[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/11541508/BRCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/BRCA-TP/11724890/BRCA-TP.mergedcluster.txt"

nPatients in clinical file=1043, in cluster file=1100, common to both=1043
[1]   12 1043
[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 
249 387  85 256  48 
  1   2   3   4   5 
249 387  85 256  48 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3   4   5 
129 195 172  86 119 
  1   2   3   4   5 
129 195 172  86 119 
[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 
524 292 223 
  1   2   3 
524 292 223 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5   6 
214 158 290 139 181  57 
  1   2   3   4   5   6 
214 158 290 139 181  57 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
320 226 477 
  1   2   3 
320 226 477 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5   6 
231 152 299 126  85 130 
  1   2   3   4   5   6 
231 152 299 126  85 130 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3   4   5 
179 131  84 101 119 
  1   2   3   4   5 
179 131  84 101 119 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3 
295 209 110 
  1   2   3 
295 209 110 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "HISTOLOGICALTYPE"                      
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "NUMBER.OF.LYMPH.NODES"                 
[18] "RACE"                                  
[19] "ETHNICITY"                             
[20] "BATCHNUMBER"                           

Input Data has 20 rows and 1043 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
          12          259          437         1321         1463          434 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN 
        1437          635          416           NA          242         1196 
TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q 
         852          584          554         3188           NA         1276 
TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X 
        2499         2246          671           NA         1948         1686 
TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
        1099         4159         1964           NA         3409         2813 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV 
        2695         3283         2298         2289           NA         1930 
TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0CY TCGA-A2-A0CZ TCGA-A2-A0D0 TCGA-A2-A0D1 
        1948         1728         1673         1616          643         1051 
TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO 
        1027          875          767         3094         2718         2442 
TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU 
        3273         2426         2263         1127         1066         1043 
TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU 
         968          905          752          735         3017         1662 
TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 
          NA           NA         1534         1347          533          521 
TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 
          NA          569          624          531          575          631 
TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH 
         990          769          554          469          666          659 
TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT 
         441          566          588         1474          965           NA 
TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 
         714          528         1119          683          616          584 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C 
         595          501         1596         3276          496          523 
TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS 
         552         2796          322          635         1206           NA 
TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
        2525           NA          996         1505         1168         1064 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
         973         1167          222          742          648          706 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG 
         820          643          666         1165         1074         1043 
TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D 
        1079          931         1139         1085         1007          965 
TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F 
         326          387          718          899          954          738 
TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY 
         722          724          661          627          679          345 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 
         322          313          343          408          447          364 
TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SC TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF 
         454          418          446          441          644          545 
TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW 
         448          368          326          336          313          285 
TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06N TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q 
         317          266           NA          396          396           31 
TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z 
         547         1614           NA           NA          791           31 
TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07C TCGA-A8-A07E 
         518         1642          274         1308         1034          608 
TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O 
         577          577          426          365          518          304 
TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z 
         334          273          243          760          304          853 
TCGA-A8-A081 TCGA-A8-A082 TCGA-A8-A083 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 
          NA          549           NA          458         1124          396 
TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08H 
          30         1156          881         1004          607           NA 
TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R 
         365           NA           NA          943          943           30 
TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A090 TCGA-A8-A091 
        1004         2830         1308         1217           NA         1004 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A094 TCGA-A8-A095 TCGA-A8-A096 TCGA-A8-A097 
         942          546           NA         1277           NA          365 
TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E 
         304          304          365           31         1522         1492 
TCGA-A8-A09G TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q 
          NA         1371          912         1006           31          761 
TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A09Z 
         273          579          457           30           NA           NA 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 
         365          579          396          640           30          396 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H 
         518         1157           29           72          330           81 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG 
          45         1172         1162         1234         1686         1125 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ 
        1180           NA         1542           31           28           69 
TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 
          30           21          451          675           34          504 
TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X 
         602          707          754           47            2           34 
TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OP 
          55           36           21           13           51           53 
TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 
          34           40           10           10            7           10 
TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK 
          19           90           54           52          244          224 
TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD 
         198            5           10           10           10          196 
TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
         141          242          213          231          218          191 
TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ 
         183           10           11           10           10           10 
TCGA-AN-A0G0 TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR 
          16           10           10          375            9           10 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L 
          10           10           10          162          170         2442 
TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T 
        1455         2031           NA         2576         2091         1456 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 
          NA          886          997          651         1587          735 
TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB 
        1140          618          680         1613          655         1542 
TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI 
        1547         2190         2335          650          798         1528 
TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 
        1887         1683         2184         3120         3019         3307 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12C TCGA-AO-A12D 
        3248         2923         2755         2359         1994         1948 
TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
        1743         1471         1266          863          448         2513 
TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J 
        1882         2141           16          541          754          819 
TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O 
        3957           NA          475          989           78         1001 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT 
         304         3386         1500           NA         2275         2636 
TCGA-AR-A0TU TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
         360          905         3009         1972           NA         2316 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH 
        1988         3101           NA         3468         2615         2298 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
        1881         1605         1559         1485         1903         1330 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AT 
        1325         1216         1310           NA         1150           NA 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H 
        2318         1864         1935         1890          615         3333 
TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
        1548         2221         2947         2388         2561           26 
TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V 
        3088         2653           NA         2312         1623         2596 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 
        1550         2548         2403         1708         2387         2226 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
        2213         1792           NA         3913           NA         1912 
TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
        1304          224         1218         1161         1198         1233 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
         620         1665          488          622           NA           NA 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I6 TCGA-B6-A0I8 TCGA-B6-A0I9 TCGA-B6-A0IA 
        4361         4550           NA           NA           NA         6719 
TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ 
          NA           NA           NA           NA           NA         5383 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ 
          NA         3836           NA         3350         3374         4285 
TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM 
        6435         2082         5749         7126           NA           NA 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT 
        5261         4929           NA           NA           NA         2721 
TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW 
        3991         4788           NA         5739           NA          547 
TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
          NA           NA         3941           NA         5672           NA 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN 
          NA           NA         1326         3088         2236         4233 
TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C 
        5176         2596         1651         1519         3152         1673 
TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 
         746         1180          622          777          867         1428 
TCGA-BH-A0B1 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 
        1148         1242         1203         1191         1471         1732 
TCGA-BH-A0B7 TCGA-BH-A0B8 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
        1733         1569         1572         1132          974          554 
TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO 
         782          756          660         1340         1876         1085 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV 
        1481          827         1633         1641         1386         1519 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 
         355         1492         1270         1339         1464         1305 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
        1394          948          713         1156          673          423 
TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT 
        1467          525          476           98           78         1170 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 
        1374         1442          495          134          477          435 
TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE 
         293         1363         1405           NA          745          943 
TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
         743          923          328          461         1149         1080 
TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HF 
         747          702         1247         1611          806          727 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HL TCGA-BH-A0HN TCGA-BH-A0HO TCGA-BH-A0HP 
         620          178           72          516           76          414 
TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX 
        1121          392         1561          829         1545          170 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F 
         728          759         1288         1363          701          268 
TCGA-BH-A18G TCGA-BH-A18H TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L 
          61           NA          220           NA           NA           NA 
TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 
          NA           NA           NA           NA           NA          210 
TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O 
          22           NA           NA           NA           NA          324 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12K 
         196          612           30         3324          272           NA 
TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q 
         363          358          358          385          358            2 
TCGA-C8-A12T TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y 
          NA          385          385          385          385           NA 
TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A133 TCGA-C8-A134 
          NA           95           54           44           NA           21 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG 
          19          117          114          375          332          345 
TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN 
         345            5          366          317           70           99 
TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z 
          NA            9            7           11           13          252 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B 
         294            1            1            1          371           30 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 
           1            7          362          635          403          626 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 
         425          431          410          643          584          431 
TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE 
         532          502          569          480          552          575 
TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK 
         366          366          426          577          611          612 
TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT 
         611          590          620          639          371          405 
TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 
         447          565          541          509          783          727 
TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG 
         839          552           81          522          463          448 
TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ 
         664          441          606          538          242          499 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW 
         482          496          193          395          461          385 
TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 
         503          466          472          116          433          430 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K 
         530          488          409          397          439          287 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T 
         499          410          146           23          307          398 
TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 
         381          373          441          563          223         1308 
TCGA-E2-A106 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B 
        1807         1047          837         1417         1229         1141 
TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P 
        1220          865          878         1434         1359         1246 
TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V 
        1163         1174         1009         1013         1318         1042 
TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 
         974          972          870          518          773          825 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 
         707          591          640          726          450          762 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G 
         710          694          526          630          658          554 
TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M 
         393          530          590          275          626          235 
TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ 
         396          595          519          428          456         2329 
TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC 
        1631         1613          911          984          867          501 
TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II 
         520         1165         1138          997         1026         1025 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
         865          689          118          675          638          337 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB 
        1648          834         1205          598          748         1231 
TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL 
          NA          574         3247         3121           NA         1309 
TCGA-E2-A1LS TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
         470          515          168          478          219          931 
TCGA-E2-A572 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 
         831         1062          605          578          280           NA 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA 
         584         1120          410          365          399         1112 
TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH 
        1203          383         1088          610          656           NA 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 
         300          362          435           19           64          186 
TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC 
          42           84          645          976          633         1224 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI 
          20         1054          200          647         1052         1084 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
        1038           24          381          405         1189          692 
TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 
          NA          392          715          733          519           21 
TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
          26          828           59           29          747           22 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
         540           23          793          560           19          478 
TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP 
         375            7          447            8          420          438 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 
         468          371         1208          258          554          575 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW 
         403          504          477          875          789          694 
TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 
         911          908         1229         1251         1210         1611 
TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA 
         907          703          562          915           NA          575 
TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
         608          187          424          320          439         1051 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 
         607         1673         1604          788          672          647 
TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 
         532          309          322          225         3342           NA 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH 
        5909         1616         1628         1309         1299         1286 
TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO 
        1883         1896         2763         2331         2352         1623 
TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 
        3361         1162         1330         2108         2019         2191 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U 
         412          551          360          352          646          203 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
         124          140          266          290          348          333 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP 
         231          519          466          447          440          450 
TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 
         352           80          118          126          137          137 
TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
         170           98          189          224          849           85 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
          64          385         1416          973         1783          841 
TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 
        1062         1106          513          752          679          620 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
         812          714         1996         1021          945          792 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PL-A8LV TCGA-PL-A8LX 
         220          428          858          600            7            5 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z 
           8          120          502          207          263          322 
TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 
         241          169          259          218          209          119 
TCGA-W8-A86G TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
         161          292          278         3042         3195 
Variable 1:'AGE':	nDistinctValues=65,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=119,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=684,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=16,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=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=31,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'BATCH.NUMBER':	nDistinctValues=58,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "NEOPLASM.DISEASESTAGE"                 
 [3] "PATHOLOGY.T.STAGE"                     
 [4] "PATHOLOGY.N.STAGE"                     
 [5] "PATHOLOGY.M.STAGE"                     
 [6] "GENDER"                                
 [7] "HISTOLOGICAL.TYPE"                     
 [8] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [9] "NUMBER.OF.LYMPH.NODES"                 
[10] "RACE"                                  
[11] "ETHNICITY"                             
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 1043 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 
272 604 125  39 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
272 604 125  39 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
272 604 125  39 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
272 604 125  39 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
491 345 114  74 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
491 345 114  74 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2  N3 
491 345 114  74 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
491 345 114  74 
PATHOLOGY.M.STAGE, nv=4, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=7, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=31, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = MRNA_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 17  3
  subtype2 36  3
  subtype3 97 19
  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       19       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        48.46        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        76.21        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 
       33.01        19.96        33.01        50.04        49.05        29.98 
TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A04A 
       33.07        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        50.24       108.72        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        98.93        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        33.99         9.99 
TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A08R TCGA-A8-A08X TCGA-AN-A04D TCGA-AN-A0AL 
        8.98        24.99         0.99        43.00         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        52.18        37.48        55.33 
TCGA-AO-A124 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12F TCGA-AQ-A04J TCGA-AR-A0TP 
      102.58       106.78        96.10        48.36        26.93       111.32 
TCGA-AR-A0TS TCGA-AR-A0TU TCGA-AR-A0U0 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
       74.79        11.84        65.36        85.97        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        53.06        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 
       28.96        33.01        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 
       37.81        63.62       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 
       43.00        15.06        38.01        37.05         9.99        30.97 
TCGA-A8-A09I TCGA-A8-A09N TCGA-A8-A09W TCGA-A8-A09X TCGA-AN-A04C TCGA-AN-A0FT 
       45.07         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       114.02        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        86.66        61.28        62.14        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   43.560   29.080   30.165   27.730   30.985   44.810   27.520 
[1] "0.3 - 92.0 (15.3)"  "1.4 - 157.4 (43.6)" "0.2 - 188.7 (29.1)"
[4] "0.2 - 211.6 (30.2)" "0.3 - 234.3 (27.7)" "0.1 - 189.0 (31.0)"
[7] "1.0 - 97.5 (44.8)"  "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        0 115   2   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      115       97      101       70       19
  M1              2        1        2        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  82  16
  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 
      16       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        53.06        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        33.01        19.96        33.01        33.01 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09R 
        1.02        50.04        49.05        29.98        33.07         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        50.24 
TCGA-AQ-A04H TCGA-AR-A0TQ TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0TZ 
       24.79        49.32        29.75        98.93        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 
       48.46        34.29        33.11        19.99        12.00        28.96 
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 
      108.72        90.58        65.56        57.30        41.62        86.66 
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        76.21 
TCGA-AR-A1AV TCGA-AR-A1AX TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IE TCGA-B6-A0IH 
       61.28        62.14       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        43.00        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        38.01        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 
       43.00        30.97        41.98        12.00        45.07         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       114.02 
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        33.99         9.99         8.98        24.99 
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        52.18 
TCGA-AO-A0J6 TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12F 
       37.48        55.33       102.58       106.78        96.10        48.36 
TCGA-AQ-A04J TCGA-AR-A0TP TCGA-AR-A0TS TCGA-AR-A0TU TCGA-AR-A0U0 TCGA-AR-A0U4 
       26.93       111.32        74.79        11.84        65.36        85.97 
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        37.81        63.62 
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 
  30.805   31.820   25.035   31.730   23.930 
[1] "0.2 - 234.3 (30.8)" "0.3 - 220.9 (31.8)" "0.1 - 189.0 (25.0)"
[4] "0.3 - 211.6 (31.7)" "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  96   2   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             96      146      111       88       54
  M1              2        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 208  32
  subtype2 340  40
  subtype3  75   9
  subtype4 223  30
  subtype5  40   8
subtype1 subtype2 subtype3 subtype4 subtype5 
     240      380       84      253       48 
subtype1 subtype2 subtype3 subtype4 subtype5 
      32       40        9       30        8 
$subtype1
TCGA-5T-A9QA TCGA-A1-A0SD TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SQ 
        0.39        14.37        13.68         7.96        39.32        18.21 
TCGA-A2-A04R TCGA-A2-A04X TCGA-A2-A0CT TCGA-A2-A0CX TCGA-A2-A0D4 TCGA-A2-A0EO 
       82.16        55.43        75.25        56.81        25.22        80.28 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0T3 
       35.05        34.29        31.82        27.12        44.88        18.71 
TCGA-A2-A0T4 TCGA-A2-A0T7 TCGA-A2-A0YG TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX 
       20.52        20.75        21.90        23.77        17.36        36.79 
TCGA-A2-A25E TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A13F TCGA-A7-A26J TCGA-A7-A2KD 
       91.92        38.30        30.61        12.72        20.61        22.32 
TCGA-A7-A4SB TCGA-A7-A4SF TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T 
       13.74        17.92        13.02         1.02        17.98        53.06 
TCGA-A8-A06U TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07G 
       29.03         1.02        53.98         9.01        43.00        18.97 
TCGA-A8-A07I TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A07W TCGA-A8-A085 TCGA-A8-A086 
       14.01        17.03        10.98         9.99        36.95        13.02 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08P 
       33.01        19.96        12.00        37.05        31.00        31.00 
TCGA-A8-A08S TCGA-A8-A092 TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09E 
       33.01        30.97        12.00         9.99         1.02        49.05 
TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09R TCGA-A8-A09W TCGA-A8-A0A4 TCGA-A8-A0A6 
       45.07        33.07         8.98         0.99        13.02        21.04 
TCGA-A8-A0A9 TCGA-AC-A23H TCGA-AC-A2BM TCGA-AC-A2FM TCGA-AC-A62V TCGA-AC-A8OP 
       13.02         2.66        38.20        26.04         0.07         1.74 
TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A0AJ TCGA-AN-A0FV 
        0.33         0.23         0.62         2.96         8.02         0.33 
TCGA-AN-A0FW TCGA-AN-A0XL TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03P TCGA-AO-A03T 
        0.36         0.33         5.59        80.28        84.69        47.87 
TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JG TCGA-AO-A0JI 
       32.78        21.40        72.00        76.77        26.24        50.24 
TCGA-AO-A0JM TCGA-AO-A12E TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H 
       71.80        57.30        61.87         0.53        17.79        24.79 
TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A54O TCGA-AR-A0TQ TCGA-AR-A0TZ TCGA-AR-A0U2 
        5.65        15.62        32.91        49.32        76.14        83.87 
TCGA-AR-A1AK TCGA-AR-A1AP TCGA-AR-A24L TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24V 
       51.25        39.98        73.02         0.85        87.22        85.35 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LK TCGA-AR-A2LL 
       79.00        56.15        72.76        58.92        42.87         7.36 
TCGA-B6-A0I9 TCGA-B6-A0IG TCGA-B6-A0RG TCGA-B6-A0RL TCGA-B6-A0RO TCGA-B6-A0WV 
       12.13       146.50        68.45        81.17       162.05        79.63 
TCGA-B6-A0WY TCGA-B6-A1KN TCGA-B6-A408 TCGA-BH-A0AU TCGA-BH-A0B4 TCGA-BH-A0BC 
      113.79       139.17        49.94        24.53        39.16        32.02 
TCGA-BH-A0BF TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DI TCGA-BH-A0DQ TCGA-BH-A0EI 
       25.71        42.90        45.83        22.13         3.22        24.43 
TCGA-BH-A0H7 TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0W3 TCGA-BH-A18L 
       23.08        51.32        27.25        50.79        23.93        26.66 
TCGA-BH-A18N TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EW 
       37.74        37.55        66.05        51.39        69.93        55.69 
TCGA-BH-A1F2 TCGA-BH-A1F8 TCGA-BH-A1FM TCGA-BH-A201 TCGA-BH-A42T TCGA-C8-A12M 
       31.53        24.66        45.63         6.90         0.99        11.77 
TCGA-C8-A12O TCGA-C8-A12Q TCGA-C8-A12W TCGA-C8-A132 TCGA-C8-A137 TCGA-C8-A1HI 
       12.66         0.07        12.66         1.45         3.85        11.34 
TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A27A 
       12.03        10.42         3.25         8.28         9.67        12.20 
TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A1J9 TCGA-D8-A1JC TCGA-D8-A1JD 
        0.23        11.90        13.25        17.49        15.78        18.15 
TCGA-D8-A1JE TCGA-D8-A1JI TCGA-D8-A1JT TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XS 
       18.90        18.97        13.32        23.90        27.58        16.31 
TCGA-D8-A1XT TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y3 TCGA-D8-A27G TCGA-D8-A27N 
        6.35        16.54        15.52        14.14        13.45         4.80 
TCGA-D8-A27R TCGA-D8-A27W TCGA-E2-A105 TCGA-E2-A109 TCGA-E2-A14O TCGA-E2-A14P 
       10.09        12.26        43.00        46.59        44.68        40.96 
TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A152 TCGA-E2-A15A 
       33.17        33.30        34.26        32.02        27.12        23.34 
TCGA-E2-A15E TCGA-E2-A15H TCGA-E2-A15O TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1IE 
       20.71        12.92        13.02        14.07        14.99        38.30 
TCGA-E2-A1IG TCGA-E2-A1LA TCGA-E2-A1LE TCGA-E2-A56Z TCGA-E9-A1NA TCGA-E9-A1NF 
       32.78        24.59        28.90         7.20        36.56        20.05 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R2 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RE 
        9.86        11.90         0.62         2.76        21.21        34.65 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A228 TCGA-E9-A22A TCGA-E9-A247 TCGA-E9-A295 
        6.58        21.27        12.53        39.09        27.22         0.72 
TCGA-E9-A2JS TCGA-E9-A5UO TCGA-E9-A5UP TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 
       17.75        13.81        14.40        16.57        15.68        28.77 
TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1PD TCGA-EW-A2FS 
       29.85        40.41        52.96        23.11        13.94        52.73 
TCGA-EW-A2FW TCGA-GI-A2C8 TCGA-LL-A5YM TCGA-LL-A6FQ TCGA-LL-A7T0 TCGA-OL-A5RZ 
       22.09         7.40        15.32         2.63         3.22        22.32 
TCGA-PL-A8LX TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA17 TCGA-Z7-A8R6 
        0.16        16.50         6.81         8.65         3.91       105.04 

