.74        13.45        14.43         9.44        16.41 
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-A107 TCGA-E2-A14Q TCGA-E2-A14U TCGA-E2-A15C TCGA-E2-A1B1 TCGA-E2-A1L6 
       34.42        38.24        43.33        22.82        53.03        54.18 
TCGA-E2-A2P5 TCGA-E2-A3DX TCGA-E2-A572 TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A2JT 
       16.93        15.72        27.32        11.90        14.30         0.76 
TCGA-E9-A3X8 TCGA-E9-A5FK TCGA-EW-A1J2 TCGA-EW-A1P1 TCGA-EW-A1PG TCGA-EW-A3E8 
       15.72         0.39        13.25        39.78        34.55        21.27 
TCGA-EW-A424 TCGA-GM-A2D9 TCGA-GM-A2DI TCGA-GM-A2DL TCGA-GM-A2DN TCGA-GM-A3NY 
       10.59        59.57        61.91        90.84        77.33        38.20 
TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YX 
       32.28        53.95        57.63        13.55        18.12        11.57 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A50Y TCGA-LQ-A4E4 
        8.28         6.67         4.60         0.66         6.90        15.91 
TCGA-MS-A51U TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A66J 
        2.79        27.65        24.10        16.87        14.10        54.51 
TCGA-OL-A66K TCGA-OL-A66L TCGA-S3-A6ZG TCGA-W8-A86G 
       33.90        31.07         6.81         5.29 

$subtype2
TCGA-A1-A0SD TCGA-A1-A0SG TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SQ TCGA-A2-A04N 
       14.37        14.27        20.88        13.68        18.21       104.81 
TCGA-A2-A04R TCGA-A2-A0CK TCGA-A2-A0CU TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0ER 
       82.16       125.59         5.19        25.22       101.72        74.40 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0SU TCGA-A2-A0T4 TCGA-A2-A0YF TCGA-A2-A0YI 
       35.05        34.29        54.64        20.52        15.42        14.50 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A25E TCGA-A7-A0CD TCGA-A7-A0CH 
       22.45        20.25        19.56        91.92        38.30        35.47 
TCGA-A7-A13F TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A56D 
       12.72        11.34        10.59        14.93        13.74        14.73 
TCGA-A8-A06P TCGA-A8-A06T TCGA-A8-A06Z TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07P 
       13.02        41.06         1.02        12.00        17.03        10.98 
TCGA-A8-A07S TCGA-A8-A07Z TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08G 
        7.99        28.04        36.95        13.02         0.99        19.96 
TCGA-A8-A08I TCGA-A8-A091 TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A0A1 TCGA-A8-A0A6 
       12.00        19.07        25.02         8.98        12.00        21.04 
TCGA-A8-A0A9 TCGA-A8-A0AD TCGA-AC-A2BM TCGA-AC-A62Y TCGA-AN-A041 TCGA-AN-A049 
       13.02        38.04        38.20         1.81         0.23         0.62 
TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XT 
        7.00         7.17         6.28         0.30         0.33         0.33 
TCGA-AN-A0XV TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A0J7 TCGA-AO-A0JF TCGA-AO-A0JJ 
        5.33        68.75        47.87        20.32        21.37        62.04 
TCGA-AO-A126 TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12H TCGA-AO-A1KQ TCGA-AQ-A04H 
       93.70        77.56        57.30        28.37        61.87        24.79 
TCGA-AQ-A54O TCGA-AR-A0TV TCGA-AR-A1AK TCGA-AR-A1AN TCGA-AR-A24R TCGA-AR-A24V 
       21.86        29.75        51.25        43.73        57.40        54.18 
TCGA-AR-A2LE TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IP 
      128.65       220.90        50.70        18.77       126.12       110.93 
TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RP TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT 
      234.28        78.02       102.77       157.41        97.48       188.68 
TCGA-B6-A0X0 TCGA-B6-A0X5 TCGA-B6-A1KI TCGA-BH-A0BA TCGA-BH-A0BD TCGA-BH-A0BJ 
      129.70        68.94        73.51        37.22        18.21        21.70 
TCGA-BH-A0BM TCGA-BH-A0C0 TCGA-BH-A0DE TCGA-BH-A0DH TCGA-BH-A0DQ TCGA-BH-A0E1 
       61.68        41.75        31.17        38.01         3.22        15.68 
TCGA-BH-A0E7 TCGA-BH-A0EI TCGA-BH-A0H0 TCGA-BH-A0H6 TCGA-BH-A0HA TCGA-BH-A0HF 
       44.81        24.43        15.16        24.56        52.96        23.90 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HW TCGA-BH-A0HY 
       20.38         5.85         2.50        13.61        51.32        50.79 
TCGA-BH-A0W3 TCGA-BH-A18I TCGA-BH-A18N TCGA-BH-A18S TCGA-BH-A1ES TCGA-BH-A1F5 
       23.93         7.23        37.74        66.05       113.82        89.16 
TCGA-BH-A1FG TCGA-BH-A1FJ TCGA-BH-A42T TCGA-C8-A12X TCGA-C8-A1HL TCGA-C8-A273 
      122.89        63.35         0.99        12.66        10.42         9.67 
TCGA-D8-A146 TCGA-D8-A1JE TCGA-D8-A1JI TCGA-D8-A1JT TCGA-D8-A1X6 TCGA-D8-A1X7 
       21.14        18.90        18.97        13.32        17.79        16.73 
TCGA-D8-A1XD TCGA-D8-A1XL TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XY TCGA-D8-A27E 
       17.16        19.92         7.96        15.85        16.54        17.42 
TCGA-E2-A106 TCGA-E2-A10A TCGA-E2-A14S TCGA-E2-A156 TCGA-E2-A15F TCGA-E2-A15I 
       59.41        40.41        33.17        23.87        21.63        17.42 
TCGA-E2-A1B4 TCGA-E2-A1BC TCGA-E2-A1IK TCGA-E2-A2P6 TCGA-E9-A1N4 TCGA-E9-A1NE 
       29.95        16.47        22.65         5.52        19.20        35.77 
TCGA-E9-A1R7 TCGA-E9-A1RB TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A229 TCGA-E9-A22H 
       21.21        20.81        35.64         0.79        13.32        24.10 
TCGA-E9-A24A TCGA-E9-A54Y TCGA-E9-A5UO TCGA-EW-A1IX TCGA-EW-A1J1 TCGA-EW-A1OX 
       12.56         0.23         0.23        39.72        18.90        29.95 
TCGA-EW-A1P0 TCGA-EW-A1P5 TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A2FS 
       41.13        23.11        13.94        10.52        14.43        52.73 
TCGA-EW-A2FW TCGA-GI-A2C8 TCGA-GM-A2DC TCGA-GM-A2DK TCGA-GM-A2DM TCGA-GM-A3NW 
       22.09         7.40        53.52        62.33        76.64       110.50 
TCGA-LL-A442 TCGA-OL-A5DA TCGA-OL-A66O 
        3.58        44.61         7.23 

$subtype3
TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SH TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN 
       43.43        48.10        47.24        31.79         7.96        39.32 
TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CQ TCGA-A2-A0CS 
       63.12        64.04        55.43        36.13        88.60        75.55 
TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0EN 
       75.25        63.45        64.04        34.55        28.77        89.36 
TCGA-A2-A0EO TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T1 
       80.28        24.72        24.16        44.88        44.28        17.13 
TCGA-A2-A0T3 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YG 
       18.71        17.46        18.90        20.75        32.55        21.90 
TCGA-A2-A0YH TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A25B 
       21.67        23.77        23.47        17.36        36.79        16.31 
TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A3XZ TCGA-A2-A4S0 TCGA-A7-A0CJ TCGA-A7-A0D9 
       17.19        18.15        31.99         8.91        30.61        37.45 
TCGA-A7-A0DB TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD 
       33.11        23.61        31.36        23.80        20.61        22.32 
TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A4SF TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A06Q 
       10.29        13.41        17.92        10.42        13.02         1.02 
TCGA-A8-A06Y TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F 
       26.01        53.98         9.01        33.01        19.99        18.97 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A084 TCGA-A8-A08B TCGA-A8-A08J TCGA-A8-A08L 
       18.97        14.01        15.06        23.08        37.05         9.99 
TCGA-A8-A08O TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A093 
       31.00        19.07        93.04        40.01        16.01        17.95 
TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D 
       41.98         9.99         9.99        12.00         1.02        13.02 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09T TCGA-A8-A09X 
       31.00        33.07        15.02         1.02        19.04        14.01 
TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A7 TCGA-A8-A0AB TCGA-AC-A23C TCGA-AC-A23E 
       19.04        13.02         0.99        17.03         0.95         2.37 
TCGA-AC-A23H TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A3YJ TCGA-AC-A62V TCGA-AN-A03X 
        2.66        26.04        50.70         1.32         0.07         0.33 
TCGA-AN-A03Y TCGA-AN-A046 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AM 
        0.33         0.33         2.96         1.71         7.36         0.16 
TCGA-AN-A0AS TCGA-AN-A0FD TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0XL TCGA-AN-A0XN 
        0.33         6.44         6.02         0.33         0.33         0.33 
TCGA-AN-A0XO TCGA-AN-A0XS TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N 
       12.33         0.33         5.59        80.28        47.84        66.77 
TCGA-AO-A03O TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J8 TCGA-AO-A0J9 
       81.63        29.13        21.40        24.16        22.36        53.03 
TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JG 
       21.53        50.70        50.86        72.00        76.77        26.24 
TCGA-AO-A0JI TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A12A TCGA-AO-A12C TCGA-AO-A12G 
       38.53        71.80        99.25        90.58        65.56        41.62 
TCGA-AO-A1KP TCGA-AO-A1KT TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AR-A0TQ TCGA-AR-A0TR 
       82.62        17.79       130.09        15.62        49.32         5.26 
TCGA-AR-A0TX TCGA-AR-A0TZ TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AP TCGA-AR-A1AS 
       64.83        76.14        83.87        76.18        39.98        40.83 