$subtype2
TCGA-A1-A0SB TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04V 
        8.52        14.27        47.24       104.81        41.95        63.12 
TCGA-A2-A04W TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP 
       64.04        36.13       136.73        64.57       112.08        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP 
       88.60       107.93        28.77       101.72        89.36       107.61 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EW TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SY 
       74.40        37.05        29.75        99.19        54.64        44.28 
TCGA-A2-A0T1 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF 
       17.13        17.46        18.90        32.55        25.28        15.42 
TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A1FZ TCGA-A2-A1G4 TCGA-A2-A1G6 
       14.50        19.33        48.46        22.45        19.56        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD 
       52.47       107.70        17.19        10.59        20.88        39.65 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XZ TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       32.75        49.48        31.99        24.39        21.30        23.21 
TCGA-A2-A4S1 TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       26.96        34.29        35.47        23.61        29.56        31.36 
TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       24.26        23.80        11.34        10.59        10.29        11.28 
TCGA-A7-A3RF TCGA-A7-A426 TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A8-A06P TCGA-A8-A07E 
       13.41        11.97        10.72        11.05        13.02        19.99 
TCGA-A8-A07J TCGA-A8-A07S TCGA-A8-A082 TCGA-A8-A08A TCGA-A8-A08T TCGA-A8-A08Z 
       12.00         7.99        18.05         0.99        93.04        40.01 
TCGA-A8-A095 TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A7 
       41.98        19.04        15.02        14.01        12.00         0.99 
TCGA-A8-A0AD TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2FB TCGA-AC-A2FF 
       38.04         2.37        10.85         1.48        40.57        55.43 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB 
       36.99        38.79        50.70         0.92         2.27         0.99 
TCGA-AC-A3HN TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ 
        0.69        22.19         1.12        19.79        23.24        24.79 
TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A8OR TCGA-AN-A046 TCGA-AN-A0FF TCGA-AN-A0FN 
        1.18         0.43         1.32         0.33         4.64         7.17 
TCGA-AN-A0FS TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XV TCGA-AO-A03U TCGA-AO-A0J5 
        6.28         0.33         0.33         5.33        59.05        24.16 
TCGA-AO-A0J8 TCGA-AO-A0JA TCGA-AO-A0JC TCGA-AO-A0JF TCGA-AO-A0JJ TCGA-AO-A125 
       22.36        21.53        50.86        21.37        62.04        99.25 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12H TCGA-AO-A1KO TCGA-AQ-A1H3 TCGA-AQ-A7U7 
      108.72       106.78        28.37        14.73        32.52         9.99 
TCGA-AR-A0TS TCGA-AR-A0TX TCGA-AR-A1AJ TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
       74.79        64.83        52.77        48.82        62.56        43.73 
TCGA-AR-A1AO TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX 
       43.56        43.07        37.81        76.21        63.62        62.14 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24T TCGA-AR-A24W TCGA-AR-A24X 
       96.89        78.51        84.20        76.01        50.96        83.77 
TCGA-AR-A252 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN 
       73.18       128.65        20.25        62.86        40.04        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I5 
       39.39        40.54        16.04        20.45        10.59       149.59 
TCGA-B6-A0IC TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0RI TCGA-B6-A0RM 
       50.70       126.12        84.59       110.93       234.28        78.02 
TCGA-B6-A0RN TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT 
      172.96       140.48        89.46       157.41        97.48       188.68 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KI 
      129.57       129.70        28.27        68.94        58.88        73.51 
TCGA-B6-A401 TCGA-B6-A40C TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B7 TCGA-BH-A0BD 
       85.35        55.00        28.50        46.95        56.98        18.21 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BZ TCGA-BH-A0C3 
       61.68        35.67        27.19        53.95        49.05        48.13 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DT 
       31.17        23.44        38.01        13.91        17.26        38.47 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 
       45.17        47.41        16.27        15.68        14.30        44.81 
TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       32.65        24.49        31.00        37.78        35.51        24.56 
TCGA-BH-A0HA TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0RX 
       52.96        20.38         5.85         2.50        13.61         5.59 
TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18G TCGA-BH-A18J TCGA-BH-A18M 
       24.95        42.35        44.81         2.01        20.12        72.56 
TCGA-BH-A18P TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EX TCGA-BH-A1F0 
       30.28       113.82        82.85        42.28        49.58        25.81 
TCGA-BH-A1F5 TCGA-BH-A1FB TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
       89.16       120.62        74.73       122.89        36.92        63.35 
TCGA-BH-A1FL TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A28O TCGA-BH-A2L8 TCGA-BH-A42U 
       55.00       144.59        72.07        10.65        20.12       109.28 
TCGA-BH-A42V TCGA-C8-A12N TCGA-C8-A12V TCGA-C8-A1HE TCGA-C8-A26V TCGA-C8-A26X 
        8.94        11.77        12.66        12.33         0.30         0.36 
TCGA-C8-A26Y TCGA-C8-A275 TCGA-C8-A3M7 TCGA-D8-A141 TCGA-D8-A145 TCGA-D8-A1JB 
        0.43         0.03         0.03        20.58        13.48        18.71 
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-A1B1 
       17.42        19.40         9.04        20.58        19.56        53.03 
TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IF TCGA-E2-A1IJ 
       29.95        32.35        28.50        16.47        37.41        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LB 
       22.65         3.88        11.08        54.18        19.66        40.47 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1NE 
        5.52        15.72        30.61        19.20        36.82        35.77 
TCGA-E9-A1NG TCGA-E9-A1R0 TCGA-E9-A1R4 TCGA-E9-A1RA TCGA-E9-A1RD TCGA-E9-A1RI 
       21.57        14.30         6.12        32.09         0.66        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-A54X TCGA-E9-A5FK 
       24.56         0.76        18.41        15.72        12.33        14.70 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J2 
       15.39        12.20        39.72         8.48        18.21        13.25 
TCGA-EW-A1OX TCGA-EW-A1P1 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PE TCGA-EW-A1PG 
       29.95        39.78        18.48        30.08        10.52        34.55 
TCGA-EW-A2FR TCGA-EW-A3E8 TCGA-EW-A424 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       55.00        21.27        10.59        59.57       194.27        53.13 
TCGA-GM-A2DD TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       43.04        42.28        61.91        62.33        90.84        76.64 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 
       77.33        53.36        38.20        43.73        66.38        72.03 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LD-A9QF 
       13.55        18.12        11.84         6.67         4.60         8.75 
TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YO TCGA-LL-A73Z 
        9.53        10.95         7.59        17.06        14.47         4.50 
TCGA-LL-A740 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 
        4.50        27.91         2.79         2.10        12.66        31.99 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A66H 
       58.62        27.65        34.92        16.87        24.72        26.70 
TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ TCGA-PL-A8LY 
       65.62        31.07         7.23        14.07        19.73         0.26 
TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-W8-A86G TCGA-XX-A899 
        5.56         8.52         7.17         6.87         5.29         9.60 
TCGA-XX-A89A TCGA-Z7-A8R5 
        9.14       100.01 

$subtype3
TCGA-A1-A0SE TCGA-A1-A0SI TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A3XU TCGA-A2-A4S2 
       43.43        20.88        75.55        63.45        29.98        21.14 
TCGA-A7-A0DB TCGA-A7-A425 TCGA-A8-A06Y TCGA-A8-A07F TCGA-A8-A07Z TCGA-A8-A084 
       33.11        14.70        26.01        18.97        28.04        15.06 
TCGA-A8-A08C TCGA-A8-A093 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A0A2 TCGA-A8-A0AB 
       28.96        17.95         9.99        12.00        19.04        17.03 
TCGA-AC-A3OD TCGA-AC-A5XS TCGA-AC-A62Y TCGA-AC-A6NO TCGA-AN-A03Y TCGA-AN-A0FK 
       14.83         1.55         1.81         1.68         0.33         7.00 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AO-A03N TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A12A 
       12.33         0.30        66.77        20.32        53.03        90.58 
TCGA-AO-A12B TCGA-AR-A0TR TCGA-AR-A1AV TCGA-AR-A24K TCGA-AR-A5QM TCGA-B6-A0IB 
       77.56         5.26        61.28        50.89        54.74       129.57 
TCGA-B6-A0IH TCGA-B6-A0RH TCGA-B6-A0RP TCGA-B6-A40B TCGA-BH-A0B5 TCGA-BH-A0BA 
      112.37       189.01       102.77       103.63        48.36        37.22 
TCGA-BH-A0BJ TCGA-BH-A0BV TCGA-BH-A0C1 TCGA-BH-A0DP TCGA-BH-A0E9 TCGA-BH-A0GZ 
       21.70        49.94        44.02        15.65        46.19        10.78 
TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A18F TCGA-BH-A18K TCGA-BH-A1EV TCGA-BH-A202 
       36.85        12.89         8.81        90.84        12.00         0.72 
TCGA-BH-A28Q TCGA-C8-A274 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1JA TCGA-D8-A1XG 
        6.44         0.03        21.14        14.17        16.50        14.73 
TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1Y1 TCGA-D8-A27V TCGA-E2-A107 TCGA-E2-A10B 
        7.96        15.85         3.81        12.53        34.42        37.51 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A15G TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1L8 
       23.24        19.43        18.21        17.10        33.73        39.62 
TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1RC TCGA-E9-A249 TCGA-E9-A3HO TCGA-EW-A1PC 
        2.10         1.38        40.24         0.95        26.07         6.15 
TCGA-GM-A3NW TCGA-LD-A66U TCGA-LL-A6FP TCGA-OL-A66K TCGA-OL-A66N TCGA-S3-AA0Z 
      110.50        21.24        11.57        33.57        26.04        10.59 

$subtype4
TCGA-A1-A0SF TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A04P TCGA-A2-A04T 
       48.10        31.79        28.01        19.20        18.02        73.84 
TCGA-A2-A04U TCGA-A2-A0CM TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 
       22.06        24.79        64.04        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        21.90        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        24.99        38.01         9.99         0.99        43.00 
TCGA-A8-A09D TCGA-A8-A09K TCGA-A8-A09N TCGA-A8-A09Q TCGA-AC-A23C TCGA-AC-A2BK 
       50.04        29.98         1.02        25.02         0.95        38.53 
TCGA-AC-A2QH TCGA-AC-A3W5 TCGA-AC-A62X TCGA-AC-A8OQ TCGA-AN-A04C TCGA-AN-A04D 
        1.02        16.57         1.12         1.12         1.78         1.71 
TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT 
        7.36         6.51         0.16         0.33         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-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        52.18        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-A0TT TCGA-AR-A0TV TCGA-AR-A0TW 
      130.09         2.56       111.32        86.66        29.75        98.93 
TCGA-AR-A0TY TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
       55.86        65.36       101.95        85.97        75.55        61.84 
TCGA-AR-A1AR TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24Q TCGA-AR-A24U TCGA-AR-A251 
       17.23        20.22       109.58       101.52        53.36        78.48 
TCGA-AR-A256 TCGA-AR-A2LR TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0IE TCGA-B6-A0IJ 
       93.83        20.38        77.62       143.38        65.72       176.98 
TCGA-B6-A0IK TCGA-B6-A0IO TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RS TCGA-B6-A0RU 
       18.77       110.14       140.88       211.56       100.70       131.21 
TCGA-B6-A0WX TCGA-B6-A0X1 TCGA-B6-A1KF TCGA-B6-A402 TCGA-BH-A0AV TCGA-BH-A0AW 
       21.47       186.48       101.52        54.28        38.79        20.45 
TCGA-BH-A0B3 TCGA-BH-A0B6 TCGA-BH-A0B9 TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BP 
       39.55        56.94        51.68        24.85        44.05        48.69 
TCGA-BH-A0BR TCGA-BH-A0BW TCGA-BH-A0C0 TCGA-BH-A0DL TCGA-BH-A0E0 TCGA-BH-A0E6 
       53.69        11.67        41.75        48.23         4.41         9.63 
TCGA-BH-A0GY TCGA-BH-A0H9 TCGA-BH-A0WA TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A18V 
       30.35        41.00        23.05        55.63         7.36        51.16 
TCGA-BH-A1EY TCGA-BH-A1F6 TCGA-BH-A1FN TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A209 
       17.69        97.48        72.07        38.60        57.83       130.16 
TCGA-C8-A12L TCGA-C8-A12P TCGA-C8-A12U TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A134 
       11.93        11.77        12.66         3.12         1.78         0.69 
TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HJ TCGA-C8-A1HM TCGA-C8-A26W 
        0.62         3.75        10.92         0.16         2.30         0.23 
TCGA-C8-A278 TCGA-C8-A27B TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A147 
        0.03         0.99        20.88        13.97        14.17        19.20 
TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM 
       12.03        12.03        20.09        20.12        20.09        19.40 
TCGA-D8-A1JP TCGA-D8-A1X5 TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XQ 
       21.01        18.58        21.83        14.50        19.92        16.41 
TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27M 
       12.99        12.66        15.32        16.04        13.05        13.48 
TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A158 
       38.60        31.96        28.60        17.03        25.41        14.79 
TCGA-E2-A159 TCGA-E2-A15M TCGA-E2-A1AZ TCGA-E2-A1II TCGA-E2-A1IO TCGA-E2-A1L7 
       25.05         7.73        60.53        33.70        20.98        27.42 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A573 TCGA-E2-A574 
      106.75       102.61        43.04        16.93        34.92        19.89 
TCGA-E2-A9RU TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1RH 
        9.21        12.00        13.12        39.55        12.59        34.59 
TCGA-E9-A226 TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A3QA 
       34.13        22.75        12.89        23.51         0.69         0.62 
TCGA-E9-A5FL TCGA-EW-A1J1 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P8 
        0.26        18.90        25.94        22.82        29.82         7.86 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PF TCGA-EW-A1PH TCGA-EW-A2FV TCGA-EW-A3U0 
       18.90        19.99        14.43        19.96        25.91        17.49 
TCGA-EW-A423 TCGA-GI-A2C9 TCGA-GM-A2DF TCGA-GM-A3XL TCGA-LD-A7W5 TCGA-LL-A441 
       10.16       109.87        42.71        69.30         4.08        11.44 
TCGA-LL-A5YN TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A8F5 TCGA-OL-A5D7 
       14.70        14.79         3.88         4.14         6.21        46.55 
TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-OL-A66I TCGA-OL-A6VO TCGA-PL-A8LV TCGA-PL-A8LZ 
       36.36        20.38        23.47        28.21         0.23         3.95 
TCGA-S3-AA10 
        7.92 

$subtype5
TCGA-A2-A0CU TCGA-A2-A0EX TCGA-A2-A0YH TCGA-A2-A1FV TCGA-A2-A1G0 TCGA-A2-A25D 
        5.19        24.72        21.67        23.47        20.25        18.15 
TCGA-A8-A091 TCGA-AC-A6IW TCGA-AO-A03R TCGA-AO-A1KP TCGA-AR-A0U3 TCGA-B6-A0IA 
       33.01         0.69        68.75        82.62       114.02       220.90 
TCGA-B6-A0WW TCGA-B6-A1KC TCGA-B6-A2IU TCGA-BH-A0AY TCGA-BH-A0B2 TCGA-BH-A0BT 
       17.98        43.59       170.17        25.55        40.83        45.57 
TCGA-BH-A0DS TCGA-BH-A0H0 TCGA-BH-A0HB TCGA-BH-A18I TCGA-BH-A1EO TCGA-BH-A1FC 
        2.56        15.16        26.50         7.23        91.99       114.15 
TCGA-BH-A1FD TCGA-BH-A204 TCGA-C8-A12X TCGA-C8-A1HG TCGA-D8-A1X6 TCGA-D8-A1XD 
       33.17        83.31        12.66        11.34        17.79        17.16 
TCGA-D8-A1XF TCGA-D8-A1Y2 TCGA-E2-A10C TCGA-E2-A15F TCGA-E2-A15R TCGA-E2-A1B0 
       15.22        14.24        40.11        21.63        17.06        53.62 
TCGA-E2-A1IN TCGA-E2-A1LG TCGA-E2-A1LK TCGA-E2-A576 TCGA-E9-A1N6 TCGA-E9-A1RB 
       22.19        18.87         8.75        19.00        13.48        20.81 
TCGA-E9-A54Y TCGA-EW-A1P0 TCGA-GM-A2DC TCGA-JL-A3YX TCGA-LL-A7SZ TCGA-LL-A9Q3 
        0.23        41.13        53.52        11.57         5.59         7.36 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.07     0.03     0.03     0.03     0.23 
subtype1 subtype2 subtype3 subtype4 subtype5 
  162.05   234.28   189.01   211.56   220.90 
subtype1 subtype2 subtype3 subtype4 subtype5 
  21.995   24.870   20.600   21.140   21.220 
[1] "0.1 - 162.1 (22.0)" "0.0 - 234.3 (24.9)" "0.0 - 189.0 (20.6)"
[4] "0.0 - 211.6 (21.1)" "0.2 - 220.9 (21.2)"
D3V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1      13       15        2        1        80        51         1
  subtype2      43       44        6        3       106        89         1
  subtype3       5        2        0        1        28        26         0
  subtype4      18       16        1        0       108        57         0
  subtype5       4        3        0        0        20        11         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
  subtype1         47         14         15        8         0       2
  subtype2         49          6         27        5         0       8
  subtype3          9          4          6        2         0       2
  subtype4         31          5         12        3         1       3
  subtype5          6          0          3        0         0       1
D3V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          13       43        5       18        4
  STAGE IA         15       44        2       16        3
  STAGE IB          2        6        0        1        0
  STAGE II          1        3        1        0        0
  STAGE IIA        80      106       28      108       20
  STAGE IIB        51       89       26       57       11
  STAGE III         1        1        0        0        0
  STAGE IIIA       47       49        9       31        6
  STAGE IIIB       14        6        4        5        0
  STAGE IIIC       15       27        6       12        3
  STAGE IV          8        5        2        3        0
  STAGE TIS         0        0        0        1        0
  STAGE X           2        8        2        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  49 159  26  15
  subtype2 143 174  60   9
  subtype3   9  57  12   7
  subtype4  49 176  22   7
  subtype5  15  28   4   1
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       49      143        9       49       15
  T2      159      174       57      176       28
  T3       26       60       12       22        4
  T4       15        9        7        7        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  96  85  41  19
  subtype2 184 135  30  30
  subtype3  36  32   6   9
  subtype4 144  69  30  13
  subtype5  21  18   6   3
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       96      184       36      144       21
  N1       85      135       32       69       18
  N2       41       30        6       30        6
  N3       19       30        9       13        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"
          vv
clus       CM0 (I+)  M0  M1  MX
  subtype1        1 216   9  23
  subtype2        3 307   5  72
  subtype3        0  70   2  13
  subtype4        0 222   3  31
  subtype5        1  39   0   8
D3V6, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4 subtype5
  CM0 (I+)        1        3        0        0        1
  M0            216      307       70      222       39
  M1              9        5        2        3        0
  MX             23       72       13       31        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"
D3V7, binary
          cls
clus         0   1
  subtype1 239  10
  subtype2 387   0
  subtype3  84   1
  subtype4 256   0
  subtype5  48   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  239   10
  subtype2  387    0
  subtype3   84    1
  subtype4  256    0
  subtype5   48    0
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE      239      387       84      256       48
  MALE         10        0        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                           216
  subtype2                          0                           226
  subtype3                          0                            52
  subtype4                          1                           226
  subtype5                          0                            34
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                             19                   0
  subtype2                            113                   0
  subtype3                             27                   0
  subtype4                              7                   5
  subtype5                              9                   1
          vv
clus       MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                                4                  3              7
  subtype2                               15                 11             22
  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         216      226       52      226       34
  INFILTRATING LOBULAR CARCINOMA         19      113       27        7        9
  MEDULLARY CARCINOMA                     0        0        0        5        1
  MIXED HISTOLOGY (PLEASE SPECIFY)        4       15        5        4        1
  MUCINOUS CARCINOMA                      3       11        0        0        1
  OTHER  SPECIFY                          7       22        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  74 175
  subtype2  93 294
  subtype3  20  65
  subtype4  79 177
  subtype5  16  32
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   74  175
  subtype2   93  294
  subtype3   20   65
  subtype4   79  177
  subtype5   16   32
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        74       93       20       79       16
  YES      175      294       65      177       32
[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                                0    20                        29
  subtype2                                1    15                        51
  subtype3                                0     2                         6
  subtype4                                0    16                        65
  subtype5                                0     3                         7
          vv
clus       WHITE
  subtype1   159
  subtype2   295
  subtype3    67
  subtype4   159
  subtype5    37
D3V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0        0
  ASIAN                                  20       15        2       16        3
  BLACK OR AFRICAN AMERICAN              29       51        6       65        7
  WHITE                                 159      295       67      159       37
[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   6 193
  subtype2  16 316
  subtype3   2  64
  subtype4  10 212
  subtype5   2  41
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6  193
  subtype2   16  316
  subtype3    2   64
  subtype4   10  212
  subtype5    2   41
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            6       16        2       10        2
  NOT HISPANIC OR LATINO      193      316       64      212       41
[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 111  18
  subtype2 174  19
  subtype3 142  29
  subtype4  82   4
  subtype5 107  10
subtype1 subtype2 subtype3 subtype4 subtype5 
     129      193      171       86      117 
subtype1 subtype2 subtype3 subtype4 subtype5 
      18       19       29        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 
       24.39        26.96        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        16.57         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       111.32        11.84        65.36 
TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AN TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AY 
       85.97        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 
      101.52        78.48        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        34.92        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        14.79         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        36.36        22.32        20.38 
TCGA-OL-A66I TCGA-OL-A6VO TCGA-PL-A8LZ 
       23.47        28.21         3.95 

$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 
      136.73       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        21.14 
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-AC-A6NO TCGA-AN-A0XL TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS 
       24.79         1.68         0.33         0.30         0.33         0.33 
TCGA-AN-A0XT TCGA-AO-A03N TCGA-AO-A0JD TCGA-AO-A0JJ TCGA-AO-A125 TCGA-AO-A126 
        0.33        66.77        72.00        62.04        99.25       108.72 
TCGA-AO-A12B TCGA-AO-A12C TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AQ-A54O TCGA-AR-A0TR 
       77.56        65.56        82.62        61.87        32.91         5.26 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AS TCGA-AR-A24L TCGA-AR-A24M 
       51.25        48.82        62.56        37.81        73.02        96.89 
TCGA-AR-A24V TCGA-AR-A2LE TCGA-AR-A2LM TCGA-AR-A2LN TCGA-B6-A0RG TCGA-B6-A0RI 
       85.35       128.65        40.04        38.17        68.45       234.28 
TCGA-B6-A0RM TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WZ 
       78.02       162.05       102.77       188.68        79.63       129.57 
TCGA-B6-A0X4 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A408 
       28.27        58.88        43.59        73.51       170.17        49.94 
TCGA-BH-A0AU TCGA-BH-A0AZ TCGA-BH-A0B5 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BM 
       24.53        28.50        48.36        37.22        32.02        61.68 
TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0H0 TCGA-BH-A0H6 
       53.95        45.57        15.65         3.22        15.16        24.56 
TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HF TCGA-BH-A0HI TCGA-BH-A0HN TCGA-BH-A0W3 
       52.96        26.50        23.90        20.38        16.96        23.93 
TCGA-BH-A0W4 TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EX TCGA-BH-A1F5 TCGA-BH-A1FG 
       24.95       113.82        82.85        49.58        89.16       122.89 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FR TCGA-BH-A28Q TCGA-C8-A26W TCGA-C8-A26Z 
       63.35        55.00       144.59         6.44         0.23         8.28 
TCGA-C8-A273 TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JI TCGA-D8-A1JS 
        9.67        15.78        18.15        18.90        18.97        12.20 
TCGA-D8-A1JT TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1XB TCGA-D8-A1XC 
       13.32        17.79        16.73        25.74        18.15         2.66 
TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1Y0 
        7.96        15.85        16.31        15.16        16.54        15.52 
TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-E2-A106 TCGA-E2-A107 
       13.08        12.53        14.50        18.51        59.41        34.42 
TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       37.51        28.44        28.87        17.42        19.40         9.04 
TCGA-E2-A1B4 TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO 
       29.95        16.47        38.30         3.88        22.19        20.98 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A56Z TCGA-E2-A570 
       11.08        54.18        39.62        19.66         7.20        30.61 
TCGA-E2-A572 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1NI TCGA-E9-A1R0 TCGA-E9-A1R3 
       27.32        19.20        36.82         9.86        14.30         2.10 
TCGA-E9-A1RD TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A229 
        0.66        21.27        35.64        34.13         0.79        13.32 
TCGA-E9-A22H TCGA-E9-A245 TCGA-E9-A249 TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A54X 
       24.10         0.85         0.95        26.07        18.41        12.33 
TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IX TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 
       14.40        15.39        39.72        18.90        13.25        16.57 
TCGA-EW-A1J6 TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 
       28.77        29.85        41.13        52.96        23.11        18.48 
TCGA-EW-A1PE TCGA-EW-A2FW TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YX TCGA-LD-A66U 
       10.52        22.09        13.55        18.12        11.57        21.24 
TCGA-LD-A7W6 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A6FP TCGA-OL-A66H TCGA-OL-A66J 
        4.60        10.95         7.59        11.57        26.70        65.62 
TCGA-OL-A66O 
        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        32.75        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        50.24        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        98.93        76.14        83.87 
TCGA-AR-A0U3 TCGA-AR-A1AP TCGA-AR-A1AT TCGA-AR-A1AV TCGA-AR-A24H TCGA-AR-A24N 
      114.02        39.98        41.82        61.28       109.58        78.51 
TCGA-AR-A24R TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A255 TCGA-AR-A2LK TCGA-AR-A2LL 
       87.22        79.00        56.15        58.92        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       103.63        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-E2-A576 TCGA-E9-A1NA TCGA-E9-A1NF TCGA-E9-A1R5 
       16.93         5.52        19.00        36.56        20.05         1.38 
TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A228 
        2.76        21.21        40.24        34.65         6.58        12.53 
TCGA-E9-A247 TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A54Y TCGA-E9-A5UO TCGA-EW-A1IW 
       27.22         0.72        17.75         0.23        13.81        12.20 
TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1PA TCGA-EW-A1PC 
       15.68        25.94        29.95        40.41        18.90         6.15 
TCGA-EW-A2FS TCGA-EW-A3E8 TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GM-A2D9 
       52.73        21.27        10.16        10.59         7.40        59.57 
TCGA-GM-A2DC TCGA-GM-A2DL TCGA-GM-A3NW TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A6FQ 
       53.52        90.84       110.50        17.06        15.32         2.63 
TCGA-LL-A740 TCGA-LL-A7T0 TCGA-LQ-A4E4 TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
        4.50         3.22        27.91        33.57        31.07        26.04 
TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH 
       16.50         6.81         8.65 

$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        48.46        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        21.30        23.21 
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        22.19         1.81         0.43         0.53 
TCGA-AQ-A1H3 TCGA-AR-A1AU TCGA-AR-A24K TCGA-AR-A24P TCGA-AR-A24T TCGA-AR-A24W 
       32.52        76.21        50.89         0.85        76.01        50.96 
TCGA-AR-A24X TCGA-AR-A254 TCGA-AR-A2LJ TCGA-AR-A5QP TCGA-B6-A0RV TCGA-B6-A0WY 
       83.77        72.76        62.86        20.45       157.41       113.79 
TCGA-BH-A0B2 TCGA-BH-A0BJ TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0E1 TCGA-BH-A0GZ 
       40.83        21.70        23.44        22.13        15.68        10.78 
TCGA-BH-A0H3 TCGA-BH-A0HP TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1FH TCGA-BH-A201 
       37.78        13.61        12.00        55.69        36.92         6.90 
TCGA-BH-A202 TCGA-BH-A28O TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HI TCGA-D8-A1JH 
        0.72        10.65        12.33        10.92        11.34        14.01 
TCGA-D8-A1JP TCGA-D8-A1JU TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XL TCGA-D8-A1XM 
       21.01        14.70        17.16        14.73        19.92        17.69 
TCGA-D8-A27E TCGA-D8-A27K TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A4Z1 TCGA-E2-A14U 
       17.42         9.44         0.76        10.09         7.33        43.33 
TCGA-E2-A1IH TCGA-E2-A1L7 TCGA-E2-A1LB TCGA-E9-A1R2 TCGA-E9-A1RA TCGA-E9-A22B 
       33.73        27.42        40.47         0.62        32.09        22.75 
TCGA-E9-A24A TCGA-E9-A3X8 TCGA-EW-A1IY TCGA-EW-A1PD TCGA-EW-A2FR TCGA-GM-A2DM 
       24.56        15.72         8.48        13.94        55.00        76.64 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-LD-A74U TCGA-MS-A51U TCGA-OL-A5RV 
       38.20        43.73        66.38         6.67         2.79        34.92 
TCGA-OL-A5RX TCGA-W8-A86G 
       16.87         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 
       21.90        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        19.79        23.24         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 
      106.78         9.99        86.66        64.83        52.77        43.56 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24O TCGA-AR-A24U TCGA-AR-A252 TCGA-AR-A2LH 
       63.62        62.14        84.20        53.36        73.18        20.25 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QQ TCGA-B6-A0RT TCGA-B6-A401 TCGA-BH-A0B6 
       39.39        40.54        10.59        89.46        85.35        56.94 
TCGA-BH-A0BF TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0DV TCGA-BH-A0RX TCGA-BH-A0W5 
       25.71        41.75        48.13        45.17         5.59        42.35 
TCGA-BH-A1EU TCGA-BH-A1F0 TCGA-BH-A1FB TCGA-BH-A1FE TCGA-BH-A1FU TCGA-BH-A209 
       42.28        25.81       120.62        74.73        72.07       130.16 
TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A1HG TCGA-C8-A278 TCGA-C8-A3M7 
       20.12       109.28         8.94        11.34         0.03         0.03 
TCGA-D8-A1JB TCGA-D8-A1Y2 TCGA-D8-A27I TCGA-D8-A27L TCGA-D8-A27M TCGA-E2-A108 
       18.71        14.24        14.43        16.41        13.48        27.52 
TCGA-E2-A1B1 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1IF TCGA-E2-A1II TCGA-E2-A1IJ 
       53.03        32.35        28.50        37.41        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1LA TCGA-E2-A3DX TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1QZ 
       22.65        24.59        15.72        35.77        21.57        11.90 
TCGA-E9-A1R4 TCGA-E9-A22A TCGA-E9-A243 TCGA-E9-A248 TCGA-E9-A2JT TCGA-E9-A3QA 
        6.12        39.09        17.06         1.94         0.76         0.62 
TCGA-EW-A1IZ TCGA-EW-A1P1 TCGA-EW-A1P7 TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FV 
       18.21        39.78        30.08        14.43        34.55        25.91 
TCGA-EW-A3U0 TCGA-GM-A2DA TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI 
       17.49       194.27        43.04        42.71        42.28        61.91 
TCGA-GM-A2DK TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A4E0 TCGA-LD-A7W5 TCGA-LL-A440 
       62.33        77.33        53.36        72.03         4.08         9.53 
TCGA-LL-A441 TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A7SZ TCGA-OL-A5RU TCGA-OL-A5RY 
       11.44        14.70        14.47         5.59        27.65        24.72 
TCGA-OL-A66P TCGA-XX-A899 TCGA-XX-A89A 
       14.07         9.60         9.14 