TCGA-AR-A1AT TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L 
       41.82        42.58        35.24       109.58        50.89        73.02 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 
       65.46        68.19        48.16        51.75        56.15        40.64 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A5QN TCGA-B6-A0I5 
       39.85        34.82        42.87         7.36        16.04       149.59 
TCGA-B6-A0I8 TCGA-B6-A0I9 TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IN 
       24.62        12.13       129.57        65.72       146.50        84.59 
TCGA-B6-A0IO TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RL TCGA-B6-A0RN TCGA-B6-A0RO 
      110.14        68.45       189.01        81.17       172.96       162.05 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X4 TCGA-B6-A1KC 
       79.63        17.98       113.79       129.57        28.27        43.59 
TCGA-B6-A1KN TCGA-B6-A408 TCGA-B6-A40B TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AY 
      139.17        49.94        82.88        24.53        20.45        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B1 TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B5 
       28.50        46.95        37.74        40.83        39.16        48.36 
TCGA-BH-A0B6 TCGA-BH-A0B8 TCGA-BH-A0BC TCGA-BH-A0BF TCGA-BH-A0BP TCGA-BH-A0BQ 
       56.94        51.58        32.02        25.71        48.69        27.19 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0C1 TCGA-BH-A0C7 
       53.69        53.95        45.57        49.94        44.02        42.90 
TCGA-BH-A0DD TCGA-BH-A0DK TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DZ TCGA-BH-A0E2 
       45.83        13.91        15.65         2.56        16.27        14.30 
TCGA-BH-A0EA TCGA-BH-A0GZ TCGA-BH-A0H5 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HB 
       32.65        10.78        35.51        23.08        41.00        26.50 
TCGA-BH-A0HL TCGA-BH-A0HN TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0W5 
        2.37        16.96        36.85        12.89        27.25        42.35 
TCGA-BH-A0W7 TCGA-BH-A18F TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18P 
       44.81         8.81        20.12        90.84        26.66        30.28 
TCGA-BH-A18R TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1EV TCGA-BH-A1EW 
       37.55        69.93        91.99        82.85        12.00        55.69 
TCGA-BH-A1EY TCGA-BH-A1F2 TCGA-BH-A1F8 TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR 
       17.69        31.53        24.66        55.00        45.63       144.59 
TCGA-BH-A204 TCGA-BH-A209 TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P 
       83.31       130.16        11.77        11.77        12.66        11.77 
TCGA-C8-A12U TCGA-C8-A132 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF 
       12.66         1.45         3.85         3.75        12.33        10.92 
TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A26V TCGA-C8-A26W 
       11.34        11.34        12.03         2.30         0.30         0.23 
TCGA-C8-A26Z TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-D8-A13Y TCGA-D8-A140 
        8.28         0.03         0.03        12.20        11.90        13.25 
TCGA-D8-A141 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JD TCGA-D8-A1JJ 
       20.58        14.17        17.49        16.50        18.15        20.09 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1X5 TCGA-D8-A1X9 TCGA-D8-A1XA 
       20.38        21.01        12.20        18.58        23.90        27.58 
TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XM 
       18.15         2.66        15.22        14.73        21.83        17.69 
TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       16.31         6.35        12.99        15.16        15.52         3.81 
TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27N TCGA-D8-A27W TCGA-E2-A105 TCGA-E2-A109 
       14.24        14.14         4.80        12.26        43.00        46.59 
TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14T 
       37.51        40.11        28.44        28.87        44.68        33.30 
TCGA-E2-A14V TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A15A 
       34.26        27.12        23.24        19.43        21.04        23.34 
TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15J TCGA-E2-A15K 
       17.29        20.71        18.21        12.92        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-A1B5 TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       14.99        32.35        17.10        38.30        37.41        32.78 
TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       33.73        28.44         3.88        22.19        20.98        11.08 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A56Z TCGA-E2-A570 
       27.42        39.62        19.66        40.47         7.20        18.05 
TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NF TCGA-E9-A1NG 
       36.82        13.48        13.12        36.56        20.05        21.57 
TCGA-E9-A1NI TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 
        9.86         0.62         2.10         6.12         1.38         2.76 
TCGA-E9-A1RA TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A226 
       32.09        40.24         0.66        34.65        21.27        34.13 
TCGA-E9-A228 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A245 TCGA-E9-A247 
       12.53        39.09        22.75        12.89         0.85        27.22 
TCGA-E9-A249 TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A3Q9 TCGA-E9-A6HE TCGA-EW-A1IW 
        0.95         0.72        17.75        18.41        15.39        12.20 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV 
        8.48        18.21        16.57        15.68        28.77        25.94 
TCGA-EW-A1OZ TCGA-EW-A1P3 TCGA-EW-A1P6 TCGA-EW-A1PA TCGA-EW-A1PC TCGA-EW-A2FV 
       40.41        52.96        18.48        18.90         6.15        25.91 
TCGA-EW-A423 TCGA-GM-A2DO TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A6FQ TCGA-LL-A7SZ 
       10.16        53.36         4.70         3.65         2.63         5.59 
TCGA-LL-A7T0 TCGA-OL-A5D8 TCGA-OL-A5RZ TCGA-OL-A66H 
        3.22         7.53        10.29        14.76 

$subtype4
TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04T TCGA-A2-A04U 
       28.01        19.20        18.02        41.95        73.84        22.06 
TCGA-A2-A0CM TCGA-A2-A0D0 TCGA-A2-A0SX TCGA-A2-A0YM TCGA-A2-A25F TCGA-A2-A3XT 
       24.79        21.14        50.43        31.73        10.59        83.01 
TCGA-A2-A3XU TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RX TCGA-A7-A0CE 
       29.98        38.40        34.98        38.37         9.01        35.31 
TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A4SE 
       35.67        31.73        10.72        24.26        23.74        21.17 
TCGA-A7-A5ZV TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A07C TCGA-A8-A07O 
       12.10        10.29         9.37         8.75        19.07         9.99 
TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A08R TCGA-AC-A2BK TCGA-AC-A62X TCGA-AC-A6IW 
        8.98         9.96         0.99        38.53         1.12         0.69 
TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FX TCGA-AN-A0XU TCGA-AO-A03U TCGA-AO-A0J4 
        7.96         7.59         0.33         0.33        59.05        17.65 
TCGA-AO-A0J6 TCGA-AO-A0JL TCGA-AO-A129 TCGA-AO-A12F TCGA-AO-A1KR TCGA-AQ-A04J 
       37.48        55.33        96.10        48.36        70.39        26.93 
TCGA-AQ-A54N TCGA-AR-A0TP TCGA-AR-A0TS TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
        2.56        82.88        37.41        55.36        75.55        61.84 
TCGA-AR-A1AJ TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AY TCGA-AR-A24Q TCGA-AR-A251 
       52.77        43.07        17.23        20.22        66.05        45.17 
TCGA-AR-A256 TCGA-AR-A2LR TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I6 TCGA-B6-A0IJ 
       93.83        20.38        77.62       143.38        32.78       176.98 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0WX TCGA-B6-A0X7 
      140.88       211.56        89.46       131.21        21.47        58.88 
TCGA-B6-A1KF TCGA-B6-A402 TCGA-BH-A0AV TCGA-BH-A0B9 TCGA-BH-A0E0 TCGA-BH-A0E6 
      101.52        54.28        38.79        51.68         4.41         9.63 
TCGA-BH-A0RX TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A1F6 
        5.59        23.05         2.01        55.63         7.36        97.48 
TCGA-BH-A1FC TCGA-C8-A12V TCGA-C8-A134 TCGA-C8-A1HJ TCGA-C8-A27B TCGA-D8-A147 
      114.15        12.66         0.69         0.16         0.99        19.20 
TCGA-D8-A1JL TCGA-D8-A1XK TCGA-D8-A1XQ TCGA-D8-A1XW TCGA-D8-A27F TCGA-D8-A27H 
       20.09        14.50        16.41        12.66        16.04        13.05 
TCGA-D8-A27M TCGA-E2-A14N TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A158 
       13.48        47.15        38.60        31.96        28.60        14.79 
TCGA-E2-A1AZ TCGA-E2-A1B6 TCGA-E2-A1II TCGA-E2-A1LG TCGA-E2-A1LI TCGA-E2-A1LK 
       60.53        28.50        33.70        18.87       102.61         8.75 
TCGA-E2-A1LS TCGA-E2-A573 TCGA-E9-A1N8 TCGA-E9-A1ND TCGA-E9-A22G TCGA-E9-A244 
       15.45        22.26        12.00        12.59        23.51         0.69 
TCGA-E9-A3QA TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A3U0 
        0.62        22.82        29.82         7.86        19.99        17.49 
TCGA-GI-A2C9 TCGA-GM-A2DF TCGA-GM-A3XL TCGA-LL-A441 TCGA-LL-A6FR TCGA-OL-A5D7 
      109.87        42.71        69.30         2.99         3.88        46.55 
TCGA-OL-A5S0 TCGA-OL-A66I 
        9.80        23.70 

$subtype5
TCGA-A2-A0CL TCGA-A2-A0CY TCGA-A2-A0D2 TCGA-A2-A0EQ TCGA-A2-A0EV TCGA-A2-A0ST 
       64.57        55.00        33.76        79.76        31.82        99.19 
TCGA-A2-A0SV TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A1G1 TCGA-A2-A3XS TCGA-A2-A3XV 