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 
  22.320   23.900   21.210   20.665   28.440 
[1] "0.2 - 211.6 (22.3)" "0.2 - 234.3 (23.9)" "0.0 - 173.0 (21.2)"
[4] "0.4 - 157.4 (20.7)" "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        9        0        0        61        31         0
  subtype2      14       15        3        2        53        56         0
  subtype3       9       11        0        1        49        38         1
  subtype4       6       12        0        1        19        19         0
  subtype5      18       12        1        0        42        19         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  subtype1         12          2          3        3       1
  subtype2         31          6         12        1       2
  subtype3         38          8         12        3       2
  subtype4         14          1         13        1       0
  subtype5         17          1          8        0       0
D4V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           6       14        9        6       18
  STAGE IA          9       15       11       12       12
  STAGE IB          0        3        0        0        1
  STAGE II          0        2        1        1        0
  STAGE IIA        61       53       49       19       42
  STAGE IIB        31       56       38       19       19
  STAGE III         0        0        1        0        1
  STAGE IIIA       12       31       38       14       17
  STAGE IIIB        2        6        8        1        1
  STAGE IIIC        3       12       12       13        8
  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  23  89  12   4
  subtype2  55 110  24   5
  subtype3  33 100  29  10
  subtype4  25  47  13   1
  subtype5  50  55  13   1
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       23       55       33       25       50
  T2       89      110      100       47       55
  T3       12       24       29       13       13
  T4        4        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 77 35 12  4
  subtype2 67 88 22 13
  subtype3 69 55 32 12
  subtype4 35 28 10 13
  subtype5 61 36 13  9
D4V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       77       67       69       35       61
  N1       35       88       55       28       36
  N2       12       22       32       10       13
  N3        4       13       12       13        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        0 106   3  20
  subtype2        1 160   1  33
  subtype3        0 135   4  33
  subtype4        0  68   1  17
  subtype5        0  95   0  24
D4V6, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4 subtype5
  CM0 (I+)        0        1        0        0        0
  M0            106      160      135       68       95
  M1              3        1        4        1        0
  MX             20       33       33       17       24
[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 129   0
  subtype2 192   3
  subtype3 169   3
  subtype4  84   2
  subtype5 119   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  129    0
  subtype2  192    3
  subtype3  169    3
  subtype4   84    2
  subtype5  119    0
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE      129      192      169       84      119
  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                           106
  subtype2                          0                           118
  subtype3                          0                           126
  subtype4                          0                            51
  subtype5                          0                            78
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                              4                   3
  subtype2                             45                   0
  subtype3                             35                   0
  subtype4                             30                   0
  subtype5                             33                   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         106      118      126       51       78
  INFILTRATING LOBULAR CARCINOMA          4       45       35       30       33
  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  85
  subtype2  60 135
  subtype3  54 118
  subtype4  23  63
  subtype5  34  85
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   44   85
  subtype2   60  135
  subtype3   54  118
  subtype4   23   63
  subtype5   34   85
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        44       60       54       23       34
  YES       85      135      118       63       85
[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                        45
  subtype2                                0     8                        20
  subtype3                                0    12                        26
  subtype4                                0     4                         8
  subtype5                                1     5                        20
          vv
clus       WHITE
  subtype1    76
  subtype2   164
  subtype3   130
  subtype4    73
  subtype5    90
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              45       20       26        8       20
  WHITE                                  76      164      130       73       90
[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   6 109
  subtype2  10 167
  subtype3  11 147
  subtype4   2  74
  subtype5   6 104
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6  109
  subtype2   10  167
  subtype3   11  147
  subtype4    2   74
  subtype5    6  104
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            6       10       11        2        6
  NOT HISPANIC OR LATINO      109      167      147       74      104
[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 102  14
subtype1 subtype2 subtype3 
     147      133      116 
subtype1 subtype2 subtype3 
      25       13       14 
$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        43.00         9.99        45.07 
TCGA-A8-A09M TCGA-A8-A09R TCGA-A8-A09X TCGA-A8-A0A7 TCGA-AN-A04D TCGA-AN-A0AK 
       33.07         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       111.32        49.32        74.79        86.66 
TCGA-AR-A0TU TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0U0 TCGA-AR-A0U1 
       11.84        29.75        98.93        55.86        65.36       101.95 
TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AO TCGA-AR-A1AQ TCGA-AR-A1AT 
      114.02        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 
       33.01         9.99        12.00         1.02        49.05         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       108.72        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        37.81        61.28 
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        48.46 
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        50.24        62.04        71.80 
TCGA-AO-A128 TCGA-AO-A12E TCGA-AQ-A04L TCGA-AR-A0TX TCGA-AR-A0TZ TCGA-AR-A0U2 
      106.78        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 
       85.97        52.77        48.82        39.98        76.21        63.62 
TCGA-AR-A1AX TCGA-B6-A0I2 TCGA-B6-A0I8 TCGA-B6-A0IK TCGA-B6-A0RG TCGA-B6-A0RH 
       62.14       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 
   29.03    26.24    33.78 
[1] "0.1 - 186.5 (29.0)" "0.2 - 146.5 (26.2)" "0.3 - 189.0 (33.8)"
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        1 113   4   2
D5V6, multiclass
          clus
vv         subtype1 subtype2 subtype3
  CM0 (I+)        0        0        1
  M0            145      128      113
  M1              8        3        4
  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 98 11
  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       11       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        49.05         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        37.81        61.28        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        48.46        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        76.21        63.62        62.14       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 
      106.78        96.10        48.36       111.32        74.79        11.84 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
       65.36       101.95        83.87        85.97        75.55        61.84 
TCGA-AR-A1AJ TCGA-AR-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        33.01         9.99        33.07 
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        50.24        62.04       108.72        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        86.66        29.75        98.93        55.86 
TCGA-AR-A0U3 TCGA-AR-A1AP TCGA-B6-A0IB TCGA-B6-A0RG TCGA-BH-A0B4 TCGA-BH-A0BF 
      114.02        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        43.00        45.07         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   31.000   31.730   27.810   27.860 
[1] "0.3 - 129.7 (28.4)" "0.2 - 173.0 (31.0)" "0.3 - 189.0 (31.7)"
[4] "0.2 - 129.6 (27.8)" "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        1 104   4   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      104       89      105       30
  M1              2        4        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 443  66
  subtype2 247  41
  subtype3 207  15
subtype1 subtype2 subtype3 
     509      288      222 
subtype1 subtype2 subtype3 
      66       41       15 
$subtype1
TCGA-5T-A9QA TCGA-A1-A0SG TCGA-A1-A0SI TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SQ 
        0.39        14.27        20.88         7.96        39.32        18.21 
TCGA-A2-A04N TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CQ 
      104.81        82.16        63.12        55.43        36.13        88.60 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0D3 TCGA-A2-A0D4 
       75.55        75.25         5.19        64.04        28.77        25.22 
TCGA-A2-A0EM TCGA-A2-A0ER TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EY 
      101.72        74.40        35.05        34.29        31.82        24.16 
TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 
       54.64        27.12        44.88        18.71        20.52        17.46 
TCGA-A2-A0YC TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YT TCGA-A2-A1FV 
       32.55        15.42        21.90        21.67        23.77        23.47 
TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1G4 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25E 
       17.36        36.79        19.56        16.31        17.19        91.92 
TCGA-A2-A4RW TCGA-A2-A4S0 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CH TCGA-A7-A0CJ 
        7.30        23.21        21.90        38.30        35.47        30.61 
TCGA-A7-A0D9 TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A26E TCGA-A7-A26H TCGA-A7-A26J 
       37.45        12.72        23.61        31.36        23.80        20.61 
TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A4SB 
       22.32        11.34        10.59        10.29        13.41        13.74 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q 
       17.92        14.73        10.42        13.02        13.02         1.02 
TCGA-A8-A06T TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 
       53.06        31.00        26.01         1.02        17.03        53.98 
TCGA-A8-A079 TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
        9.01        18.97        18.97        14.01        12.00        17.03 
TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A082 TCGA-A8-A084 
       10.98         7.99         9.99        28.04        18.05        15.06 
TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G 
       36.95        13.02         0.99        28.96        33.01        19.96 
TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z 
       12.00        37.05        31.00        33.01        93.04        40.01 
TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 
       33.01        30.97        17.95        41.98        12.00         9.99 
TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K 
       12.00         1.02        50.04        49.05        45.07        29.98 
TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       33.07         1.02        25.02         8.98        19.04        15.02 
TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD 
        0.99        12.00        19.04        13.02        17.03        38.04 
TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FM TCGA-AC-A3TN 
        0.95         2.37         1.48        38.20        26.04         1.12 
TCGA-AC-A3W6 TCGA-AC-A3YJ TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6NO TCGA-AC-A8OR 
       19.79        24.79         0.07         1.81         1.68         1.32 
TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A 
        0.33         0.33         0.23         0.33         0.62         2.96 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FT 
        8.02         7.36         6.44         4.64         7.00         6.02 
TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR 
        0.36         0.33         0.33        12.33         0.30         0.33 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03N 
        0.33         0.33         5.33         5.59        80.28        66.77 
TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03T TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J5 
       81.63        84.69        47.87        29.13        21.40        24.16 
TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0JA TCGA-AO-A0JI TCGA-AO-A0JM TCGA-AO-A125 
       20.32        22.36        21.53        50.24        71.80        99.25 
TCGA-AO-A126 TCGA-AO-A12B TCGA-AO-A12C TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KP 
      108.72        77.56        65.56        41.62        28.37        82.62 
TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A0Y5 TCGA-AQ-A1H2 
       61.87         0.53        17.79        24.79         5.65        15.62 
TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TV 
       32.52        32.91        49.32         5.26        86.66        29.75 
TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AN 
       98.93        55.86        76.14        83.87       114.02        43.73 
TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A24H TCGA-AR-A24K 
       39.98        37.81        61.28        63.62       109.58        50.89 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24V 
       73.02        96.89        78.51         0.85        87.22        85.35 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A2LE TCGA-AR-A2LK TCGA-AR-A2LL 
       83.77        79.00        56.15       128.65        42.87         7.36 
TCGA-B6-A0I5 TCGA-B6-A0I8 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IG 
      149.59        24.62       220.90       129.57        50.70       146.50 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
      126.12        84.59       110.14        68.45       189.01       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0WS 
       81.17        78.02       172.96       162.05       102.77        97.48 
TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 
      188.68        79.63        17.98       129.57       129.70        28.27 
TCGA-B6-A0X5 TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A408 
       68.94        43.59        73.51       170.17        85.35        49.94 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AY TCGA-BH-A0B1 TCGA-BH-A0B4 
      103.63        55.00        24.53        25.55        37.74        39.16 
TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B8 TCGA-BH-A0BD TCGA-BH-A0BR TCGA-BH-A0BS 
       48.36        56.94        51.58        18.21        53.69        53.95 
TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0C1 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DH 
       45.57        49.94        44.02        42.90        45.83        38.01 
TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0EB 
        3.22         2.56        15.68        14.30        44.81        24.49 
TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 
       24.43        10.78        15.16        24.56        23.08        41.00 
TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HL TCGA-BH-A0HN TCGA-BH-A0HO 
       52.96        26.50        20.38         2.37        16.96         2.50 
TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0W3 
       36.85        12.89        51.32        27.25        50.79        23.93 
TCGA-BH-A0W7 TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18P 
       44.81        20.12        90.84        26.66        37.74        30.28 
TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET 
       66.05        51.39        69.93        91.99       113.82        82.85 
TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EY TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F8 
       12.00        55.69        17.69        31.53        89.16        24.66 
TCGA-BH-A1FD TCGA-BH-A1FG TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR 
       33.17       122.89        63.35        55.00        45.63       144.59 
TCGA-BH-A204 TCGA-BH-A28Q TCGA-BH-A42T TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O 
       83.31         6.44         0.99        11.77        11.77        12.66 
TCGA-C8-A12U TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A138 TCGA-C8-A1HE 
       12.66        12.66        12.66         3.12         3.75        12.33 
TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W 
       11.34        11.34        10.42         3.25         0.30         0.23 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A27A TCGA-C8-A3M8 TCGA-D8-A140 
        8.28         9.67         0.03        12.20         0.23        13.25 
TCGA-D8-A141 TCGA-D8-A1J9 TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JI 
       20.58        17.49        15.78        18.15        18.90        18.97 
TCGA-D8-A1JJ TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1X5 
       20.09        20.38        21.01        12.20        13.32        18.58 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC 
       17.79        16.73        23.90        27.58        18.15         2.66 
TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XL TCGA-D8-A1XO TCGA-D8-A1XR 
       17.16        15.22        14.73        19.92         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-A1Y2 TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27N TCGA-D8-A27R 
        3.81        14.24        17.42        13.45         4.80        10.09 
TCGA-D8-A27T TCGA-D8-A27W TCGA-D8-A3Z6 TCGA-E2-A105 TCGA-E2-A106 TCGA-E2-A107 
       13.08        12.26        18.51        43.00        59.41        34.42 
TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F 
       46.59        40.41        37.51        40.11        28.44        28.87 
TCGA-E2-A14O TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A153 
       44.68        33.17        33.30        34.26        32.02        23.24 
TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D 
       19.43        21.04        23.87        23.34        22.82        17.29 
TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       21.63        18.21        12.92        19.40         9.04        20.58 
TCGA-E2-A15O TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B4 TCGA-E2-A1BD 
       13.02        17.06        14.07        14.99        29.95        17.10 
TCGA-E2-A1IE TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN 
       38.30        32.78        33.73        22.65         3.88        22.19 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A2P5 
       27.42        39.62        19.66        24.59        40.47        16.93 
TCGA-E2-A2P6 TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A572 TCGA-E2-A576 TCGA-E2-A9RU 
        5.52         7.20        30.61        27.32        19.00         9.21 
TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1NA TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI 
       36.82        13.48        36.56        20.05        21.57         9.86 
TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 
        0.62         2.10         6.12         1.38         2.76        21.21 
TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF 
       32.09        20.81        40.24         0.66        34.65         6.58 
TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       21.27        35.64        34.13        12.53        13.32        39.09 
TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A249 
       22.75        12.89        24.10         0.85        27.22         0.95 
TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A54X 
       24.56         0.72        17.75        26.07        18.41        12.33 
TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
       13.81        14.40        15.39        39.72         8.48        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OX TCGA-EW-A1OY 
       18.90        16.57        15.68        28.77        29.95        29.85 
TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1PA 
       40.41        41.13        52.96        23.11        18.48        18.90 
TCGA-EW-A1PE TCGA-EW-A2FW TCGA-EW-A423 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GM-A2D9 
       10.52        22.09        10.16        10.59         7.40        59.57 
TCGA-GM-A2DC TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-JL-A3YX 
       53.52        90.84        76.64        77.33        53.36        11.57 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A6FP TCGA-LL-A6FQ 
       10.95         7.59        15.32        14.70        11.57         2.63 
TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OL-A5D8 TCGA-OL-A5DA 
        5.59         3.22         7.36        27.91        31.99        58.62 
TCGA-OL-A66H TCGA-OL-A66K TCGA-OL-A66O TCGA-PL-A8LX TCGA-S3-A6ZF TCGA-S3-A6ZG 
       26.70        33.57         7.23         0.16        16.50         6.81 
TCGA-S3-A6ZH TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA17 TCGA-Z7-A8R6 
        8.65         5.56         8.52         3.91       105.04 

$subtype2
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-A04W TCGA-A2-A0CM TCGA-A2-A0CX TCGA-A2-A0CY 
       73.84        22.06        64.04        24.79        56.81        55.00 
TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0EQ TCGA-A2-A0ST TCGA-A2-A0SX 
       21.14        34.55        33.76        79.76        99.19        50.43 
TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T7 TCGA-A2-A0YE TCGA-A2-A0YJ 
       17.52        17.13         8.38        20.75        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-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 
       32.75        49.48        38.40        34.98        31.99        38.37 
TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A7-A0CE TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E 
       24.39        26.96        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-A06R TCGA-A8-A06U TCGA-A8-A07B 
       10.29         9.37         8.75        17.98        29.03        43.00 
TCGA-A8-A07C TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A08B TCGA-A8-A08L 
       33.99         9.99         8.98        24.99        38.01         9.99 
TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A09X TCGA-A8-A0A7 TCGA-AC-A23H TCGA-AC-A2BK 
        0.99        43.00        14.01         0.99         2.66        38.53 
TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A3W5 TCGA-AC-A62X TCGA-AC-A6IW TCGA-AC-A8OQ 
        1.02         2.27        16.57         1.12         0.69         1.12 
TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS 
        1.78         1.71         6.51         0.16         0.33         0.33 
TCGA-AN-A0AT TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0G0 
        0.33         7.96         7.59         0.33         0.33         0.53 
TCGA-AN-A0XN TCGA-AN-A0XU TCGA-AO-A03M TCGA-AO-A03U TCGA-AO-A0J2 TCGA-AO-A0J4 
        0.33         0.33        47.84        59.05        32.78        52.18 
TCGA-AO-A0J6 TCGA-AO-A0JB TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JL TCGA-AO-A124 
       37.48        50.70        72.00        76.77        55.33       102.58 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A1KR TCGA-AQ-A04J 
      106.78        96.10        64.04        48.36        70.39        26.93 
TCGA-AQ-A04L TCGA-AQ-A54N TCGA-AR-A0TP TCGA-AR-A0TS TCGA-AR-A0TU TCGA-AR-A0TX 
      130.09         2.56       111.32        74.79        11.84        64.83 
TCGA-AR-A0U0 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AO 
       65.36        85.97        75.55        61.84        52.77        43.56 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AT TCGA-AR-A1AY TCGA-AR-A24Q TCGA-AR-A24U 
       43.07        17.23        41.82        20.22       101.52        53.36 
TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LR TCGA-AR-A5QQ TCGA-B6-A0I1 
       78.48        72.76        93.83        20.38        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I6 TCGA-B6-A0I9 TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IQ 
      143.38        32.78        12.13       176.98        18.77       140.88 
TCGA-B6-A0RE TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0WX TCGA-B6-A0X1 
      211.56       100.70        89.46       131.21        21.47       186.48 
TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A402 TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0B3 
      101.52       139.17        54.28        38.79        20.45        39.55 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BW 
       56.98        51.68        25.71        24.85        44.05        11.67 
TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0DL TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E6 
       49.05        41.75        48.23        16.27         4.41         9.63 
TCGA-BH-A0EE TCGA-BH-A0GY TCGA-BH-A0RX TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18Q 
       31.00        30.35         5.59        23.05         2.01        55.63 
TCGA-BH-A18R TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1F6 
       37.55         7.36        51.16        49.58        25.81        97.48 
TCGA-BH-A1FC TCGA-BH-A1FN TCGA-BH-A1FU TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 
      114.15        72.07        72.07         0.72        38.60        57.83 
TCGA-BH-A209 TCGA-C8-A12L TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12V TCGA-C8-A131 
      130.16        11.93        11.77         0.07        12.66         1.78 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HF TCGA-C8-A1HJ 
        1.45         0.69         0.62         3.85        10.92         0.16 
TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A275 TCGA-C8-A278 
       12.03         2.30         0.36         0.43         0.03         0.03 
TCGA-C8-A27B TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A147 
        0.99        11.90        20.88        13.97        14.17        19.20 
TCGA-D8-A1J8 TCGA-D8-A1JA TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JK TCGA-D8-A1JL 
       14.17        16.50        12.03        12.03        20.12        20.09 
TCGA-D8-A1JM TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XQ TCGA-D8-A1XT TCGA-D8-A1XW 
       19.40        21.83        14.50        16.41         6.35        12.66 
TCGA-D8-A1Y3 TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27M TCGA-E2-A14N TCGA-E2-A14P 
       14.14        16.04        13.05        13.48        47.15        40.96 
TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A158 
       38.60        31.96        28.60        25.41        27.12        14.79 
TCGA-E2-A159 TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B6 TCGA-E2-A1II TCGA-E2-A1LE 
       25.05        60.53        53.62        28.50        33.70        28.90 
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-A1N9 TCGA-E9-A1NC TCGA-E9-A1ND 
       34.92        19.89        12.00        13.12        39.55        12.59 
TCGA-E9-A1RH TCGA-E9-A22G TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A3QA 
       34.59        23.51        17.06         0.69         1.94         0.62 
TCGA-E9-A5FL TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P7 TCGA-EW-A1P8 
        0.26        25.94        22.82        29.82        30.08         7.86 
TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A3U0 TCGA-GI-A2C9 
       19.99         6.15        19.96        55.00        17.49       109.87 
TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A3XL TCGA-JL-A3YW 
       53.13        43.04        42.71        42.28        69.30        11.84 
TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YL TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FR 
        8.75        11.44        17.06        14.47        14.79         3.88 
TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A8F5 TCGA-OL-A5D6 TCGA-OL-A5D7 
        4.14         4.50         4.50         6.21        12.66        46.55 
TCGA-OL-A5RW TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66I TCGA-OL-A66P 
       36.36        24.72        22.32        20.38        23.47        14.07 
TCGA-OL-A6VO TCGA-PL-A8LV TCGA-PL-A8LZ TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA15 
       28.21         0.23         3.95        10.59         7.92         6.87 