       27.12        17.52         8.38        19.20        33.93        14.07 
TCGA-A2-A3XW TCGA-A2-A4RW TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A26I TCGA-A7-A4SD 
       49.48         7.30        12.00         3.42        21.73        14.50 
TCGA-A8-A06R TCGA-A8-A06U TCGA-A8-A075 TCGA-A8-A07W TCGA-A8-A082 TCGA-A8-A08X 
       17.98        29.03        17.03         9.99        18.05        33.99 
TCGA-A8-A097 TCGA-A8-A09K TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A5XS TCGA-AC-A6IX 
       12.00        29.98         1.02         2.27         1.55         0.43 
TCGA-AN-A04C TCGA-AN-A0AJ TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FW 
        1.78         8.02         6.51         0.33         0.33         0.36 
TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0G0 TCGA-AO-A0J2 TCGA-AO-A124 TCGA-AO-A12D 
        0.33         0.33         0.53        32.78       102.58        64.04 
TCGA-AO-A1KS TCGA-AQ-A0Y5 TCGA-AR-A0TT TCGA-AR-A0TY TCGA-AR-A1AO TCGA-AR-A1AX 
        0.53         5.65        56.88        55.86        43.56        36.26 
TCGA-AR-A24S TCGA-AR-A24U TCGA-AR-A5QQ TCGA-B6-A0RS TCGA-BH-A0B3 TCGA-BH-A0B7 
       62.07        53.36        10.59       100.70        39.55        56.98 
TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BW TCGA-BH-A0C3 TCGA-BH-A0DL TCGA-BH-A0EE 
       24.85        44.05        11.67        48.13        48.23        31.00 
TCGA-BH-A0GY TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1F0 TCGA-BH-A1FN TCGA-BH-A1FU 
       30.35        51.39        51.16        25.81        72.07        72.07 
TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 TCGA-C8-A12L TCGA-C8-A12Q TCGA-C8-A12W 
        0.72        38.60        57.83        11.93         0.07        12.66 
TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A135 TCGA-C8-A1HN TCGA-C8-A26X TCGA-C8-A26Y 
        3.12         1.78         0.62         3.25         0.36         0.43 
TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A1JC TCGA-D8-A1JF TCGA-D8-A1JG 
       20.88        13.97        14.17        15.78        12.03        12.03 
TCGA-D8-A1JK TCGA-D8-A1XZ TCGA-D8-A27R TCGA-E2-A108 TCGA-E2-A14P TCGA-E2-A14W 
       20.12        15.32        10.09        27.52        40.96        32.02 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A159 TCGA-E2-A1B0 TCGA-E2-A1LA TCGA-E2-A1LE 
       17.03        25.41        25.05        53.62        24.59        28.90 
TCGA-E2-A1LH TCGA-E2-A1LL TCGA-E2-A574 TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A243 
      106.75        43.04        19.89         6.58        34.59        17.06 
TCGA-E9-A248 TCGA-E9-A5FL TCGA-EW-A1OY TCGA-EW-A1P7 TCGA-EW-A1PH TCGA-EW-A2FR 
        1.94         0.26        29.85        30.08        19.96        55.00 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DH TCGA-JL-A3YW TCGA-LL-A5YL 
      194.27        53.13        43.04        42.28        11.84         5.56 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A8F5 
        3.19         3.25         4.14         4.50         4.50         6.21 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5RW TCGA-OL-A66N TCGA-OL-A66P 
        2.10        12.66        26.20        18.21         4.44 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.03     0.23     0.03     0.16     0.07 
subtype1 subtype2 subtype3 subtype4 subtype5 
  170.17   234.28   189.01   211.56   194.27 
subtype1 subtype2 subtype3 subtype4 subtype5 
  19.725   21.630   22.045   23.605   18.210 
[1] "0.0 - 170.2 (19.7)" "0.2 - 234.3 (21.6)" "0.0 - 189.0 (22.0)"
[4] "0.2 - 211.6 (23.6)" "0.1 - 194.3 (18.2)"
D10V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1      13       16        2        6        33        39         1
  subtype2      16       17        4        0        59        47         0
  subtype3      34       26        3        1       133        87         1
  subtype4       7       14        0        0        63        24         0
  subtype5      10        6        1        2        47        26         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
  subtype1         23          1         20        1         0       0
  subtype2         26          8          2        0         0       3
  subtype3         58         14         23       10         1      10
  subtype4         11          0          5        1         0       3
  subtype5         18          3          8        4         0       1
D10V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          13       16       34        7       10
  STAGE IA         16       17       26       14        6
  STAGE IB          2        4        3        0        1
  STAGE II          6        0        1        0        2
  STAGE IIA        33       59      133       63       47
  STAGE IIB        39       47       87       24       26
  STAGE III         1        0        1        0        0
  STAGE IIIA       23       26       58       11       18
  STAGE IIIB        1        8       14        0        3
  STAGE IIIC       20        2       23        5        8
  STAGE IV          1        0       10        1        4
  STAGE TIS         0        0        1        0        0
  STAGE X           0        3       10        3        1
[1] 13  5
[1] 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
  subtype1  48  71  35   1
  subtype2  60  96  18   7
  subtype3  94 243  41  22
  subtype4  28  88  10   2
  subtype5  33  78  11   4
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       48       60       94       28       33
  T2       71       96      243       88       78
  T3       35       18       41       10       11
  T4        1        7       22        2        4
[1] 4 5
[1] 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
  subtype1  66  54  14  21
  subtype2  82  74  19   2
  subtype3 176 136  49  31
  subtype4  85  30   8   5
  subtype5  61  35  19   9
D10V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       66       82      176       85       61
  N1       54       74      136       30       35
  N2       14       19       49        8       19
  N3       21        2       31        5        9
[1] 4 5
[1] 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
  subtype1        0 115   1  39
  subtype2        1 159   0  22
  subtype3        1 352  10  38
  subtype4        0 113   1  15
  subtype5        0 104   4  18
D10V6, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4 subtype5
  CM0 (I+)        0        1        1        0        0
  M0            115      159      352      113      104
  M1              1        0       10        1        4
  MX             39       22       38       15       18
[1] 4 5
[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
  subtype1 155   0
  subtype2 178   4
  subtype3 395   6
  subtype4 129   0
  subtype5 125   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  155    0
  subtype2  178    4
  subtype3  395    6
  subtype4  129    0
  subtype5  125    1
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE      155      178      395      129      125
  MALE          0        4        6        0        1
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  subtype1                          0                            58
  subtype2                          0                           135
  subtype3                          0                           318
  subtype4                          1                           114
  subtype5                          0                           110
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                             91                   0
  subtype2                             20                   0
  subtype3                             45                   1
  subtype4                              1                   4
  subtype5                              8                   0
          vv
clus       MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                                3                  1              2
  subtype2                                9                  6             12
  subtype3                               14                  7             16
  subtype4                                1                  0              7
  subtype5                                1                  0              7
D10V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  INFILTRATING CARCINOMA NOS              0        0        0        1        0
  INFILTRATING DUCTAL CARCINOMA          58      135      318      114      110
  INFILTRATING LOBULAR CARCINOMA         91       20       45        1        8
  MEDULLARY CARCINOMA                     0        0        1        4        0
  MIXED HISTOLOGY (PLEASE SPECIFY)        3        9       14        1        1
  MUCINOUS CARCINOMA                      1        6        7        0        0
  OTHER  SPECIFY                          2       12       16        7        7
[1] 7 5
[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
  subtype1  22 133
  subtype2  57 125
  subtype3 122 279
  subtype4  39  90
  subtype5  38  88
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22  133
  subtype2   57  125
  subtype3  122  279
  subtype4   39   90
  subtype5   38   88
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        22       57      122       39       38
  YES      133      125      279       90       88
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     6                        19
  subtype2                                0     7                        17
  subtype3                                1    29                        37
  subtype4                                0     5                        44
  subtype5                                0    10                        21
          vv
clus       WHITE
  subtype1   129
  subtype2   132
  subtype3   291
  subtype4    74
  subtype5    83
D10V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1        0        0
  ASIAN                                   6        7       29        5       10
  BLACK OR AFRICAN AMERICAN              19       17       37       44       21
  WHITE                                 129      132      291       74       83
[1] 4 5
[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
  subtype1   6 139
  subtype2  12 127
  subtype3  11 315
  subtype4   3 108
  subtype5   4 106
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6  139
  subtype2   12  127
  subtype3   11  315
  subtype4    3  108
  subtype5    4  106
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            6       12       11        3        4
  NOT HISPANIC OR LATINO      139      127      315      108      106
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = MIRSEQ_MATURE_CNMF
D11V1, survival
          sevent
clus2        0   1
  subtype1 210  34
  subtype2 210  14
  subtype3 163  28
subtype1 subtype2 subtype3 
     244      224      191 
subtype1 subtype2 subtype3 
      34       14       28 
$subtype1
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SI TCGA-A1-A0SN 
        8.52        14.37        48.10        14.27        20.88        39.32 
TCGA-A1-A0SQ TCGA-A2-A04W TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0D3 TCGA-A2-A0ES 
       18.21        64.04        75.55        63.45        28.77        37.05 
TCGA-A2-A0EW TCGA-A2-A0T3 TCGA-A2-A1FW TCGA-A2-A1FZ TCGA-A2-A1G4 TCGA-A2-A25B 
       29.75        18.71        17.36        22.45        19.56        16.31 
TCGA-A2-A25C TCGA-A2-A25E TCGA-A7-A0DB TCGA-A7-A13F TCGA-A7-A13G TCGA-AC-A23C 
       17.19        91.92        33.11        12.72        23.61         0.95 
TCGA-AC-A23E TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2FG TCGA-AO-A03V TCGA-AO-A12A 
        2.37         2.66         1.48        36.99        29.13        90.58 
TCGA-AO-A12B TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KT TCGA-AQ-A1H2 
       77.56        28.37        14.73        82.62        17.79        15.62 
TCGA-AR-A0TY TCGA-AR-A1AK TCGA-AR-A1AN TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AT 
       55.86        51.25        43.73        39.98        40.83        41.82 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       46.32        42.58        35.24        73.02        65.46        68.19 
TCGA-AR-A24R TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 
       57.40        54.18        50.96        48.16        51.75        56.15 
TCGA-AR-A252 TCGA-AR-A255 TCGA-B6-A0RH TCGA-B6-A0WS TCGA-B6-A0X0 TCGA-B6-A1KI 
       40.64        34.82       189.01        97.48       129.70        73.51 
TCGA-B6-A1KN TCGA-BH-A0AU TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B5 TCGA-BH-A0B7 
      139.17        24.53        28.50        46.95        48.36        56.98 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0C7 TCGA-BH-A0DE 
       48.69        27.19        53.69        53.95        42.90        31.17 
TCGA-BH-A0DG TCGA-BH-A0DT TCGA-BH-A0DX TCGA-BH-A0EA TCGA-BH-A0EI TCGA-BH-A0H3 
       23.44        38.47        47.41        32.65        24.43        37.78 
TCGA-BH-A0H5 TCGA-BH-A0HA TCGA-BH-A0HN TCGA-BH-A0W7 TCGA-BH-A18F TCGA-BH-A18I 
       35.51        52.96        16.96        44.81         8.81         7.23 
TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18S TCGA-BH-A1EN 
       20.12        90.84        37.74        30.28        66.05        69.93 
TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EV TCGA-BH-A1EY TCGA-BH-A1F2 
       91.99       113.82        82.85        12.00        17.69        31.53 
TCGA-BH-A1F5 TCGA-BH-A1F8 TCGA-BH-A1FE TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM 
       89.16        24.66        74.73        63.35        55.00        45.63 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A204 TCGA-BH-A208 
      144.59        72.07         6.90         0.72        83.31        57.83 
TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12Q TCGA-C8-A12X TCGA-C8-A132 
       11.77        11.77        12.66         0.07        12.66         1.45 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HI TCGA-C8-A1HK 
        0.62         3.85         3.75        12.33        11.34        12.03 
TCGA-C8-A1HL TCGA-C8-A1HN TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A146 
       10.42         3.25        11.90        13.25        20.58        21.14 
TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF 
       14.17        17.49        15.78        18.15        18.90        12.03 
TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ 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-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1XA TCGA-D8-A1XB 
       13.32        18.58        17.79        16.73        27.58        18.15 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XO TCGA-D8-A1XR 
        2.66        17.16        15.22        14.73         7.96        15.85 
TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 
       16.31        12.99        15.16        16.54        15.32        15.52 
TCGA-D8-A1Y1 TCGA-D8-A27V TCGA-E2-A10A TCGA-E2-A14O TCGA-E2-A14S TCGA-E2-A14T 
        3.81        12.53        40.41        44.68        33.17        33.30 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 
       34.26        32.02        27.12        23.24        19.43        21.04 
TCGA-E2-A156 TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I 
       23.87        22.82        17.29        18.21        12.92        17.42 
TCGA-E2-A15J TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15R TCGA-E2-A15S 
       19.40        20.58         7.73        13.02        17.06        14.07 
TCGA-E2-A15T TCGA-E2-A1B4 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF 
       14.99        29.95        16.47        17.10        38.30        37.41 
TCGA-E2-A1IG TCGA-E2-A1IJ TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       32.78        28.44         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-A1LS 
       54.18        39.62        19.66        24.59        40.47        15.45 
TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG 
       36.82        13.48        13.12        35.77        20.05        21.57 
TCGA-E9-A1NI TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA 
        9.86         6.12         1.38         2.76        21.21        32.09 
TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A227 
       40.24        34.65         6.58        21.27        35.64         0.79 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A247 
       12.53        13.32        22.75        12.89        24.10        27.22 
TCGA-E9-A249 TCGA-E9-A24A TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1J1 
        0.95        12.56        12.20        39.72         8.48        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-A1P0 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1PD 
       29.85        40.41        41.13        23.11        18.48        13.94 
TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A2FS TCGA-EW-A2FW 
       10.52        14.43        52.73        22.09 

$subtype2
TCGA-A2-A04N TCGA-A2-A0CK TCGA-A2-A0CO TCGA-A2-A0CR TCGA-A2-A0EP TCGA-A2-A1FV 
      104.81       125.59       112.08       107.93       107.61        23.47 
TCGA-A2-A1FX TCGA-A2-A1G0 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25D 
       36.79        20.25        16.47        52.47       107.70        18.15 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XW TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 
       20.88        39.65        49.48         7.30         8.81         8.91 
TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26H TCGA-A7-A26J 
        6.74         3.42        29.56        31.36        23.80        20.61 
TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J1 TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA 
       11.34        10.59        11.28        14.70        11.97        14.93 
TCGA-A7-A4SB TCGA-A7-A4SC TCGA-A7-A56D TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VX 
       13.74        14.66        14.73        10.72        11.05        10.42 
TCGA-AC-A23G TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FK TCGA-AC-A2FM 
       10.85        38.20        40.57        55.43        38.79        26.04 
TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
       50.70         0.92         0.99         0.69        14.83         9.40 
TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62Y 
        1.12         1.68         1.55         1.32         1.55         1.81 
TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AQ-A7U7 
        1.18         0.43         1.74        13.22        21.86         9.99 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AX TCGA-AR-A24K TCGA-AR-A24O TCGA-AR-A24P 
       48.82        62.56        36.26        50.89        65.69         0.85 
TCGA-AR-A24T TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM 
       53.26       128.65        20.25        42.87         7.36        40.04 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP 
       17.10        20.81        16.96        54.74        16.04        20.45 
TCGA-B6-A0IH TCGA-B6-A0RQ TCGA-B6-A1KC TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A408 
      112.37       140.48        43.59       170.17        85.35        49.94 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0B6 TCGA-BH-A0BO TCGA-BH-A0BZ TCGA-BH-A0C1 
       82.88        55.00        56.94        35.67        49.05        44.02 
TCGA-BH-A0C3 TCGA-BH-A0DI TCGA-BH-A0DO TCGA-BH-A0DV TCGA-BH-A0E2 TCGA-BH-A0E9 
       48.13        22.13        17.26        45.17        14.30        46.19 
TCGA-BH-A0HL TCGA-BH-A18M TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1FB 
        2.37        72.56        42.28        55.69        49.58       120.62 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T 
      122.89        36.92        10.65         6.44        20.12         0.99 
TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A26W TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 