$subtype3
TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SH TCGA-A1-A0SJ TCGA-A2-A0CK 
       14.37        43.43        48.10        47.24        13.68       136.73 
TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CV TCGA-A2-A0CZ 
       64.57       112.08        92.48       107.93        63.45        53.13 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ES TCGA-A2-A0EW TCGA-A2-A0EX 
       89.36        80.28       107.61        37.05        29.75        24.72 
TCGA-A2-A0SY TCGA-A2-A0T6 TCGA-A2-A0YD TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL 
       44.28        18.90        25.28        14.50        19.33        48.46 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25D 
       22.45        20.25        16.47        52.47       107.70        18.15 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A4RY TCGA-A2-A4S2 TCGA-A7-A0CG TCGA-A7-A0DB 
       20.88        39.65        21.30        21.14        34.29        33.11 
TCGA-A7-A13H TCGA-A7-A3J1 TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SC 
       29.56        11.28        14.70        11.97        14.93        14.66 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A8-A07E TCGA-A8-A08O TCGA-A8-A09A TCGA-A8-A0A4 
       10.72        11.05        19.99        31.00         9.99        13.02 
TCGA-A8-A0A6 TCGA-AC-A23G TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
       21.04        10.85        40.57        55.43        36.99        38.79 
TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
       50.70         0.92         0.99         0.69        14.83        22.19 
TCGA-AC-A3YI TCGA-AC-A5XS TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A8OP TCGA-AN-A0FN 
       23.24         1.55         1.18         0.43         1.74         7.17 
TCGA-AN-A0FS TCGA-AN-A0XL TCGA-AO-A03R TCGA-AO-A0J9 TCGA-AO-A0JC TCGA-AO-A0JF 
        6.28         0.33        68.75        53.03        50.86        21.37 
TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A12A TCGA-AO-A12E TCGA-AO-A1KO TCGA-AQ-A7U7 
       26.24        62.04        90.58        57.30        14.73         9.99 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AU TCGA-AR-A1AX TCGA-AR-A24O 
       51.25        48.82        62.56        76.21        62.14        84.20 
TCGA-AR-A24T TCGA-AR-A24W TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A2LH TCGA-AR-A2LJ 
       76.01        50.96        73.18        58.92        20.25        62.86 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN 
       40.04        38.17        39.39        40.54        54.74        16.04 
TCGA-AR-A5QP TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IP TCGA-B6-A0RQ TCGA-B6-A0RV 
       20.45        65.72       112.37       110.93       140.48       157.41 
TCGA-B6-A0WY TCGA-B6-A0X7 TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0BA TCGA-BH-A0BC 
      113.79        58.88        28.50        46.95        37.22        32.02 
TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0C3 
       21.70        61.68        35.67        48.69        27.19        48.13 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DP 
       31.17        23.44        22.13        13.91        17.26        15.65 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0H3 
       38.47        45.17        47.41        46.19        32.65        37.78 
TCGA-BH-A0H5 TCGA-BH-A0HF TCGA-BH-A0HK TCGA-BH-A0HP TCGA-BH-A0W4 TCGA-BH-A0W5 
       35.51        23.90         5.85        13.61        24.95        42.35 
TCGA-BH-A18F TCGA-BH-A18I TCGA-BH-A18M TCGA-BH-A1EU TCGA-BH-A1FB TCGA-BH-A1FE 
        8.81         7.23        72.56        42.28       120.62        74.73 
TCGA-BH-A1FH TCGA-BH-A201 TCGA-BH-A28O TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V 
       36.92         6.90        10.65        20.12       109.28         8.94 
TCGA-C8-A3M7 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1JB TCGA-D8-A1JH TCGA-D8-A1JU 
        0.03        13.48        21.14        18.71        14.01        14.70 
TCGA-D8-A1X8 TCGA-D8-A1XM TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27P 
       25.74        17.69        14.43         9.44        16.41         0.76 
TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A4Z1 TCGA-E2-A108 TCGA-E2-A14Q TCGA-E2-A14U 
       12.53        14.50         7.33        27.52        38.24        43.33 
TCGA-E2-A14Z TCGA-E2-A15E TCGA-E2-A15I TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A1B1 
       17.03        20.71        17.42         7.73        19.56        53.03 
TCGA-E2-A1B5 TCGA-E2-A1BC TCGA-E2-A1IF TCGA-E2-A1IJ TCGA-E2-A1IO TCGA-E2-A1IU 
       32.35        16.47        37.41        28.44        20.98        11.08 
TCGA-E2-A1L6 TCGA-E2-A3DX TCGA-E9-A1N4 TCGA-E9-A1NE TCGA-E9-A1QZ TCGA-E9-A1R0 
       54.18        15.72        19.20        35.77        11.90        14.30 
TCGA-E9-A227 TCGA-E9-A2JT TCGA-E9-A3X8 TCGA-E9-A5FK TCGA-EW-A1IW TCGA-EW-A1J2 
        0.79         0.76        15.72        14.70        12.20        13.25 
TCGA-EW-A1P1 TCGA-EW-A1PD TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FS TCGA-EW-A2FV 
       39.78        13.94        14.43        34.55        52.73        25.91 
TCGA-EW-A3E8 TCGA-GM-A2DA TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A3NW TCGA-GM-A3NY 
       21.27       194.27        61.91        62.33       110.50        38.20 
TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-LD-A66U 
       43.73        66.38        72.03        13.55        18.12        21.24 
TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LL-A440 TCGA-MS-A51U TCGA-OK-A5Q2 
        6.67         4.08         4.60         9.53         2.79         2.10 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66N 
       27.65        34.92        16.87        65.62        31.07        26.04 
TCGA-PL-A8LY TCGA-S3-AA14 TCGA-W8-A86G TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
        0.26         7.17         5.29         9.60         9.14       100.01 

subtype1 subtype2 subtype3 
    0.03     0.03     0.03 
subtype1 subtype2 subtype3 
  234.28   211.56   194.27 
subtype1 subtype2 subtype3 
   21.90    22.57    25.51 
[1] "0.0 - 234.3 (21.9)" "0.0 - 211.6 (22.6)" "0.0 - 194.3 (25.5)"
D7V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1      42       36        7        1       171       118         1
  subtype2      16       25        0        1       127        65         0
  subtype3      25       22        3        3        49        55         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
  subtype1         80         22         25       11         0      10
  subtype2         30          6         12        5         0       4
  subtype3         32          1         26        2         1       3
D7V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          42       16       25
  STAGE IA         36       25       22
  STAGE IB          7        0        3
  STAGE II          1        1        3
  STAGE IIA       171      127       49
  STAGE IIB       118       65       55
  STAGE III         1        0        1
  STAGE IIIA       80       30       32
  STAGE IIIB       22        6        1
  STAGE IIIC       25       12       26
  STAGE IV         11        5        2
  STAGE TIS         0        0        1
  STAGE X          10        4        3
[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 131 312  53  27
  subtype2  66 188  27  10
  subtype3  74 101  45   2
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1      131       66       74
  T2      312      188      101
  T3       53       27       45
  T4       27       10        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"
          vv
clus        N0  N1  N2  N3
  subtype1 229 182  68  32
  subtype2 161  89  25  13
  subtype3  99  73  20  29
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0      229      161       99
  N1      182       89       73
  N2       68       25       20
  N3       32       13       29
[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        1 444  12  67
  subtype2        1 251   5  35
  subtype3        3 173   2  45
D7V6, multiclass
          clus
vv         subtype1 subtype2 subtype3
  CM0 (I+)        1        1        3
  M0            444      251      173
  M1             12        5        2
  MX             67       35       45
[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"
D7V7, binary
          cls
clus         0   1
  subtype1 514  10
  subtype2 292   0
  subtype3 222   1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  514   10
  subtype2  292    0
  subtype3  222    1
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      514      292      222
  MALE         10        0        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 CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  subtype1                          0                           405
  subtype2                          1                           257
  subtype3                          0                           106
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                             64                   0
  subtype2                              7                   6
  subtype3                            104                   0
          vv
clus       MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                               17                 14             24
  subtype2                                2                  0             18
  subtype3                               10                  1              2
D7V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  INFILTRATING CARCINOMA NOS              0        1        0
  INFILTRATING DUCTAL CARCINOMA         405      257      106
  INFILTRATING LOBULAR CARCINOMA         64        7      104
  MEDULLARY CARCINOMA                     0        6        0
  MIXED HISTOLOGY (PLEASE SPECIFY)       17        2       10
  MUCINOUS CARCINOMA                     14        0        1
  OTHER  SPECIFY                         24       18        2
[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"
D7V9, binary
          cls
clus         0   1
  subtype1 150 374
  subtype2  79 213
  subtype3  56 167
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  150  374
  subtype2   79  213
  subtype3   56  167
     clus
vv    subtype1 subtype2 subtype3
  NO       150       79       56
  YES      374      213      167
[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"
D7V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    31                        62
  subtype2                                1    22                        77
  subtype3                                0     4                        21
          vv
clus       WHITE
  subtype1   364
  subtype2   173
  subtype3   189
D7V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0
  ASIAN                                  31       22        4
  BLACK OR AFRICAN AMERICAN              62       77       21
  WHITE                                 364      173      189
[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"
D7V12, binary
          cls
clus         0   1
  subtype1  21 400
  subtype2   7 245
  subtype3   8 187
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21  400
  subtype2    7  245
  subtype3    8  187
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           21        7        8
  NOT HISPANIC OR LATINO      400      245      187
[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(8) Variable = MRNASEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2        0   1
  subtype1 183  26
  subtype2 124  30
  subtype3 266  20
  subtype4 121  14
  subtype5 158  22
  subtype6  45  10
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
     209      154      286      135      180       55 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      26       30       20       14       22       10 
$subtype1
TCGA-5T-A9QA TCGA-A1-A0SG TCGA-A1-A0SJ TCGA-A2-A04N TCGA-A2-A04R TCGA-A2-A04V 
        0.39        14.27        13.68       104.81        82.16        63.12 
TCGA-A2-A0CU TCGA-A2-A0D4 TCGA-A2-A0ER TCGA-A2-A0SU TCGA-A2-A0T3 TCGA-A2-A0YC 
        5.19        25.22        74.40        54.64        18.71        32.55 
TCGA-A2-A0YF TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1G4 TCGA-A2-A25C 
       15.42        23.47        17.36        36.79        19.56        17.19 
TCGA-A2-A25E TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A13F TCGA-A7-A26J 
       91.92        38.30        30.61        37.45        12.72        20.61 
TCGA-A7-A2KD TCGA-A7-A3IZ TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06T TCGA-A8-A06U 
       22.32        10.59        13.02        13.02        53.06        29.03 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A07Z 
       26.01         1.02         9.01        17.03        10.98        28.04 
TCGA-A8-A082 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08G TCGA-A8-A08Z TCGA-A8-A091 
       18.05        36.95        13.02        19.96        40.01        33.01 
TCGA-A8-A093 TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09K 
       17.95        12.00         1.02        50.04        49.05        29.98 
TCGA-A8-A09M TCGA-A8-A09T TCGA-A8-A0A9 TCGA-AC-A23E TCGA-AC-A2BM TCGA-AC-A2FM 
       33.07        19.04        13.02         2.37        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-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XR TCGA-AO-A03P TCGA-AO-A03V 
        0.36         0.33         0.33         0.33        84.69        29.13 
TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0JI TCGA-AO-A126 TCGA-AO-A12C TCGA-AO-A1KP 
       21.40        24.16        50.24       108.72        65.56        82.62 
TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A1H2 TCGA-AQ-A54O 
       61.87         0.53        17.79        24.79        15.62        32.91 
TCGA-AR-A0TV TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AS 
       29.75        55.86        76.14        83.87       114.02        37.81 
TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24R TCGA-AR-A24V TCGA-AR-A24Z TCGA-AR-A2LK 
       50.89        73.02        87.22        85.35        79.00        42.87 
TCGA-AR-A2LL TCGA-B6-A0IB TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0RL 
        7.36       129.57       126.12        84.59       110.14        81.17 
TCGA-B6-A0RM TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WZ TCGA-B6-A1KC TCGA-BH-A0AU 
       78.02       188.68        79.63       129.57        43.59        24.53 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0E7 TCGA-BH-A0EI TCGA-BH-A0H0 
       42.90        45.83        31.17        44.81        24.43        15.16 
TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HL TCGA-BH-A0HW TCGA-BH-A18L 
       24.56        41.00        52.96         2.37        51.32        26.66 
TCGA-BH-A18N TCGA-BH-A1ES TCGA-BH-A1F5 TCGA-BH-A1FD TCGA-BH-A1FG TCGA-BH-A204 
       37.74       113.82        89.16        33.17       122.89        83.31 
TCGA-BH-A42T TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12X TCGA-C8-A1HG TCGA-C8-A1HI 
        0.99        11.77        11.77        12.66        11.34        11.34 
TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A27A 
       10.42         3.25         0.30         8.28         9.67        12.20 
TCGA-C8-A3M8 TCGA-D8-A140 TCGA-D8-A1JD TCGA-D8-A1JT TCGA-D8-A1X5 TCGA-D8-A1X6 
        0.23        13.25        18.15        13.32        18.58        17.79 
TCGA-D8-A1XA TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1Y1 
       27.58        17.16        15.22        16.31        12.99         3.81 
TCGA-D8-A27W TCGA-E2-A105 TCGA-E2-A106 TCGA-E2-A109 TCGA-E2-A14O TCGA-E2-A14S 
       12.26        43.00        59.41        46.59        44.68        33.17 
TCGA-E2-A14T TCGA-E2-A14W TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A15F 
       33.30        32.02        23.24        19.43        21.04        21.63 
TCGA-E2-A15H TCGA-E2-A15J TCGA-E2-A15O TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
       12.92        19.40        13.02        17.06        14.07        14.99 
TCGA-E2-A1IE TCGA-E2-A1IG TCGA-E2-A1IN TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA 
       38.30        32.78        22.19        27.42        19.66        24.59 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A576 TCGA-E9-A1N5 TCGA-E9-A1NG TCGA-E9-A1NI 
        7.20        30.61        19.00        36.82        21.57         9.86 
TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RC 
        0.62         2.10         1.38         2.76        21.21        40.24 
TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A228 TCGA-E9-A229 
       34.65        21.27        35.64        34.13        12.53        13.32 
TCGA-E9-A22B TCGA-E9-A247 TCGA-E9-A2JS TCGA-E9-A3HO TCGA-E9-A5UP TCGA-EW-A1J1 
       22.75        27.22        17.75        26.07        14.40        18.90 
TCGA-EW-A1J6 TCGA-EW-A1P0 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1PA TCGA-EW-A1PD 
       28.77        41.13        23.11        18.48        18.90        13.94 
TCGA-EW-A2FS TCGA-EW-A2FW TCGA-GM-A2DC TCGA-GM-A2DK TCGA-LL-A5YM TCGA-LL-A7T0 
       52.73        22.09        53.52        62.33        15.32         3.22 
TCGA-OL-A5D8 TCGA-OL-A66O TCGA-S3-AA11 TCGA-S3-AA12 TCGA-Z7-A8R6 
       31.99         7.23         5.56         8.52       105.04 

$subtype2
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-A0CW TCGA-A2-A0CX TCGA-A2-A0CY TCGA-A2-A0D1 TCGA-A2-A0EV 
       36.13        64.04        56.81        55.00        34.55        31.82 
TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YT TCGA-A2-A25B 
       27.12        44.88        21.90        21.67        23.77        16.31 
TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A26H TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A6VX 
       26.96        21.90        23.80        17.92        14.73        10.42 
TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07B 
        1.02        17.98        31.00        17.03        53.98        43.00 
TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07W TCGA-A8-A084 TCGA-A8-A08B TCGA-A8-A08F 
       18.97        14.01         9.99        15.06        38.01        33.01 
TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A092 
       37.05         9.99        31.00        33.01        93.04        30.97 
TCGA-A8-A097 TCGA-A8-A09I TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09W TCGA-AC-A23C 
       12.00        45.07         1.02         8.98         0.99         0.95 
TCGA-AC-A23H TCGA-AC-A2QH TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0AS 
        2.66         1.02         8.02         7.36         0.16         0.33 
TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XW TCGA-AO-A03N 
        6.02         0.33         0.33        12.33         5.59        66.77 
TCGA-AO-A03O TCGA-AO-A0JM TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AR-A0TW TCGA-AR-A1AT 
       81.63        71.80       130.09         5.65        98.93        41.82 
TCGA-AR-A24H TCGA-AR-A250 TCGA-AR-A254 TCGA-B6-A0I8 TCGA-B6-A0I9 TCGA-B6-A0IG 
      109.58        56.15        72.76        24.62        12.13       146.50 
TCGA-B6-A0RH TCGA-B6-A0RO TCGA-B6-A0WW TCGA-B6-A1KN TCGA-B6-A408 TCGA-B6-A40B 
      189.01       162.05        17.98       139.17        49.94       103.63 
TCGA-BH-A0B4 TCGA-BH-A0BR TCGA-BH-A0BT TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0DZ 
       39.16        53.69        45.57        49.05        44.02        16.27 
TCGA-BH-A0H7 TCGA-BH-A0HU TCGA-BH-A0HY TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18P 
       23.08        12.89        50.79        20.12        90.84        30.28 
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-A1F8 TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A202 TCGA-C8-A12O TCGA-C8-A12P 
       24.66        45.63        72.07         0.72        12.66        11.77 
TCGA-C8-A12U TCGA-C8-A12W TCGA-C8-A130 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HF 
       12.66        12.66         3.12         3.85         3.75        10.92 
TCGA-C8-A1HM TCGA-C8-A274 TCGA-D8-A13Y TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA 
        2.30         0.03        11.90        14.17        17.49        16.50 
TCGA-D8-A1JC TCGA-D8-A1JJ TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1X9 TCGA-D8-A1XJ 
       15.78        20.09        20.38        21.01        23.90        21.83 
TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y3 TCGA-D8-A27N TCGA-D8-A27R TCGA-E2-A107 
       16.54        15.32        14.14         4.80        10.09        34.42 
TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A14V TCGA-E2-A152 TCGA-E2-A15A TCGA-E2-A2P5 
       40.11        28.44        34.26        27.12        23.34        16.93 
TCGA-E2-A9RU TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NF TCGA-E9-A1R4 
        9.21        13.48        13.12        36.56        20.05         6.12 
TCGA-E9-A1RB TCGA-E9-A1RF TCGA-E9-A22A TCGA-E9-A22E TCGA-EW-A1OY TCGA-EW-A1PC 
       20.81         6.58        39.09        12.89        29.85         6.15 
TCGA-EW-A2FR TCGA-EW-A423 TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-JL-A3YX TCGA-LL-A6FP 
       55.00        10.16         7.40        59.57        11.57        11.57 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OL-A5RZ TCGA-S3-A6ZF 
        7.36        27.91        22.32        16.50 