      109.28         8.94         0.23         0.43         8.28         9.67 
TCGA-C8-A274 TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A145 TCGA-D8-A1JB TCGA-D8-A1JU 
        0.03         0.03         0.23        13.48        18.71        14.70 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XM TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27G 
       25.74        23.90        17.69        14.24        17.42        13.45 
TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R 
       14.43         9.44        16.41         4.80         0.76        10.09 
TCGA-D8-A27T TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A14Q 
       13.08        12.26        14.50        18.51         7.33        38.24 
TCGA-E2-A14U TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15P TCGA-E2-A1B1 TCGA-E2-A1B5 
       43.33        20.71        21.63        19.56        53.03        32.35 
TCGA-E2-A1IH TCGA-E2-A1IK TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z 
       33.73        22.65        16.93         5.52        15.72         7.20 
TCGA-E2-A570 TCGA-E2-A572 TCGA-E9-A1N4 TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R3 
       18.05        27.32        19.20        11.90        14.30         2.10 
TCGA-E9-A1RD TCGA-E9-A226 TCGA-E9-A245 TCGA-E9-A295 TCGA-E9-A2JT TCGA-E9-A3Q9 
        0.66        34.13         0.85         0.72         0.76        18.41 
TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE 
       15.72         0.23         0.39         0.26         0.23        15.39 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1PA TCGA-EW-A1PG TCGA-EW-A2FV TCGA-EW-A3E8 
       39.78        52.96        18.90        34.55        25.91        21.27 
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-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-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV 
      110.50        38.20        32.28        53.95        57.63        13.55 
TCGA-GM-A5PX TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 
       18.12        11.57         8.28         6.67         4.60         0.66 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN 
        2.99         3.58         6.90         5.56         4.70         3.65 
TCGA-LL-A6FQ TCGA-LL-A73Z TCGA-LL-A740 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 
        2.63         4.50         4.50        15.91         2.79         2.10 
TCGA-OL-A5D6 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY 
       12.66        44.61        27.65        24.10        16.87        14.10 
TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O 
       14.76        54.51        33.90        31.07        18.21         7.23 
TCGA-S3-A6ZG TCGA-W8-A86G 
        6.81         5.29 

$subtype3
TCGA-A2-A04U TCGA-A2-A0CL TCGA-A2-A0CW TCGA-A2-A1G1 TCGA-A2-A25F TCGA-A2-A3XS 
       22.06        64.57        64.04        19.20        10.59        33.93 
TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ 
       83.01        29.98        14.07        38.40        34.98        31.99 
TCGA-A2-A3Y0 TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E 
       38.37         9.01        12.00        35.67        31.73        10.72 
TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3J0 TCGA-A7-A3RF 
       24.26        23.74        21.73        22.32        10.29        13.41 
TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A6VV TCGA-A7-A6VW 
       14.50        21.17        17.92        12.10        10.29         9.37 
TCGA-A7-A6VY TCGA-AC-A2BK TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A3W5 TCGA-AC-A62V 
        8.75        38.53         1.02         2.27         1.81         0.07 
TCGA-AC-A62X TCGA-AC-A6IW TCGA-AN-A0AT TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A1KQ 
        1.12         0.69         0.33        64.04        48.36        61.87 
TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AR-A0TS TCGA-AR-A1AH 
       70.39         0.53         5.65         2.56        37.41        75.55 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AO TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AY 
       61.84        52.77        43.56        43.07        17.23        20.22 
TCGA-AR-A24H TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24U TCGA-AR-A251 TCGA-AR-A254 
      109.58        66.05        62.07        53.36        45.17        39.85 
TCGA-AR-A256 TCGA-AR-A2LR TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A1KF TCGA-B6-A402 
       93.83        20.38        10.59        77.62       101.52        54.28 
TCGA-BH-A0AV TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BT TCGA-BH-A0BW 
       38.79        25.71        24.85        44.05        45.57        11.67 
TCGA-BH-A0DD TCGA-BH-A0DL TCGA-BH-A18G TCGA-BH-A18L TCGA-BH-A18Q TCGA-BH-A18R 
       45.83        48.23         2.01        26.66        55.63        37.55 
TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1F0 TCGA-BH-A1F6 TCGA-BH-A1FC 
        7.36        51.39        51.16        25.81        97.48       114.15 
TCGA-BH-A1FN TCGA-BH-A203 TCGA-BH-A209 TCGA-C8-A12L TCGA-C8-A12P TCGA-C8-A12U 
       72.07        38.60       130.16        11.93        11.77        12.66 
TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A1HF 
       12.66        12.66         3.12         1.78         0.69        10.92 
TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HM TCGA-C8-A26V TCGA-C8-A26X TCGA-C8-A275 
       11.34         0.16         2.30         0.30         0.36         0.03 
TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A143 
        0.03        12.20         0.99        20.88        13.97        14.17 
TCGA-D8-A147 TCGA-D8-A1JA TCGA-D8-A1JG TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1XJ 
       19.20        16.50        12.03        20.12        20.09        21.83 
TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XQ TCGA-D8-A1XT TCGA-D8-A1XW TCGA-D8-A1Y3 
       14.50        19.92        16.41         6.35        12.66        14.14 
TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27M TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14R 
       16.04        13.05        13.48        47.15        40.96        38.60 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A158 TCGA-E2-A159 
       31.96        28.60        17.03        25.41        14.79        25.05 
TCGA-E2-A15A TCGA-E2-A15K TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B6 TCGA-E2-A1II 
       23.34         9.04        60.53        53.62        28.50        33.70 
TCGA-E2-A1L7 TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK 
       27.42        28.90        18.87       106.75       102.61         8.75 
TCGA-E2-A1LL TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N8 TCGA-E9-A1NA TCGA-E9-A1ND 
       43.04        22.26        19.89        12.00        36.56        12.59 
TCGA-E9-A1R2 TCGA-E9-A1RB TCGA-E9-A1RH TCGA-E9-A22A TCGA-E9-A22G TCGA-E9-A243 
        0.62        20.81        34.59        39.09        23.51        17.06 
TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A2JS TCGA-E9-A3QA TCGA-EW-A1IZ TCGA-EW-A1OW 
        0.69         1.94        17.75         0.62        18.21        22.82 
TCGA-EW-A1P4 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PH 
       29.82        30.08         7.86        19.99         6.15        19.96 
TCGA-EW-A2FR TCGA-EW-A3U0 TCGA-GI-A2C9 TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH 
       55.00        17.49       109.87        43.04        42.71        42.28 
TCGA-GM-A2DO TCGA-GM-A3XL TCGA-JL-A3YW TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FR 
       53.36        69.30        11.84         3.19         3.25         3.88 
TCGA-LL-A73Y TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-OL-A5D7 TCGA-OL-A5D8 
        4.14         5.59         3.22         6.21        46.55         7.53 
TCGA-OL-A5RW TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66I TCGA-OL-A66P 
       26.20        10.29         9.80        23.70         4.44 

subtype1 subtype2 subtype3 
    0.07     0.03     0.03 
subtype1 subtype2 subtype3 
  189.01   194.27   130.16 
subtype1 subtype2 subtype3 
   21.83    17.18    20.22 
[1] "0.1 - 189.0 (21.8)" "0.0 - 194.3 (17.2)" "0.0 - 130.2 (20.2)"
D11V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1      34       23        1        2        81        59         0
  subtype2      19       19        4        7        54        55         2
  subtype3      16        9        0        0        91        39         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  subtype1         34          6          6        2       2
  subtype2         31          4         30        2       0
  subtype3         24          3          7        1       3
D11V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          34       19       16
  STAGE IA         23       19        9
  STAGE IB          1        4        0
  STAGE II          2        7        0
  STAGE IIA        81       54       91
  STAGE IIB        59       55       39
  STAGE III         0        2        0
  STAGE IIIA       34       31       24
  STAGE IIIB        6        4        3
  STAGE IIIC        6       30        7
  STAGE IV          2        2        1
  STAGE X           2        0        3
[1] 12  3
[1] 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
  subtype1  94 129  18   9
  subtype2  60 120  43   4
  subtype3  42 130  16   6
D11V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       94       60       42
  T2      129      120      130
  T3       18       43       16
  T4        9        4        6
[1] 4 3
[1] 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
  subtype1 117  96  26   7
  subtype2  93  79  21  31
  subtype3 109  56  21   7
D11V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0      117       93      109
  N1       96       79       56
  N2       26       21       21
  N3        7       31        7
[1] 4 3
[1] 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
  subtype1        2 218   2  28
  subtype2        0 165   2  60
  subtype3        0 160   1  33
D11V6, multiclass
          clus
vv         subtype1 subtype2 subtype3
  CM0 (I+)        2        0        0
  M0            218      165      160
  M1              2        2        1
  MX             28       60       33
[1] 4 3
[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
  subtype1 246   4
  subtype2 226   1
  subtype3 191   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  246    4
  subtype2  226    1
  subtype3  191    3
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      246      226      191
  MALE          4        1        3
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  subtype1                          0                           198
  subtype2                          0                            98
  subtype3                          1                           168
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                             20                   0
  subtype2                            112                   0
  subtype3                              7                   5
          vv
clus       MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                               13                  5             14
  subtype2                                5                  7              5
  subtype3                                1                  2             10
D11V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  INFILTRATING CARCINOMA NOS              0        0        1
  INFILTRATING DUCTAL CARCINOMA         198       98      168
  INFILTRATING LOBULAR CARCINOMA         20      112        7
  MEDULLARY CARCINOMA                     0        0        5
  MIXED HISTOLOGY (PLEASE SPECIFY)       13        5        1
  MUCINOUS CARCINOMA                      5        7        2
  OTHER  SPECIFY                         14        5       10
[1] 7 3
[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
  subtype1  81 169
  subtype2  36 191
  subtype3  57 137
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   81  169
  subtype2   36  191
  subtype3   57  137
     clus
vv    subtype1 subtype2 subtype3
  NO        81       36       57
  YES      169      191      137
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1    20                        14   214
  subtype2    11                        37   176
  subtype3    21                        61   111
D11V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                           20       11       21
  BLACK OR AFRICAN AMERICAN       14       37       61
  WHITE                          214      176      111
[1] 3 3
[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
  subtype1  16 221
  subtype2  12 202
  subtype3   6 180
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16  221
  subtype2   12  202
  subtype3    6  180
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           16       12        6
  NOT HISPANIC OR LATINO      221      202      180
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D12V1, survival
          sevent
clus2        0   1
  subtype1 101  16
  subtype2  54  12
  subtype3 160  23
  subtype4 105  12
  subtype5 106   4
  subtype6  57   9
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
     117       66      183      117      110       66 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      16       12       23       12        4        9 
$subtype1
TCGA-A1-A0SB TCGA-A2-A04U TCGA-A2-A1G1 TCGA-A2-A25F TCGA-A2-A3XS TCGA-A2-A3XT 
        8.52        22.06        19.20        10.59        33.93        83.01 
TCGA-A2-A3XU TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RX TCGA-A7-A0DA 
       29.98        38.40        34.98        38.37         9.01        35.67 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A4SE TCGA-A7-A5ZV 
       31.73        10.72        24.26        23.74        21.17        12.10 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY TCGA-AC-A2BK TCGA-AC-A2QH TCGA-AC-A2QJ 
       10.29         9.37         8.75        38.53         1.02         2.27 
TCGA-AC-A62X TCGA-AC-A6IW TCGA-AN-A0AT TCGA-AO-A12F TCGA-AO-A1KR TCGA-AQ-A54N 
        1.12         0.69         0.33        48.36        70.39         2.56 
TCGA-AR-A0TS TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AO TCGA-AR-A1AQ 
       37.41        75.55        61.84        52.77        43.56        43.07 
TCGA-AR-A1AR TCGA-AR-A1AY TCGA-AR-A24L TCGA-AR-A24Q TCGA-AR-A251 TCGA-AR-A256 
       17.23        20.22        73.02        66.05        45.17        93.83 
TCGA-AR-A2LR TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A1KF TCGA-B6-A402 TCGA-BH-A0AV 
       20.38        10.59        77.62       101.52        54.28        38.79 
TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BT TCGA-BH-A0BW TCGA-BH-A0DL TCGA-BH-A18G 
       24.85        44.05        45.57        11.67        48.23         2.01 
TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1F0 TCGA-BH-A1F6 TCGA-BH-A1FC 
       55.63         7.36        51.16        25.81        97.48       114.15 
TCGA-C8-A12V TCGA-C8-A134 TCGA-C8-A1HJ TCGA-C8-A27B TCGA-D8-A142 TCGA-D8-A147 
       12.66         0.69         0.16         0.99        13.97        19.20 
TCGA-D8-A1JL TCGA-D8-A1X5 TCGA-D8-A1XK TCGA-D8-A1XQ TCGA-D8-A1XW TCGA-D8-A27F 
       20.09        18.58        14.50        16.41        12.66        16.04 
TCGA-D8-A27H TCGA-D8-A27M TCGA-E2-A14N TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Y 
       13.05        13.48        47.15        38.60        31.96        28.60 
TCGA-E2-A150 TCGA-E2-A158 TCGA-E2-A1AZ TCGA-E2-A1B6 TCGA-E2-A1II TCGA-E2-A1LG 
       25.41        14.79        60.53        28.50        33.70        18.87 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A573 TCGA-E2-A574 
      106.75       102.61         8.75        43.04        22.26        19.89 
TCGA-E9-A1N8 TCGA-E9-A1ND TCGA-E9-A22G TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A3QA 
       12.00        12.59        23.51        17.06         0.69         0.62 
TCGA-E9-A5FL TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PB 
        0.26        22.82        29.82        30.08         7.86        19.99 
TCGA-EW-A1PH TCGA-EW-A3U0 TCGA-GI-A2C9 TCGA-GM-A2DF TCGA-GM-A3XL TCGA-LL-A441 
       19.96        17.49       109.87        42.71        69.30         2.99 
TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A8F5 TCGA-OL-A5D7 TCGA-OL-A5RW 
        3.25         3.88         4.14         6.21        46.55        26.20 
TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66I 
       14.10         9.80        23.70 

$subtype2
TCGA-A1-A0SD TCGA-A2-A0CV TCGA-A2-A0ES TCGA-A2-A0EW TCGA-A2-A1FZ TCGA-A2-A1G6 
       14.37        63.45        37.05        29.75        22.45        16.47 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A6IV TCGA-AO-A1KO TCGA-AQ-A1H3 TCGA-AR-A0TY 
       55.43        36.99         1.18        14.73        13.22        55.86 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A24P TCGA-AR-A24T TCGA-AR-A24W 
       51.25        48.82        43.73         0.85        53.26        50.96 
TCGA-B6-A0IH TCGA-B6-A1KI TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BZ TCGA-BH-A0DE 
      112.37        73.51        35.67        27.19        49.05        31.17 
TCGA-BH-A0DI TCGA-BH-A0DO TCGA-BH-A0DT TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0H3 
       22.13        17.26        38.47        46.19        32.65        37.78 
TCGA-BH-A18F TCGA-BH-A18M TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1FB 
        8.81        72.56        91.99        82.85        42.28       120.62 
TCGA-BH-A1FE TCGA-BH-A1FH TCGA-BH-A1FL TCGA-BH-A201 TCGA-D8-A145 TCGA-D8-A146 
       74.73        36.92        55.00         6.90        13.48        21.14 
TCGA-D8-A1JB TCGA-D8-A1JH TCGA-D8-A1JU TCGA-D8-A27P TCGA-E2-A14Q TCGA-E2-A15P 
       18.71        14.01        14.70         0.76        38.24        19.56 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1IF TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IL 
       53.03        29.95        37.41        33.73        28.44         3.88 
TCGA-E2-A1L6 TCGA-E9-A1NE TCGA-E9-A1QZ TCGA-E9-A1RI TCGA-EW-A1IX TCGA-EW-A1J2 
       54.18        35.77        11.90        35.64        39.72        13.25 
TCGA-EW-A1P1 TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-OL-A66J 
       39.78        13.94        10.52        14.43        34.55        54.51 

$subtype3
TCGA-A1-A0SF TCGA-A1-A0SI TCGA-A1-A0SN TCGA-A2-A04W TCGA-A2-A0CS TCGA-A2-A0CW 
       48.10        20.88        39.32        64.04        75.55        64.04 
TCGA-A2-A0D3 TCGA-A2-A0T3 TCGA-A2-A1FW TCGA-A2-A25B TCGA-A2-A3XZ TCGA-A7-A13F 
       28.77        18.71        17.36        16.31        31.99        12.72 
TCGA-A7-A13G TCGA-A7-A26I TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23H TCGA-AC-A2B8 
       23.61        21.73         0.95         2.37         2.66         1.48 
TCGA-AO-A03V TCGA-AO-A12A TCGA-AO-A1KP TCGA-AO-A1KT TCGA-AQ-A1H2 TCGA-AR-A1AP 
       29.13        90.58        82.62        17.79        15.62        39.98 
TCGA-AR-A1AS TCGA-AR-A1AT TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A24H 
       40.83        41.82        46.32        42.58        35.24       109.58 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24R TCGA-AR-A24V TCGA-AR-A24X 
       65.46        68.19        65.69        57.40        54.18        48.16 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A255 TCGA-B6-A0RH TCGA-B6-A0WS 
       51.75        56.15        40.64        34.82       189.01        97.48 
TCGA-B6-A0X0 TCGA-B6-A1KN TCGA-B6-A408 TCGA-B6-A40B TCGA-BH-A0AU TCGA-BH-A0AZ 
      129.70       139.17        49.94        82.88        24.53        28.50 
TCGA-BH-A0B0 TCGA-BH-A0B5 TCGA-BH-A0BF TCGA-BH-A0BP TCGA-BH-A0BR TCGA-BH-A0BS 
       46.95        48.36        25.71        48.69        53.69        53.95 
TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0DG TCGA-BH-A0DX TCGA-BH-A0E2 TCGA-BH-A0EI 
       44.02        45.83        23.44        47.41        14.30        24.43 
TCGA-BH-A0H5 TCGA-BH-A0HA TCGA-BH-A0HN TCGA-BH-A0W7 TCGA-BH-A18I TCGA-BH-A18J 
       35.51        52.96        16.96        44.81         7.23        20.12 
TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A1EN 
       90.84        26.66        30.28        37.55        66.05        69.93 
TCGA-BH-A1ES TCGA-BH-A1EV TCGA-BH-A1EY TCGA-BH-A1F2 TCGA-BH-A1F8 TCGA-BH-A1FJ 
      113.82        12.00        17.69        31.53        24.66        63.35 
TCGA-BH-A1FM TCGA-BH-A208 TCGA-BH-A209 TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P 
       45.63        57.83       130.16        11.77        12.66        11.77 
TCGA-C8-A12U TCGA-C8-A132 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF 
       12.66         1.45         3.85         3.75        12.33        10.92 
TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A27A 
       11.34        11.34        12.03         2.30         3.25        12.20 
TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA 
       11.90        13.25        20.58        14.17        17.49        16.50 
TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JJ TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS 
       18.15        18.90        20.09        20.38        21.01        12.20 
TCGA-D8-A1X7 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG 
       16.73        27.58        18.15        17.16        15.22        14.73 
TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1Y0 
        7.96        15.85        16.31        12.99        16.54        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27V TCGA-E2-A14O TCGA-E2-A14T TCGA-E2-A14V 
        3.81        14.14        12.53        44.68        33.30        34.26 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A15A TCGA-E2-A15C 
       27.12        23.24        19.43        21.04        23.34        22.82 
TCGA-E2-A15D TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       17.29        18.21        12.92        17.42        19.40         9.04 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A1B5 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IG 
       20.58         7.73        32.35        16.47        17.10        32.78 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 
       22.19        20.98        11.08        27.42        39.62        19.66 
TCGA-E2-A570 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NF TCGA-E9-A1NG 
       18.05        13.48        13.12        36.56        20.05        21.57 
TCGA-E9-A1NI TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RC 
        9.86         6.12         1.38         2.76        32.09        40.24 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A229 TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A247 
        6.58        21.27        13.32        12.89        24.10        27.22 
TCGA-E9-A249 TCGA-EW-A1IW TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J3 TCGA-EW-A1J5 
        0.95        12.20         8.48        18.21        16.57        15.68 
TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OZ TCGA-EW-A1P3 TCGA-EW-A1P6 TCGA-EW-A1PC 
       28.77        25.94        40.41        52.96        18.48         6.15 
TCGA-LL-A5YN TCGA-OL-A5D8 TCGA-OL-A5RZ 
        3.65         7.53        10.29 

$subtype4
TCGA-A1-A0SG TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1G0 
       14.27        18.21       104.81        23.47        36.79        20.25 
TCGA-A2-A1G4 TCGA-A2-A25C TCGA-A2-A25E TCGA-A2-A3XW TCGA-A2-A4S0 TCGA-A7-A0DB 
       19.56        17.19        91.92        49.48         8.91        33.11 
TCGA-A7-A26E TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ 
       31.36        23.80        20.61        22.32        11.34        10.59 
TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A4SF TCGA-A7-A6VX TCGA-AC-A2BM TCGA-AC-A2FM 
       10.29        13.41        17.92        10.42        38.20        26.04 
TCGA-AC-A3YJ TCGA-AC-A62Y TCGA-AO-A12B TCGA-AO-A12H TCGA-AQ-A54O TCGA-AR-A24K 
        1.32         1.81        77.56        28.37        21.86        50.89 
TCGA-AR-A2LK TCGA-AR-A2LL TCGA-B6-A1KC TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0HL 
       42.87         7.36        43.59        48.13        42.90         2.37 
TCGA-BH-A18N TCGA-BH-A1EW TCGA-BH-A1F5 TCGA-BH-A1FG TCGA-BH-A1FR TCGA-BH-A204 
       37.74        55.69        89.16       122.89       144.59        83.31 
TCGA-C8-A12M TCGA-C8-A12X TCGA-C8-A1HL TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Z 
       11.77        12.66        10.42         0.30         0.23         8.28 
TCGA-C8-A273 TCGA-C8-A275 TCGA-D8-A1JI TCGA-D8-A1JT TCGA-D8-A1X6 TCGA-D8-A1X8 
        9.67         0.03        18.97        13.32        17.79        25.74 
TCGA-D8-A1X9 TCGA-D8-A1XC TCGA-D8-A1XJ TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XV 
       23.90         2.66        21.83        19.92        17.69        15.16 
TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27R TCGA-D8-A27W TCGA-E2-A10A TCGA-E2-A14S 
       14.24        17.42        10.09        12.26        40.41        33.17 
TCGA-E2-A14Z TCGA-E2-A156 TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15O TCGA-E2-A15R 
       17.03        23.87        20.71        21.63        13.02        17.06 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1IE TCGA-E2-A1IK TCGA-E2-A2P6 TCGA-E2-A56Z 
       14.07        14.99        38.30        22.65         5.52         7.20 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R7 TCGA-E9-A1RB 
       19.20        36.82         0.62         2.10        21.21        20.81 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A22A 
        0.66        34.65        34.13         0.79        12.53        39.09 
TCGA-E9-A22B TCGA-E9-A245 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A3Q9 
       22.75         0.85        12.56         0.72        17.75        18.41 
TCGA-E9-A54Y TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1J1 TCGA-EW-A1OX TCGA-EW-A1P0 
        0.23         0.23        15.39        18.90        29.95        41.13 
TCGA-EW-A1P5 TCGA-EW-A1PA TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-GM-A2DC 
       23.11        18.90        52.73        25.91        22.09        53.52 
TCGA-GM-A2DM TCGA-GM-A3NW TCGA-LL-A442 TCGA-LL-A5YM TCGA-LL-A6FQ TCGA-LL-A7SZ 
       76.64       110.50         3.58         4.70         2.63         5.59 
TCGA-LL-A7T0 TCGA-OL-A66H TCGA-OL-A66O 
        3.22        14.76         7.23 

$subtype5
TCGA-A2-A0CK TCGA-A2-A0CO TCGA-A2-A0CR TCGA-A2-A0EP TCGA-A2-A259 TCGA-A2-A25A 
      125.59       112.08       107.93       107.61        52.47       107.70 
TCGA-A2-A25D TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A4RY TCGA-A2-A4S2 TCGA-A7-A13H 
       18.15        20.88        39.65         8.81         6.74        29.56 
TCGA-A7-A3J1 TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SC 
       11.28        14.70        11.97        14.93        13.74        14.66 
TCGA-A7-A56D TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-AC-A23G TCGA-AC-A2FB TCGA-AC-A2FK 
       14.73        10.72        11.05        10.85        40.57        38.79 
TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
       50.70         0.92         0.99         0.69        14.83         9.40 
TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A5XS TCGA-AC-A6IX TCGA-AC-A8OP 
        1.12         1.68         1.55         1.55         0.43         1.74 
TCGA-AQ-A7U7 TCGA-AR-A1AM TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LM TCGA-AR-A2LN 
        9.99        62.56       128.65        20.25        40.04        17.10 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0RQ 
       20.81        16.96        54.74        16.04        20.45       140.48 
TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A40C TCGA-BH-A0B6 TCGA-BH-A0DV TCGA-BH-A28O 
      170.17        85.35        55.00        56.94        45.17        10.65 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A274 
        6.44        20.12         0.99       109.28         8.94         0.03 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A27G TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
        0.03         0.23        13.45        14.43         9.44        16.41 
TCGA-D8-A27T TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A14U TCGA-E2-A3DX 
       13.08        14.50        18.51         7.33        43.33        15.72 
TCGA-E2-A572 TCGA-E9-A1R0 TCGA-E9-A2JT TCGA-E9-A3X8 TCGA-E9-A5FK TCGA-EW-A3E8 
       27.32        14.30         0.76        15.72         0.39        21.27 
TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DI TCGA-GM-A2DK 
       10.16        10.59         7.40        59.57        61.91        62.33 
TCGA-GM-A2DL TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN 
       90.84        77.33        53.36        38.20        32.28        53.95 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U 
       57.63        13.55        18.12        11.57         8.28         6.67 
TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A50Y TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 
        4.60         0.66         6.90        15.91         2.79         2.10 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A66K TCGA-OL-A66L 
       44.61        27.65        24.10        16.87        33.90        31.07 
TCGA-S3-A6ZG TCGA-W8-A86G 
        6.81         5.29 

$subtype6
TCGA-A2-A0CL TCGA-A2-A3XV TCGA-A2-A4RW TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A4SD 
       64.57        14.07         7.30        12.00         3.42        14.50 
TCGA-AC-A3W5 TCGA-AC-A62V TCGA-AO-A12D TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AQ-A0Y5 
        1.81         0.07        64.04        61.87         0.53         5.65 
TCGA-AR-A1AX TCGA-AR-A24S TCGA-AR-A24U TCGA-AR-A254 TCGA-BH-A0B7 TCGA-BH-A18U 