$subtype3
TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SH TCGA-A2-A0CK TCGA-A2-A0CL 
       14.37        43.43        48.10        47.24       136.73        64.57 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CZ 
      112.08        92.48       107.93        75.25        63.45        53.13 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ES TCGA-A2-A0EU 
       89.36        80.28       107.61        79.76        37.05        34.29 
TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0SY TCGA-A2-A0T4 TCGA-A2-A0T6 TCGA-A2-A0T7 
       29.75        24.72        44.28        20.52        18.90        20.75 
TCGA-A2-A0YD TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G6 
       25.28        19.33        48.46        22.45        20.25        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25D TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XW 
       52.47       107.70        18.15        20.88        39.65        49.48 
TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S2 TCGA-A7-A0CG TCGA-A7-A0DB TCGA-A7-A13H 
        7.30        21.30        21.14        34.29        33.11        29.56 
TCGA-A7-A26E TCGA-A7-A3J1 TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB 
       31.36        11.28        14.70        11.97        14.93        13.74 
TCGA-A7-A4SC TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A8-A07E TCGA-A8-A07J TCGA-A8-A08I 
       14.66        10.72        11.05        19.99        12.00        12.00 
TCGA-A8-A08O TCGA-A8-A09A TCGA-A8-A09Q TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 
       31.00         9.99        25.02        12.00        19.04        13.02 
TCGA-A8-A0A6 TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG 
       21.04        10.85         1.48        40.57        55.43        36.99 
TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD 
       38.79        50.70         0.92         0.99         0.69        14.83 
TCGA-AC-A3QP TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A5XS TCGA-AC-A6IV TCGA-AC-A6IX 
       22.19        19.79        23.24         1.55         1.18         0.43 
TCGA-AC-A8OP TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0XL 
        1.74         0.33         0.62         7.17         6.28         0.33 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03R TCGA-AO-A03T 
        0.33         0.33        80.28        47.84        68.75        47.87 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JF 
       53.03        21.53        50.70        50.86        72.00        21.37 
TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A12A TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A1KO 
       26.24        62.04        90.58        57.30        41.62        14.73 
TCGA-AQ-A7U7 TCGA-AR-A0TQ TCGA-AR-A0TT TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM 
        9.99        49.32        86.66        51.25        48.82        62.56 
TCGA-AR-A1AN TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24O TCGA-AR-A24T 
       43.73        76.21        63.62        62.14        84.20        76.01 
TCGA-AR-A24W TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN 
       50.96        73.18        58.92        62.86        40.04        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0IE 
       39.39        40.54        54.74        16.04        20.45        65.72 
TCGA-B6-A0IH TCGA-B6-A0IP TCGA-B6-A0RG TCGA-B6-A0RI TCGA-B6-A0RQ TCGA-B6-A0RV 
      112.37       110.93        68.45       234.28       140.48       157.41 
TCGA-B6-A0WS TCGA-B6-A0WY TCGA-B6-A0X0 TCGA-B6-A0X7 TCGA-B6-A2IU TCGA-B6-A401 
       97.48       113.79       129.70        58.88       170.17        85.35 
TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B1 TCGA-BH-A0B6 TCGA-BH-A0B8 
       25.55        28.50        46.95        37.74        56.94        51.58 
TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BM 
       37.22        32.02        18.21        25.71        21.70        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0DG 
       35.67        48.69        27.19        41.75        48.13        23.44 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ 
       38.01        22.13        13.91        17.26        15.65         3.22 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0E2 TCGA-BH-A0E9 TCGA-BH-A0EA 
       38.47        45.17        47.41        14.30        46.19        32.65 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0HB TCGA-BH-A0HF 
       30.35        10.78        37.78        35.51        26.50        23.90 
TCGA-BH-A0HK TCGA-BH-A0HP TCGA-BH-A0HX TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A18F 
        5.85        13.61        27.25        24.95        42.35         8.81 
TCGA-BH-A18I TCGA-BH-A18M TCGA-BH-A18R TCGA-BH-A1EO TCGA-BH-A1EU TCGA-BH-A1EW 
        7.23        72.56        37.55        91.99        42.28        55.69 
TCGA-BH-A1FB TCGA-BH-A1FE TCGA-BH-A1FH TCGA-BH-A201 TCGA-BH-A209 TCGA-BH-A28O 
      120.62        74.73        36.92         6.90       130.16        10.65 
TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A132 TCGA-C8-A26W TCGA-C8-A3M7 TCGA-D8-A145 
      109.28         8.94         1.45         0.23         0.03        13.48 
TCGA-D8-A1JB TCGA-D8-A1JH TCGA-D8-A1JU TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1Y0 
       18.71        14.01        14.70        19.92        17.69        15.52 
TCGA-D8-A1Y2 TCGA-D8-A27G TCGA-D8-A27I TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 
       14.24        13.45        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-A1IH TCGA-E2-A1IJ TCGA-E2-A1IO TCGA-E2-A1L6 TCGA-E2-A2P6 
       37.41        33.73        28.44        20.98        54.18         5.52 
TCGA-E2-A3DX TCGA-E9-A1NE TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A295 TCGA-E9-A2JT 
       15.72        35.77        11.90        14.30         0.72         0.76 
TCGA-E9-A3X8 TCGA-E9-A5FK TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ 
       15.72        14.70        15.39        12.20        39.72        18.21 
TCGA-EW-A1J2 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OZ TCGA-EW-A1P1 TCGA-EW-A1P3 
       13.25        15.68        25.94        40.41        39.78        52.96 
TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FV TCGA-EW-A3E8 TCGA-EW-A424 TCGA-GM-A2DA 
       14.43        34.55        25.91        21.27        10.59       194.27 
TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DL TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3XG 
       42.28        61.91        90.84        53.36       110.50        43.73 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-LD-A66U TCGA-LD-A74U 
       66.38        72.03        13.55        18.12        21.24         6.67 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A7SZ 
        4.08         4.60         9.53        17.06        14.70         5.59 
TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5DA TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A66J 
        2.79         2.10        58.62        34.92        16.87        65.62 
TCGA-OL-A66L TCGA-OL-A66N TCGA-PL-A8LY TCGA-S3-A6ZH TCGA-S3-AA14 TCGA-S3-AA17 
       31.07        26.04         0.26         8.65         7.17         3.91 
TCGA-W8-A86G TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
        5.29         9.60         9.14       100.01 

$subtype4
TCGA-A1-A0SQ TCGA-A2-A0CQ TCGA-A2-A0CS TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0ET 
       18.21        88.60        75.55        28.77       101.72        35.05 
TCGA-A2-A0T5 TCGA-A2-A0YI TCGA-A2-A4S0 TCGA-A7-A0CH TCGA-A7-A13G TCGA-A7-A3IY 
       17.46        14.50        23.21        35.47        23.61        11.34 
TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A8-A07G TCGA-A8-A07S TCGA-A8-A08A TCGA-A8-A08C 
       10.29        13.41        18.97         7.99         0.99        28.96 
TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09V TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A3TN 
       41.98         9.99        15.02        17.03        38.04         1.12 
TCGA-AC-A3YJ TCGA-AC-A62Y TCGA-AC-A6NO TCGA-AC-A8OR TCGA-AN-A0FF TCGA-AN-A0FK 
       24.79         1.81         1.68         1.32         4.64         7.00 
TCGA-AN-A0XP TCGA-AN-A0XV TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A125 TCGA-AO-A12B 
        0.30         5.33        20.32        22.36        99.25        77.56 
TCGA-AO-A12H TCGA-AQ-A1H3 TCGA-AR-A0TR TCGA-AR-A1AP TCGA-AR-A1AV TCGA-AR-A24M 
       28.37        32.52         5.26        39.98        61.28        96.89 
TCGA-AR-A24N TCGA-AR-A24P TCGA-AR-A24X TCGA-AR-A2LE TCGA-B6-A0I5 TCGA-B6-A0IA 
       78.51         0.85        83.77       128.65       149.59       220.90 
TCGA-B6-A0IC TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A1KI 
       50.70       172.96       102.77        28.27        68.94        73.51 
TCGA-B6-A40C TCGA-BH-A0B5 TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0DS TCGA-BH-A0E1 
       55.00        48.36        53.95        49.94         2.56        15.68 
TCGA-BH-A0EB TCGA-BH-A0HI TCGA-BH-A0HN TCGA-BH-A0HO TCGA-BH-A0HQ TCGA-BH-A0W3 
       24.49        20.38        16.96         2.50        36.85        23.93 
TCGA-BH-A0W7 TCGA-BH-A18S TCGA-BH-A1ET TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FR 
       44.81        66.05        82.85        63.35        55.00       144.59 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-C8-A1HE TCGA-D8-A141 TCGA-D8-A146 TCGA-D8-A1JE 
        6.44        20.12        12.33        20.58        21.14        18.90 
TCGA-D8-A1JI TCGA-D8-A1JS TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1XB TCGA-D8-A1XC 
       18.97        12.20        16.73        25.74        18.15         2.66 
TCGA-D8-A1XG TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XV TCGA-D8-A27E TCGA-D8-A27K 
       14.73         7.96        15.85        15.16        17.42         9.44 
TCGA-D8-A27L TCGA-D8-A27P TCGA-D8-A3Z6 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A156 
       16.41         0.76        18.51        40.41        37.51        23.87 
TCGA-E2-A15D TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15P 
       17.29        18.21        17.42         9.04        20.58        19.56 
TCGA-E2-A1B4 TCGA-E2-A1BD TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IU TCGA-E2-A1L8 
       29.95        17.10        22.65         3.88        11.08        39.62 
TCGA-E2-A572 TCGA-E9-A1N4 TCGA-E9-A1RA TCGA-E9-A1RD TCGA-E9-A227 TCGA-E9-A22H 
       27.32        19.20        32.09         0.66         0.79        24.10 
TCGA-E9-A245 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A3Q9 TCGA-E9-A54X TCGA-E9-A5UO 
        0.85         0.95        24.56        18.41        12.33        13.81 
TCGA-EW-A1IY TCGA-EW-A1J3 TCGA-EW-A1OX TCGA-EW-A1PE TCGA-GM-A2DM TCGA-GM-A2DN 
        8.48        16.57        29.95        10.52        76.64        77.33 
TCGA-GM-A3NY TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A6FQ TCGA-OL-A5RU TCGA-OL-A66H 
       38.20        10.95         7.59         2.63        27.65        26.70 
TCGA-OL-A66K TCGA-PL-A8LX TCGA-S3-A6ZG 
       33.57         0.16         6.81 

$subtype5
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        24.39        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        33.99         9.99         8.98 
TCGA-A8-A07U TCGA-A8-A08R TCGA-AC-A2BK TCGA-AC-A2QJ TCGA-AC-A62X TCGA-AC-A6IW 
       24.99         0.99        38.53         2.27         1.12         0.69 
TCGA-AC-A8OQ TCGA-AN-A04D TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FJ 
        1.12         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        52.18 
TCGA-AO-A0J6 TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12F 
       37.48        55.33       102.58       106.78        96.10        48.36 
TCGA-AO-A1KR TCGA-AQ-A04J TCGA-AQ-A54N TCGA-AR-A0TP TCGA-AR-A0TS TCGA-AR-A0TU 
       70.39        26.93         2.56       111.32        74.79        11.84 
TCGA-AR-A0U0 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AQ 
       65.36        85.97        75.55        61.84        52.77        43.07 
TCGA-AR-A1AR TCGA-AR-A1AY TCGA-AR-A24Q TCGA-AR-A251 TCGA-AR-A256 TCGA-AR-A2LR 
       17.23        20.22       101.52        78.48        93.83        20.38 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I6 TCGA-B6-A0IJ TCGA-B6-A0IQ 
       10.59        77.62       143.38        32.78       176.98       140.88 
TCGA-B6-A0RE TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0WX TCGA-B6-A0X1 TCGA-B6-A1KF 
      211.56        89.46       131.21        21.47       186.48       101.52 
TCGA-B6-A402 TCGA-BH-A0AV TCGA-BH-A0B3 TCGA-BH-A0B9 TCGA-BH-A0BG TCGA-BH-A0BL 
       54.28        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-A18Q TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1F0 TCGA-BH-A1F6 
        2.01        55.63         7.36        51.16        25.81        97.48 
TCGA-BH-A1FC TCGA-C8-A12V TCGA-C8-A134 TCGA-C8-A1HJ TCGA-C8-A27B TCGA-D8-A142 
      114.15        12.66         0.69         0.16         0.99        13.97 
TCGA-D8-A147 TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1XK TCGA-D8-A1XQ TCGA-D8-A1XW 
       19.20        20.09        19.40        14.50        16.41        12.66 
TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27M TCGA-E2-A14N TCGA-E2-A14R TCGA-E2-A14X 
       16.04        13.05        13.48        47.15        38.60        31.96 
TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A1AZ TCGA-E2-A1B6 
       28.60        25.41        14.79        25.05        60.53        28.50 
TCGA-E2-A1II TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL 
       33.70        18.87       106.75       102.61         8.75        43.04 
TCGA-E2-A1LS TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N8 TCGA-E9-A1NC TCGA-E9-A1ND 
       15.45        34.92        19.89        12.00        39.55        12.59 
TCGA-E9-A22G TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A3QA TCGA-E9-A5FL TCGA-EW-A1OW 
       23.51        17.06         0.69         0.62         0.26        22.82 
TCGA-EW-A1P4 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A1PH TCGA-EW-A3U0 
       29.82        30.08         7.86        19.99        19.96        17.49 
TCGA-GI-A2C9 TCGA-GM-A2DF TCGA-GM-A3XL TCGA-LL-A441 TCGA-LL-A5YP TCGA-LL-A6FR 
      109.87        42.71        69.30        11.44        14.79         3.88 
TCGA-LL-A73Y TCGA-LL-A8F5 TCGA-OL-A5D7 TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-OL-A66I 
        4.14         6.21        46.55        36.36        20.38        23.47 
TCGA-OL-A6VO TCGA-PL-A8LV TCGA-PL-A8LZ TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA15 
       28.21         0.23         3.95        10.59         7.92         6.87 

$subtype6
TCGA-A2-A0EY TCGA-A2-A0T1 TCGA-A2-A3XV TCGA-A2-A3XZ TCGA-A8-A08X TCGA-A8-A09X 
       24.16        17.13        32.75        31.99        43.00        14.01 
TCGA-A8-A0A7 TCGA-AC-A3W5 TCGA-AN-A04C TCGA-AO-A0J2 TCGA-AO-A0JE TCGA-AO-A12D 
        0.99        16.57         1.78        32.78        76.77        64.04 
TCGA-AR-A0TX TCGA-AR-A1AO TCGA-AR-A24U TCGA-AR-A2LH TCGA-B6-A0IK TCGA-B6-A0RS 
       64.83        43.56        53.36        20.25        18.77       100.70 
TCGA-BH-A0AW TCGA-BH-A0B7 TCGA-BH-A0EE TCGA-BH-A1FU TCGA-BH-A203 TCGA-BH-A208 
       20.45        56.98        31.00        72.07        38.60        57.83 
TCGA-C8-A12L TCGA-C8-A12Q TCGA-C8-A131 TCGA-C8-A135 TCGA-C8-A1HK TCGA-C8-A26X 
       11.93         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-LD-A9QF TCGA-LL-A5YO TCGA-LL-A73Z TCGA-LL-A740 TCGA-OL-A5D6 TCGA-OL-A5RY 
        8.75        14.47         4.50         4.50        12.66        24.72 
TCGA-OL-A66P 
       14.07 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.07     0.03     0.03     0.16     0.16     0.03 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  188.68   189.01   234.28   220.90   211.56   100.70 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  22.750   20.945   26.845   20.120   23.260   20.120 
[1] "0.1 - 188.7 (22.8)" "0.0 - 189.0 (20.9)" "0.0 - 234.3 (26.8)"
[4] "0.2 - 220.9 (20.1)" "0.2 - 211.6 (23.3)" "0.0 - 100.7 (20.1)"
D8V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1      16       13        6        1        66        56         1
  subtype2       7        7        0        1        49        34         0
  subtype3      33       23        3        3        75        71         0
  subtype4      14       18        1        0        50        27         0
  subtype5      12       16        0        0        84        39         0
  subtype6       1        6        0        0        23        11         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
  subtype1         33          8          7        3         0       4
  subtype2         31          8         11        7         0       3
  subtype3         41          3         31        2         1       4
  subtype4         16          5          3        2         0       3
  subtype5         15          4          5        3         0       2
  subtype6          6          1          6        1         0       1
D8V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I          16        7       33       14       12        1
  STAGE IA         13        7       23       18       16        6
  STAGE IB          6        0        3        1        0        0
  STAGE II          1        1        3        0        0        0
  STAGE IIA        66       49       75       50       84       23
  STAGE IIB        56       34       71       27       39       11
  STAGE III         1        0        0        0        0        1
  STAGE IIIA       33       31       41       16       15        6
  STAGE IIIB        8        8        3        5        4        1
  STAGE IIIC        7       11       31        3        5        6
  STAGE IV          3        7        2        2        3        1
  STAGE TIS         0        0        1        0        0        0
  STAGE X           4        3        4        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  55 126  22  10
  subtype2  23 107  18  10
  subtype3  87 142  56   4
  subtype4  48  75   9   7
  subtype5  39 119  16   6
  subtype6  19  32   4   2
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1       55       23       87       48       39       19
  T2      126      107      142       75      119       32
  T3       22       18       56        9       16        4
  T4       10       10        4        7        6        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  86  87  24  10
  subtype2  62  45  31  13
  subtype3 130  99  25  33
  subtype4  75  45  13   5
  subtype5 114  48  13   6
  subtype6  22  20   7   7
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0       86       62      130       75      114       22
  N1       87       45       99       45       48       20
  N2       24       31       25       13       13        7
  N3       10       13       33        5        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        0 189   4  21
  subtype2        0 130   7  21
  subtype3        4 226   2  58
  subtype4        0 116   2  21
  subtype5        1 157   3  20
  subtype6        0  50   1   6
D8V6, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  CM0 (I+)        0        0        4        0        1        0
  M0            189      130      226      116      157       50
  M1              4        7        2        2        3        1
  MX             21       21       58       21       20        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 206   8
  subtype2 156   2
  subtype3 290   0
  subtype4 138   1
  subtype5 181   0
  subtype6  57   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  206    8
  subtype2  156    2
  subtype3  290    0
  subtype4  138    1
  subtype5  181    0
  subtype6   57    0
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE      206      156      290      138      181       57
  MALE          8        2        0        1        0        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                          0                           183
  subtype2                          0                           135
  subtype3                          0                           152
  subtype4                          0                            87
  subtype5                          1                           159
  subtype6                          0                            52
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                             13                   0
  subtype2                             14                   0
  subtype3                            121                   1
  subtype4                             21                   0
  subtype5                              1                   5
  subtype6                              5                   0
          vv
clus       MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                                6                  2             10
  subtype2                                4                  0              5
  subtype3                                9                  1              6
  subtype4                                9                 12             10
  subtype5                                1                  0             13
  subtype6                                0                  0              0
D8V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  INFILTRATING CARCINOMA NOS              0        0        0        0        1
  INFILTRATING DUCTAL CARCINOMA         183      135      152       87      159
  INFILTRATING LOBULAR CARCINOMA         13       14      121       21        1
  MEDULLARY CARCINOMA                     0        0        1        0        5
  MIXED HISTOLOGY (PLEASE SPECIFY)        6        4        9        9        1
  MUCINOUS CARCINOMA                      2        0        1       12        0
  OTHER  SPECIFY                         10        5        6       10       13
                                  clus
vv                                 subtype6
  INFILTRATING CARCINOMA NOS              0
  INFILTRATING DUCTAL CARCINOMA          52
  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  67 147
  subtype2  33 125
  subtype3  76 214
  subtype4  38 101
  subtype5  57 124
  subtype6  14  43
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   67  147
  subtype2   33  125
  subtype3   76  214
  subtype4   38  101
  subtype5   57  124
  subtype6   14   43
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO        67       33       76       38       57       14
  YES      147      125      214      101      124       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    18                        27
  subtype2                                0    14                        15
  subtype3                                0     8                        32
  subtype4                                0     2                        14
  subtype5                                0     5                        60
  subtype6                                1    10                        12
          vv
clus       WHITE
  subtype1   140
  subtype2   103
  subtype3   235
  subtype4   112
  subtype5   108
  subtype6    28
D8V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        0        0
  ASIAN                                  18       14        8        2        5
  BLACK OR AFRICAN AMERICAN              27       15       32       14       60
  WHITE                                 140      103      235      112      108
                                  clus
vv                                 subtype6
  AMERICAN INDIAN OR ALASKA NATIVE        1
  ASIAN                                  10
  BLACK OR AFRICAN AMERICAN              12
  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   8 166
  subtype2   3 121
  subtype3  13 232
  subtype4   6 112
  subtype5   6 153
  subtype6   0  48
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8  166
  subtype2    3  121
  subtype3   13  232
  subtype4    6  112
  subtype5    6  153
  subtype6    0   48
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            8        3       13        6        6        0
  NOT HISPANIC OR LATINO      166      121      232      112      153       48
[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 267  47
  subtype2 209  16
  subtype3 408  56
subtype1 subtype2 subtype3 
     314      225      464 
subtype1 subtype2 subtype3 
      47       16       56 
$subtype1
TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R 
       31.79        28.01        19.20        18.02        41.95        82.16 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04X TCGA-A2-A0CL TCGA-A2-A0CM 
       73.84        22.06        63.12        55.43        64.57        24.79 
TCGA-A2-A0CW TCGA-A2-A0CY TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D4 
       64.04        55.00        21.14        34.55        33.76        25.22 
TCGA-A2-A0EQ TCGA-A2-A0ST TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0T0 TCGA-A2-A0T2 
       79.76        99.19        44.88        50.43        17.52         8.38 
TCGA-A2-A0YG TCGA-A2-A0YM TCGA-A2-A1G1 TCGA-A2-A25F TCGA-A2-A3XS TCGA-A2-A3XT 
       21.90        31.73        19.20        10.59        33.93        83.01 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4S0 
       29.98        32.75        38.40        34.98        38.37        23.21 
TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E 
       26.96        21.90        35.31        35.67        31.73        10.72 
TCGA-A7-A26F TCGA-A7-A26I TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A4SD TCGA-A7-A4SF 
       24.26        21.73        10.29        13.41        14.50        17.92 
TCGA-A7-A5ZV TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06R 
       12.10        10.29         9.37         8.75        13.02        17.98 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07C TCGA-A8-A07G TCGA-A8-A07L TCGA-A8-A07O 
       53.98         9.01        33.99        18.97        17.03         9.99 
TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A082 TCGA-A8-A08B TCGA-A8-A08L 
        8.98        24.99         9.99        18.05        38.01         9.99 
TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A09I TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A0A7 
        0.99        43.00        45.07        25.02         8.98         0.99 
TCGA-AC-A2BK TCGA-AC-A2QH TCGA-AC-A3W5 TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IW 
       38.53         1.02        16.57         0.07         1.12         0.69 
TCGA-AC-A8OQ TCGA-AN-A03Y TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ 
        1.12         0.33         2.96         1.78         1.71         8.02 
TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FJ 
        7.36         6.51         0.16         0.33         0.33         7.96 
TCGA-AN-A0FL TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY 
        7.59         6.02         0.33         0.36         0.33         0.33 
TCGA-AN-A0FZ TCGA-AN-A0G0 TCGA-AN-A0XO TCGA-AN-A0XU TCGA-AO-A03M TCGA-AO-A03O 
        0.33         0.53        12.33         0.33        47.84        81.63 
TCGA-AO-A03R TCGA-AO-A03U TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J6 
       68.75        59.05        32.78        21.40        52.18        37.48 
TCGA-AO-A0J7 TCGA-AO-A0JE TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A129 TCGA-AO-A12D 
       20.32        76.77        55.33       102.58        96.10        64.04 
TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AR-A0TP 
       48.36        61.87        70.39         5.65         2.56       111.32 
TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 
       49.32        74.79        86.66        83.87       114.02        85.97 
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-AR-A24H TCGA-AR-A24Q TCGA-AR-A24U TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A256 
      109.58       101.52        53.36        78.48        72.76        93.83 
TCGA-AR-A2LR TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I6 TCGA-B6-A0I9 
       20.38        10.59        77.62       143.38        32.78        12.13 
TCGA-B6-A0IJ TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0WY 
      176.98       140.88       211.56       100.70        89.46       113.79 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A402 TCGA-BH-A0AV 
       28.27        68.94        58.88       101.52        54.28        38.79 
TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0B3 TCGA-BH-A0B9 TCGA-BH-A0BF TCGA-BH-A0BG 
       20.45        25.55        39.55        51.68        25.71        24.85 
TCGA-BH-A0BL TCGA-BH-A0BT TCGA-BH-A0BW TCGA-BH-A0C0 TCGA-BH-A0DD TCGA-BH-A0DL 
       44.05        45.57        11.67        41.75        45.83        48.23 
TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0EE TCGA-BH-A0GY TCGA-BH-A0RX TCGA-BH-A0WA 
        4.41         9.63        31.00        30.35         5.59        23.05 
TCGA-BH-A18G TCGA-BH-A18L TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18T TCGA-BH-A18U 
        2.01        26.66        55.63        37.55         7.36        51.39 
TCGA-BH-A18V TCGA-BH-A1F0 TCGA-BH-A1F6 TCGA-BH-A1FC TCGA-BH-A1FM TCGA-BH-A1FN 
       51.16        25.81        97.48       114.15        45.63        72.07 
TCGA-BH-A203 TCGA-BH-A209 TCGA-C8-A12L TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U 
       38.60       130.16        11.93        11.77         0.07        12.66 
TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A135 
       12.66        12.66         3.12         1.78         0.69         0.62 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A275 
       10.92        11.34         0.16         2.30         3.25         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-A1JC TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JJ 
       19.20        16.50        15.78        12.03        12.03        20.09 
TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1X5 TCGA-D8-A1XF TCGA-D8-A1XJ TCGA-D8-A1XK 
       20.12        20.09        18.58        15.22        21.83        14.50 
TCGA-D8-A1XL TCGA-D8-A1XQ TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XZ 
       19.92        16.41         6.35        15.16        12.66        15.32 
TCGA-D8-A1Y3 TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27M TCGA-E2-A14P TCGA-E2-A14R 
       14.14        16.04        13.05        13.48        40.96        38.60 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 
       34.26        32.02        31.96        28.60        17.03        25.41 
TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15K TCGA-E2-A1AZ TCGA-E2-A1B0 
       14.79        25.05        23.34         9.04        60.53        53.62 
TCGA-E2-A1B6 TCGA-E2-A1II TCGA-E2-A1L7 TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH 
       28.50        33.70        27.42        28.90        18.87       106.75 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A9RU 
      102.61         8.75        43.04        34.92        19.89         9.21 
TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1ND TCGA-E9-A1RB 
       13.48        12.00        13.12        36.56        12.59        20.81 
TCGA-E9-A1RH TCGA-E9-A22G TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A2JS 
       34.59        23.51        17.06         0.69         1.94        17.75 
TCGA-E9-A3QA TCGA-E9-A5FL TCGA-E9-A5UO TCGA-EW-A1IZ TCGA-EW-A1OW TCGA-EW-A1OY 
        0.62         0.26        13.81        18.21        22.82        29.85 
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        14.70 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A7SZ TCGA-LL-A7T0 
       14.47        14.79         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        31.99        36.36        22.32        20.38 
TCGA-OL-A66I TCGA-OL-A66P TCGA-OL-A6VO TCGA-PL-A8LV TCGA-PL-A8LZ TCGA-S3-AA0Z 
       23.47        14.07        28.21         0.23         3.95        10.59 
TCGA-S3-AA10 TCGA-S3-AA12 
        7.92         8.52 

$subtype2
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CU TCGA-A2-A0CZ TCGA-A2-A0EM 
      112.08        92.48       107.93         5.19        53.13       101.72 
TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ES TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
       80.28       107.61        37.05        31.82        29.75        24.72 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A1G6 TCGA-A2-A259 
       18.90        20.75        19.33        48.46        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25D TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XW TCGA-A2-A3XZ 
      107.70        18.15        20.88        39.65        49.48        31.99 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S2 TCGA-A7-A0CG TCGA-A7-A0DB 
        7.30        24.39        21.30        21.14        34.29        33.11 
TCGA-A7-A13H TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A3IZ TCGA-A7-A3J1 TCGA-A7-A425 
       29.56        23.74        23.80        10.59        11.28        14.70 
TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SC TCGA-A7-A4SE TCGA-A7-A56D 
       11.97        14.93        13.74        14.66        21.17        14.73 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A0AB TCGA-AC-A23G 
       10.72        11.05        12.00         9.99        17.03        10.85 
TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QJ 
       40.57        55.43        38.79        26.04        50.70         2.27 
TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3W6 TCGA-AC-A3YI 
        0.99         0.69        14.83        22.19        19.79        23.24 
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-A0XV TCGA-AO-A03T TCGA-AO-A12E TCGA-AO-A1KO TCGA-AQ-A04J 
        6.28         5.33        47.87        57.30        14.73        26.93 
TCGA-AQ-A1H3 TCGA-AQ-A7U7 TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AO TCGA-AR-A1AU 
       32.52         9.99        48.82        62.56        43.56        76.21 
TCGA-AR-A1AX TCGA-AR-A24K TCGA-AR-A24T TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LL 
       62.14        50.89        76.01        20.25        62.86         7.36 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN 
       40.04        38.17        39.39        40.54        54.74        16.04 
TCGA-AR-A5QP TCGA-B6-A0IH TCGA-B6-A0RQ TCGA-B6-A0RU TCGA-B6-A0WX TCGA-B6-A1KC 
       20.45       112.37       140.48       131.21        21.47        43.59 
TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0B6 TCGA-BH-A0BA 
      170.17        85.35       103.63        55.00        56.94        37.22 
TCGA-BH-A0BD TCGA-BH-A0BO TCGA-BH-A0BZ TCGA-BH-A0DI TCGA-BH-A0DO TCGA-BH-A0E9 
       18.21        35.67        49.05        22.13        17.26        46.19 
TCGA-BH-A0HP TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A18M TCGA-BH-A1EU TCGA-BH-A1EW 
       13.61        24.95        42.35        72.56        42.28        55.69 
TCGA-BH-A1EX TCGA-BH-A1FB TCGA-BH-A1FH TCGA-BH-A1FU TCGA-BH-A28O TCGA-BH-A28Q 
       49.58       120.62        36.92        72.07        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A137 TCGA-C8-A26W 
       20.12         0.99       109.28         8.94         3.85         0.23 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A3M7 TCGA-D8-A1JB TCGA-D8-A1JU TCGA-D8-A1X8 
        0.36         0.43         0.03        18.71        14.70        25.74 
TCGA-D8-A1XM TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27I TCGA-D8-A27L 
       17.69        14.24        17.42        13.45        14.43        16.41 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27W TCGA-D8-A3Z5 
        4.80         0.76        10.09        13.08        12.26        14.50 
TCGA-D8-A4Z1 TCGA-E2-A108 TCGA-E2-A14N TCGA-E2-A14Q TCGA-E2-A14U TCGA-E2-A15E 
        7.33        27.52        47.15        38.24        43.33        20.71 
TCGA-E2-A1B1 TCGA-E2-A1IH TCGA-E2-A2P5 TCGA-E2-A3DX TCGA-E2-A572 TCGA-E2-A576 
       53.03        33.73        16.93        15.72        27.32        19.00 
TCGA-E9-A1N4 TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R3 TCGA-E9-A1RD TCGA-E9-A226 
       19.20        11.90        14.30         2.10         0.66        34.13 
TCGA-E9-A22A TCGA-E9-A295 TCGA-E9-A2JT TCGA-E9-A3X8 TCGA-E9-A5FK TCGA-EW-A1IW 
       39.09         0.72         0.76        15.72        14.70        12.20 
TCGA-EW-A1P1 TCGA-EW-A1PA TCGA-EW-A1PG TCGA-EW-A3E8 TCGA-EW-A424 TCGA-GM-A2DA 
       39.78        18.90        34.55        21.27        10.59       194.27 
TCGA-GM-A2DC TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DN TCGA-GM-A3NW 
       53.52        61.91        62.33        90.84        77.33       110.50 
TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YX 
       43.73        66.38        72.03        13.55        18.12        11.57 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 
       21.24         6.67         4.08         4.60         8.75         9.53 
TCGA-LL-A441 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A6FQ TCGA-LL-A73Z 
       11.44         7.59        17.06        15.32         2.63         4.50 
TCGA-LL-A740 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5DA 
        4.50        27.91         2.79         2.10        12.66        58.62 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A66H TCGA-OL-A66J 
       27.65        34.92        16.87        24.72        26.70        65.62 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A6VQ TCGA-PL-A8LY 
       33.57        31.07        26.04         7.23        19.73         0.26 
TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-W8-A86G 
        6.81         8.65         5.56         7.17         6.87         5.29 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
        9.60         9.14       100.01 

$subtype3
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        0.39         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SQ 
       47.24        20.88        13.68         7.96        39.32        18.21 
TCGA-A2-A04N TCGA-A2-A04W TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CQ TCGA-A2-A0CS 
      104.81        64.04        36.13       136.73        88.60        75.55 
TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0D3 TCGA-A2-A0EN TCGA-A2-A0ER TCGA-A2-A0ET 
       75.25        63.45        28.77        89.36        74.40        35.05 
TCGA-A2-A0EU TCGA-A2-A0EY TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SY TCGA-A2-A0T1 
       34.29        24.16        54.64        27.12        44.28        17.13 
TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF 
       18.71        20.52        17.46        32.55        25.28        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-A1G0 TCGA-A2-A1G4 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25E 
       22.45        20.25        19.56        16.31        17.19        91.92 
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-A3IY TCGA-A7-A6VX TCGA-A8-A06P 
       31.36        20.61        22.32        11.34        10.42        13.02 
TCGA-A8-A06Q TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 
        1.02        53.06        29.03        26.01         1.02        17.03 
TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07P 
       43.00        19.99        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-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08S TCGA-A8-A08T 
       19.96        12.00        37.05        31.00        33.01        93.04 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 
       40.01        33.01        30.97        17.95        41.98         9.99 
TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09M 
       12.00         1.02        50.04        49.05        29.98        33.07 
TCGA-A8-A09N TCGA-A8-A09T TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 
        1.02        19.04        14.01        12.00        19.04        13.02 
TCGA-A8-A0A6 TCGA-A8-A0A9 TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23H 
       21.04        13.02        38.04         0.95         2.37         2.66 
TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FG TCGA-AC-A2QI TCGA-AC-A3TN TCGA-AC-A3YJ 
        1.48        38.20        36.99         0.92         1.12        24.79 
TCGA-AC-A6NO TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 
        1.68         1.32         0.33         0.23         0.33         0.62 
TCGA-AN-A0AS TCGA-AN-A0FD TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0XL TCGA-AN-A0XN 
        0.33         6.44         7.00         7.17         0.33         0.33 
TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XW TCGA-AO-A03L 
        0.30         0.33         0.33         0.33         5.59        80.28 
TCGA-AO-A03N TCGA-AO-A03V TCGA-AO-A0J5 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA 
       66.77        29.13        24.16        22.36        53.03        21.53 
TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI 
       50.70        50.86        72.00        21.37        26.24        50.24 
TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A 
       62.04        71.80        99.25       108.72       106.78        90.58 
TCGA-AO-A12B TCGA-AO-A12C TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KP TCGA-AO-A1KS 
       77.56        65.56        41.62        28.37        82.62         0.53 
TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A54O TCGA-AR-A0TR 
       17.79        24.79       130.09        15.62        32.91         5.26 
TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A1AK TCGA-AR-A1AN 
       29.75        64.83        55.86        76.14        51.25        43.73 
TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AT TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A24L 
       39.98        37.81        41.82        61.28        63.62        73.02 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24V 
       96.89        78.51        84.20         0.85        87.22        85.35 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A255 
       50.96        83.77        79.00        56.15        73.18        58.92 
TCGA-AR-A2LE TCGA-AR-A2LK TCGA-B6-A0I5 TCGA-B6-A0I8 TCGA-B6-A0IA TCGA-B6-A0IB 
      128.65        42.87       149.59        24.62       220.90       129.57 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
       50.70        65.72       146.50        18.77       126.12        84.59 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL 
      110.14       110.93        68.45       189.01       234.28        81.17 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RV TCGA-B6-A0WS 
       78.02       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-A1KI 
      188.68        79.63        17.98       129.57       129.70        73.51 
TCGA-B6-A1KN TCGA-B6-A408 TCGA-BH-A0AU TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B1 
      139.17        49.94        24.53        28.50        46.95        37.74 
TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B8 TCGA-BH-A0BC 
       40.83        39.16        48.36        56.98        51.58        32.02 
TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       21.70        61.68        48.69        27.19        53.69        53.95 
TCGA-BH-A0BV TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DG 
       49.94        44.02        48.13        42.90        31.17        23.44 
TCGA-BH-A0DH TCGA-BH-A0DK TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT 
       38.01        13.91        15.65         3.22         2.56        38.47 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 
       45.17        47.41        16.27        15.68        14.30        44.81 
TCGA-BH-A0EA TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       32.65        24.43        10.78        15.16        37.78        35.51 
TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HF 
       24.56        23.08        41.00        52.96        26.50        23.90 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HL TCGA-BH-A0HN TCGA-BH-A0HO TCGA-BH-A0HQ 
       20.38         5.85         2.37        16.96         2.50        36.85 
TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0W3 TCGA-BH-A0W7 
       12.89        51.32        27.25        50.79        23.93        44.81 
TCGA-BH-A18F TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18N TCGA-BH-A18P 
        8.81         7.23        20.12        90.84        37.74        30.28 
TCGA-BH-A18S TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EV 
       66.05        69.93        91.99       113.82        82.85        12.00 
TCGA-BH-A1EY TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F8 TCGA-BH-A1FE TCGA-BH-A1FG 
       17.69        31.53        89.16        24.66        74.73       122.89 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A204 
       63.35        55.00       144.59         6.90         0.72        83.31 
TCGA-BH-A208 TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12X TCGA-C8-A132 
       57.83        11.77        11.77        12.66        12.66         1.45 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A26V 
        3.75        12.33        11.34        12.03        10.42         0.30 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A3M8 TCGA-D8-A13Y TCGA-D8-A140 
        8.28         9.67         0.03         0.23        11.90        13.25 
TCGA-D8-A141 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JD 
       20.58        13.48        21.14        14.17        17.49        18.15 
TCGA-D8-A1JE TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS 
       18.90        14.01        18.97        20.38        21.01        12.20 
TCGA-D8-A1JT TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB 
       13.32        17.79        16.73        23.90        27.58        18.15 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS 
        2.66        17.16        14.73         7.96        15.85        16.31 
TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A27K TCGA-D8-A27V 
       12.99        16.54        15.52         3.81         9.44        12.53 
TCGA-D8-A3Z6 TCGA-E2-A105 TCGA-E2-A106 TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10A 
       18.51        43.00        59.41        34.42        46.59        40.41 
TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14S 
       37.51        40.11        28.44        28.87        44.68        33.17 
TCGA-E2-A14T TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 
       33.30        27.12        23.24        19.43        21.04        23.87 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I 
       22.82        17.29        21.63        18.21        12.92        17.42 
TCGA-E2-A15J TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R 
       19.40        20.58         7.73        13.02        19.56        17.06 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1BC TCGA-E2-A1BD 
       14.07        14.99        29.95        32.35        16.47        17.10 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       38.30        37.41        32.78        28.44        22.65         3.88 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L8 TCGA-E2-A1L9 
       22.19        20.98        11.08        54.18        39.62        19.66 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LS TCGA-E2-A2P6 TCGA-E2-A56Z TCGA-E2-A570 
       24.59        40.47        15.45         5.52         7.20        30.61 
TCGA-E9-A1N5 TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1R2 
       36.82        35.77        20.05        21.57         9.86         0.62 
TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RC 
        6.12         1.38         2.76        21.21        32.09        40.24 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 
       34.65         6.58        21.27        35.64         0.79        12.53 
TCGA-E9-A229 TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A245 TCGA-E9-A247 
       13.32        22.75        12.89        24.10         0.85        27.22 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A3Q9 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5UP 
        0.95        24.56        18.41        12.33         0.23        14.40 
TCGA-E9-A6HE TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 
       15.39        39.72         8.48        18.90        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1P0 
       15.68        28.77        25.94        29.95        40.41        41.13 
TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
       52.96        23.11        18.48        13.94        10.52        14.43 
TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DM 
       52.73        25.91        22.09         7.40        59.57        76.64 
TCGA-GM-A3NY TCGA-LL-A442 TCGA-LL-A6FP TCGA-LL-A9Q3 TCGA-PL-A8LX TCGA-S3-A6ZF 
       38.20        10.95        11.57         7.36         0.16        16.50 
TCGA-S3-AA17 TCGA-Z7-A8R6 
        3.91       105.04 