       36.26        62.07        53.36        39.85        56.98        51.39 
TCGA-BH-A1EX TCGA-BH-A1FN TCGA-BH-A1FU TCGA-BH-A202 TCGA-BH-A203 TCGA-C8-A12L 
       49.58        72.07        72.07         0.72        38.60        11.93 
TCGA-C8-A12Q TCGA-C8-A12W TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A135 TCGA-C8-A26X 
        0.07        12.66         3.12         1.78         0.62         0.36 
TCGA-C8-A26Y TCGA-C8-A278 TCGA-D8-A13Z TCGA-D8-A143 TCGA-D8-A1JC TCGA-D8-A1JF 
        0.43         0.03        20.88        14.17        15.78        12.03 
TCGA-D8-A1JG TCGA-D8-A1JK TCGA-D8-A1XT TCGA-D8-A1XZ TCGA-D8-A27N TCGA-E2-A14P 
       12.03        20.12         6.35        15.32         4.80        40.96 
TCGA-E2-A14W TCGA-E2-A159 TCGA-E2-A1B0 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       32.02        25.05        53.62        24.59        40.47        28.90 
TCGA-E2-A1LS TCGA-E2-A2P5 TCGA-E9-A1RH TCGA-E9-A248 TCGA-EW-A1OY TCGA-EW-A2FR 
       15.45        16.93        34.59         1.94        29.85        55.00 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DH TCGA-JL-A3YW TCGA-LL-A5YL 
      194.27        53.13        43.04        42.28        11.84         5.56 
TCGA-LL-A5YO TCGA-LL-A73Z TCGA-LL-A740 TCGA-OL-A5D6 TCGA-OL-A66N TCGA-OL-A66P 
        3.19         4.50         4.50        12.66        18.21         4.44 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.16     0.76     0.95     0.03     0.03     0.03 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  114.15   120.62   189.01   144.59   170.17   194.27 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  22.060   35.655   20.880   18.900   15.720   15.385 
[1] "0.2 - 114.2 (22.1)" "0.8 - 120.6 (35.7)" "0.9 - 189.0 (20.9)"
[4] "0.0 - 144.6 (18.9)" "0.0 - 170.2 (15.7)" "0.0 - 194.3 (15.4)"
D12V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1      11        6        1        0        58        27         0
  subtype2      12        7        0        1        19        15         0
  subtype3      25       20        2        0        58        40         0
  subtype4       8        5        1        1        44        36         1
  subtype5       9        9        1        6        23        26         1
  subtype6       4        4        0        1        24         9         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  subtype1          9          1          3        0       1
  subtype2          7          0          4        1       0
  subtype3         28          4          6        2       3
  subtype4         17          4          6        0       0
  subtype5         15          2         18        0       0
  subtype6         13          2          6        2       1
D12V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I          11       12       25        8        9        4
  STAGE IA          6        7       20        5        9        4
  STAGE IB          1        0        2        1        1        0
  STAGE II          0        1        0        1        6        1
  STAGE IIA        58       19       58       44       23       24
  STAGE IIB        27       15       40       36       26        9
  STAGE III         0        0        0        1        1        0
  STAGE IIIA        9        7       28       17       15       13
  STAGE IIIB        1        0        4        4        2        2
  STAGE IIIC        3        4        6        6       18        6
  STAGE IV          0        1        2        0        0        2
  STAGE X           1        0        3        0        0        1
[1] 12  6
[1] 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
  subtype1  29  76  10   3
  subtype2  32  28   6   0
  subtype3  62 101  17   8
  subtype4  25  79  15   4
  subtype5  30  52  26   2
  subtype6  18  43   3   2
D12V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1       29       32       62       25       30       18
  T2       76       28      101       79       52       43
  T3       10        6       17       15       26        3
  T4        3        0        8        4        2        2
[1] 4 6
[1] 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
  subtype1 74 34  7  3
  subtype2 29 30  3  4
  subtype3 94 61 22  7
  subtype4 47 54 13  6
  subtype5 47 35  9 19
  subtype6 28 17 14  6
D12V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0       74       29       94       47       47       28
  N1       34       30       61       54       35       17
  N2        7        3       22       13        9       14
  N3        3        4        7        6       19        6
[1] 4 6
[1] 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
  subtype1        0  97   0  21
  subtype2        0  55   1  10
  subtype3        2 164   2  20
  subtype4        0 100   0  23
  subtype5        0  74   0  36
  subtype6        0  53   2  11
D12V6, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  CM0 (I+)        0        0        2        0        0        0
  M0             97       55      164      100       74       53
  M1              0        1        2        0        0        2
  MX             21       10       20       23       36       11
[1] 4 6
[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
  subtype1 118   0
  subtype2  65   1
  subtype3 185   3
  subtype4 122   1
  subtype5 110   0
  subtype6  63   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  118    0
  subtype2   65    1
  subtype3  185    3
  subtype4  122    1
  subtype5  110    0
  subtype6   63    3
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE      118       65      185      122      110       63
  MALE          0        1        3        1        0        3
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  subtype1                          1                           102
  subtype2                          0                            46
  subtype3                          0                           155
  subtype4                          0                            78
  subtype5                          0                            25
  subtype6                          0                            58
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                              1                   4
  subtype2                             17                   0
  subtype3                             16                   1
  subtype4                             15                   0
  subtype5                             83                   0
  subtype6                              7                   0
          vv
clus       MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                                0                  0             10
  subtype2                                1                  0              2
  subtype3                               10                  1              5
  subtype4                                7                 12             11
  subtype5                                1                  1              0
  subtype6                                0                  0              1
D12V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  INFILTRATING CARCINOMA NOS              1        0        0        0        0
  INFILTRATING DUCTAL CARCINOMA         102       46      155       78       25
  INFILTRATING LOBULAR CARCINOMA          1       17       16       15       83
  MEDULLARY CARCINOMA                     4        0        1        0        0
  MIXED HISTOLOGY (PLEASE SPECIFY)        0        1       10        7        1
  MUCINOUS CARCINOMA                      0        0        1       12        1
  OTHER  SPECIFY                         10        2        5       11        0
                                  clus
vv                                 subtype6
  INFILTRATING CARCINOMA NOS              0
  INFILTRATING DUCTAL CARCINOMA          58
  INFILTRATING LOBULAR CARCINOMA          7
  MEDULLARY CARCINOMA                     0
  MIXED HISTOLOGY (PLEASE SPECIFY)        0
  MUCINOUS CARCINOMA                      0
  OTHER  SPECIFY                          1
[1] 7 6
[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
  subtype1  33  85
  subtype2  17  49
  subtype3  58 130
  subtype4  41  82
  subtype5   6 104
  subtype6  19  47
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   33   85
  subtype2   17   49
  subtype3   58  130
  subtype4   41   82
  subtype5    6  104
  subtype6   19   47
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO        33       17       58       41        6       19
  YES       85       49      130       82      104       47
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     5                        45    67
  subtype2     3                         1    62
  subtype3    20                        17   150
  subtype4     9                        18    95
  subtype5     5                        17    86
  subtype6    10                        14    41
D12V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            5        3       20        9        5
  BLACK OR AFRICAN AMERICAN       45        1       17       18       17
  WHITE                           67       62      150       95       86
                           clus
vv                          subtype6
  ASIAN                           10
  BLACK OR AFRICAN AMERICAN       14
  WHITE                           41
[1] 3 6
[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
  subtype1   6 105
  subtype2   7  55
  subtype3   6 170
  subtype4   9 110
  subtype5   5  99
  subtype6   1  64
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6  105
  subtype2    7   55
  subtype3    6  170
  subtype4    9  110
  subtype5    5   99
  subtype6    1   64
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            6        7        6        9        5        1
  NOT HISPANIC OR LATINO      105       55      170      110       99       64
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