subtype1 subtype2 subtype3 
    0.03     0.03     0.03 
subtype1 subtype2 subtype3 
  211.56   194.27   234.28 
subtype1 subtype2 subtype3 
  21.565   20.710   24.015 
[1] "0.0 - 211.6 (21.6)" "0.0 - 194.3 (20.7)" "0.0 - 234.3 (24.0)"
D9V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1      18       18        1        0       140        68         0
  subtype2      14       24        3        4        58        54         1
  subtype3      51       40        6        1       144       111         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
  subtype1         43          7         13        6         0       5
  subtype2         31          5         29        2         0       1
  subtype3         66         16         20        9         1      11
D9V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          18       14       51
  STAGE IA         18       24       40
  STAGE IB          1        3        6
  STAGE II          0        4        1
  STAGE IIA       140       58      144
  STAGE IIB        68       54      111
  STAGE III         0        1        1
  STAGE IIIA       43       31       66
  STAGE IIIB        7        5       16
  STAGE IIIC       13       29       20
  STAGE IV          6        2        9
  STAGE TIS         0        0        1
  STAGE X           5        1       11
[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  61 218  29  11
  subtype2  64 115  42   5
  subtype3 145 256  51  23
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       61       64      145
  T2      218      115      256
  T3       29       42       51
  T4       11        5       23
[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 172  91  38  15
  subtype2  99  75  19  30
  subtype3 212 172  54  27
D9V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0      172       99      212
  N1       91       75      172
  N2       38       19       54
  N3       15       30       27
[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        0 274   6  40
  subtype2        2 165   2  57
  subtype3        3 413  10  51
D9V6, multiclass
          clus
vv         subtype1 subtype2 subtype3
  CM0 (I+)        0        2        3
  M0            274      165      413
  M1              6        2       10
  MX             40       57       51
[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 316   4
  subtype2 226   0
  subtype3 470   7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  316    4
  subtype2  226    0
  subtype3  470    7
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      316      226      470
  MALE          4        0        7
[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                          1                           283
  subtype2                          0                           101
  subtype3                          0                           370
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                              8                   6
  subtype2                            112                   0
  subtype3                             54                   0
          vv
clus       MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                                3                  5             13
  subtype2                                4                  3              6
  subtype3                               21                  7             25
D9V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  INFILTRATING CARCINOMA NOS              1        0        0
  INFILTRATING DUCTAL CARCINOMA         283      101      370
  INFILTRATING LOBULAR CARCINOMA          8      112       54
  MEDULLARY CARCINOMA                     6        0        0
  MIXED HISTOLOGY (PLEASE SPECIFY)        3        4       21
  MUCINOUS CARCINOMA                      5        3        7
  OTHER  SPECIFY                         13        6       25
[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  97 223
  subtype2  38 188
  subtype3 143 334
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   97  223
  subtype2   38  188
  subtype3  143  334
     clus
vv    subtype1 subtype2 subtype3
  NO        97       38      143
  YES      223      188      334
[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    23                        80
  subtype2                                0     8                        40
  subtype3                                1    26                        39
          vv
clus       WHITE
  subtype1   193
  subtype2   171
  subtype3   354
D9V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1
  ASIAN                                  23        8       26
  BLACK OR AFRICAN AMERICAN              80       40       39
  WHITE                                 193      171      354
[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   8 266
  subtype2   9 202
  subtype3  19 357
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8  266
  subtype2    9  202
  subtype3   19  357
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            8        9       19
  NOT HISPANIC OR LATINO      266      202      357
[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 183  39
  subtype2 128  22
  subtype3 272  26
  subtype4 114  10
  subtype5  75   5
  subtype6 112  17
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
     222      150      298      124       80      129 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      39       22       26       10        5       17 
$subtype1
TCGA-5T-A9QA TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CW 
        0.39        13.68        31.79        64.04        55.43        64.04 
TCGA-A2-A0D1 TCGA-A2-A0EY TCGA-A2-A0SW TCGA-A2-A0T1 TCGA-A2-A0T3 TCGA-A2-A0YG 
       34.55        24.16        44.88        17.13        18.71        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-A25E TCGA-A2-A4S0 TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13F 
       17.19        91.92        23.21        37.45        33.11        12.72 
TCGA-A7-A26E TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3J0 TCGA-A7-A3RF 
       31.36        21.73        20.61        22.32        10.29        13.41 
TCGA-A7-A4SF TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B 
       17.92        13.02         1.02        53.98         9.01        43.00 
TCGA-A8-A07I TCGA-A8-A084 TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08S 
       14.01        15.06        37.05         9.99        31.00        33.01 
TCGA-A8-A09D TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09X TCGA-AC-A23C TCGA-AC-A23H 
       50.04        45.07        33.07        14.01         0.95         2.66 
TCGA-AC-A2B8 TCGA-AN-A03X TCGA-AN-A046 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AK 
        1.48         0.33         0.33         2.96         1.71         7.36 
TCGA-AN-A0AM TCGA-AN-A0FT TCGA-AN-A0XN TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03O 
        0.16         6.02         0.33        80.28        47.84        81.63 
TCGA-AO-A03V TCGA-AO-A0J5 TCGA-AO-A0J7 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC 
       29.13        24.16        20.32        21.53        50.70        50.86 
TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JM TCGA-AO-A12G TCGA-AO-A1KP TCGA-AO-A1KT 
       72.00        76.77        71.80        41.62        82.62        17.79 
TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AR-A0TQ TCGA-AR-A0TX TCGA-AR-A0TZ TCGA-AR-A1AS 
      130.09        15.62        49.32        64.83        76.14        37.81 
TCGA-AR-A1AT TCGA-AR-A1AW TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A254 
       41.82        63.62        79.00        56.15        73.18        72.76 
TCGA-B6-A0I8 TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IN TCGA-B6-A0RL 
       24.62       129.57        65.72       146.50        84.59        81.17 
TCGA-B6-A0WS TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X4 TCGA-B6-A1KC TCGA-BH-A0AU 
       97.48       113.79       129.57        28.27        43.59        24.53 
TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B1 TCGA-BH-A0B4 TCGA-BH-A0B6 
       20.45        25.55        28.50        37.74        39.16        56.94 
TCGA-BH-A0B8 TCGA-BH-A0BC TCGA-BH-A0BP TCGA-BH-A0BV TCGA-BH-A0C7 TCGA-BH-A0DD 
       51.58        32.02        48.69        49.94        42.90        45.83 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H5 
       47.41        16.27        30.35        10.78        15.16        35.51 
TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HL 
       23.08        41.00        52.96        26.50        20.38         2.37 
TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A18L TCGA-BH-A18R TCGA-BH-A1EN TCGA-BH-A1EO 
       12.89        27.25        26.66        37.55        69.93        91.99 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1F2 TCGA-BH-A1F8 
      113.82        82.85        12.00        55.69        31.53        24.66 
TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A204 TCGA-C8-A12M TCGA-C8-A12P TCGA-C8-A12Q 
       45.63       144.59        83.31        11.77        11.77         0.07 
TCGA-C8-A12U TCGA-C8-A132 TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK 
       12.66         1.45        10.92        11.34        11.34        12.03 
TCGA-C8-A1HM TCGA-C8-A274 TCGA-C8-A278 TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 
        2.30         0.03         0.03        11.90        13.25        20.58 
TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JD TCGA-D8-A1JJ TCGA-D8-A1JN 
       14.17        17.49        16.50        18.15        20.09        20.38 
TCGA-D8-A1JP TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG 
       21.01        27.58         2.66        17.16        15.22        14.73 
TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1Y0 TCGA-D8-A1Y3 TCGA-D8-A27V TCGA-E2-A105 
        6.35        15.16        15.52        14.14        12.53        43.00 
TCGA-E2-A109 TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A14O TCGA-E2-A14T TCGA-E2-A152 
       46.59        40.11        28.44        44.68        33.30        27.12 
TCGA-E2-A155 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15H TCGA-E2-A15K TCGA-E2-A15M 
       21.04        23.34        22.82        12.92         9.04         7.73 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B5 TCGA-E2-A1IE 
       19.56        17.06        14.07        14.99        32.35        38.30 
TCGA-E2-A1IG TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A1LB TCGA-E2-A9RU TCGA-E9-A1N6 
       32.78        20.98        27.42        40.47         9.21        13.48 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1R2 
       13.12        36.56        35.77        20.05        21.57         0.62 
TCGA-E9-A1R4 TCGA-E9-A1R6 TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A228 TCGA-E9-A229 
        6.12         2.76        34.65        21.27        12.53        13.32 
TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A3Q9 
       22.75        12.89        24.10         0.85        27.22        18.41 
TCGA-EW-A1IZ TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OZ TCGA-EW-A1PC TCGA-EW-A2FV 
       18.21        28.77        25.94        40.41         6.15        25.91 
TCGA-EW-A423 TCGA-LL-A5YN TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-OL-A5D8 TCGA-OL-A5RZ 
       10.16        14.70         5.59         3.22        31.99        22.32 

$subtype2
TCGA-A1-A0SB TCGA-A1-A0SM TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A0CL TCGA-A2-A0CT 
        8.52         7.96        18.02        41.95        64.57        75.25 
TCGA-A2-A0CY TCGA-A2-A0D2 TCGA-A2-A0EQ TCGA-A2-A0EV TCGA-A2-A0ST TCGA-A2-A0SV 
       55.00        33.76        79.76        31.82        99.19        27.12 
TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A1G1 TCGA-A2-A3XS TCGA-A2-A3XV TCGA-A2-A4RW 
       17.52         8.38        19.20        33.93        32.75         7.30 
TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A4SD TCGA-A8-A06R TCGA-A8-A06U TCGA-A8-A075 
       26.96        21.90        14.50        17.98        29.03        17.03 
TCGA-A8-A07W TCGA-A8-A082 TCGA-A8-A08B TCGA-A8-A08X TCGA-A8-A095 TCGA-A8-A097 
        9.99        18.05        38.01        43.00        41.98        12.00 
TCGA-A8-A09K TCGA-A8-A0A7 TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A5XS TCGA-AC-A62V 
       29.98         0.99         1.02         2.27         1.55         0.07 
TCGA-AC-A6IX TCGA-AN-A04C TCGA-AN-A0AJ TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AT 
        0.43         1.78         8.02         6.51         0.33         0.33 
TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0G0 TCGA-AO-A0J2 
        0.33         0.36         0.33         0.33         0.53        32.78 
TCGA-AO-A0J3 TCGA-AO-A124 TCGA-AO-A12C TCGA-AO-A12D TCGA-AO-A1KS TCGA-AQ-A0Y5 
       21.40       102.58        65.56        64.04         0.53         5.65 
TCGA-AR-A0TT TCGA-AR-A0TY TCGA-AR-A0U2 TCGA-AR-A1AO TCGA-AR-A1AU TCGA-AR-A1AX 
       86.66        55.86        83.87        43.56        76.21        62.14 
TCGA-AR-A24L TCGA-AR-A24U TCGA-AR-A251 TCGA-AR-A5QQ TCGA-B6-A0I9 TCGA-B6-A0IO 
       73.02        53.36        78.48        10.59        12.13       110.14 
TCGA-B6-A0RG TCGA-B6-A0RS TCGA-BH-A0B3 TCGA-BH-A0B7 TCGA-BH-A0BG TCGA-BH-A0BL 
       68.45       100.70        39.55        56.98        24.85        44.05 
TCGA-BH-A0BT TCGA-BH-A0BW TCGA-BH-A0C3 TCGA-BH-A0DL TCGA-BH-A0EE TCGA-BH-A0RX 
       45.57        11.67        48.13        48.23        31.00         5.59 
TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1F0 TCGA-BH-A1FN TCGA-BH-A1FU TCGA-BH-A202 
       51.39        51.16        25.81        72.07        72.07         0.72 
TCGA-BH-A203 TCGA-BH-A208 TCGA-C8-A12L TCGA-C8-A12W TCGA-C8-A130 TCGA-C8-A131 
       38.60        57.83        11.93        12.66         3.12         1.78 
TCGA-C8-A135 TCGA-C8-A1HN TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A275 TCGA-C8-A27A 
        0.62         3.25         0.36         0.43         0.03        12.20 
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-A1X5 TCGA-D8-A1XU TCGA-D8-A1XZ TCGA-D8-A27R TCGA-E2-A108 
       20.12        18.58        12.99        15.32        10.09        27.52 
TCGA-E2-A14P TCGA-E2-A14W TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A159 TCGA-E2-A15F 
       40.96        32.02        17.03        25.41        25.05        21.63 
TCGA-E2-A15I TCGA-E2-A1B0 TCGA-E2-A1LA TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LL 
       17.42        53.62        24.59        28.90       106.75        43.04 
TCGA-E2-A1LS TCGA-E2-A574 TCGA-E9-A1R5 TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A243 
       15.45        19.89         1.38         6.58        34.59        17.06 
TCGA-E9-A248 TCGA-E9-A5FL TCGA-EW-A1OY TCGA-EW-A1P1 TCGA-EW-A1P7 TCGA-EW-A1PH 
        1.94         0.26        29.85        39.78        30.08        19.96 
TCGA-EW-A2FR TCGA-EW-A2FS TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DH 
       55.00        52.73       194.27        53.13        43.04        42.28 
TCGA-JL-A3YW TCGA-LL-A5YL TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A73Y TCGA-LL-A73Z 
       11.84        17.06        14.47        14.79         4.14         4.50 
TCGA-LL-A8F5 TCGA-OK-A5Q2 TCGA-OL-A5RW TCGA-OL-A66N TCGA-OL-A66P TCGA-S3-AA15 
        6.21         2.10        36.36        26.04        14.07         6.87 

$subtype3
TCGA-A1-A0SD TCGA-A1-A0SI TCGA-A2-A04N TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CO 
       14.37        20.88       104.81        36.13       136.73       112.08 
TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CU TCGA-A2-A0CZ TCGA-A2-A0EM TCGA-A2-A0EP 
       92.48       107.93         5.19        53.13       101.72       107.61 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EU TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0SU 
       74.40        37.05        34.29        29.75        24.72        54.64 
TCGA-A2-A0T4 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL 
       20.52        32.55        25.28        14.50        19.33        48.46 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25D 
       22.45        20.25        16.47        52.47       107.70        18.15 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XW TCGA-A2-A3XZ TCGA-A2-A4RY TCGA-A2-A4S2 
       20.88        39.65        49.48        31.99        21.30        21.14 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A13H TCGA-A7-A26H TCGA-A7-A3IZ TCGA-A7-A3J1 
       34.29        35.47        29.56        23.80        10.59        11.28 
TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SC TCGA-A7-A56D 
       14.70        11.97        14.93        13.74        14.66        14.73 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VX TCGA-A8-A07J TCGA-A8-A08A TCGA-A8-A0A1 
       10.72        11.05        10.42        12.00         0.99        12.00 
TCGA-A8-A0A6 TCGA-AC-A23G TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG 
       21.04        10.85        38.20        40.57        55.43        36.99 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3HN 
       38.79        26.04        50.70         0.92         0.99         0.69 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI 
       14.83        22.19         1.12        16.57        19.79        23.24 
TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A8OP TCGA-AN-A049 TCGA-AN-A0FF TCGA-AN-A0FN 
        1.81         1.18         1.74         0.62         4.64         7.17 
TCGA-AN-A0FS TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A0JF 
        6.28         0.33         5.33        68.75        47.87        21.37 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12E 
       26.24        50.24        62.04       108.72       106.78        57.30 
TCGA-AO-A1KO TCGA-AQ-A1H3 TCGA-AQ-A7U7 TCGA-AR-A0TR TCGA-AR-A1AK TCGA-AR-A1AL 
       14.73        32.52         9.99         5.26        51.25        48.82 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A24K TCGA-AR-A24M TCGA-AR-A24O TCGA-AR-A24P 
       62.56        43.73        50.89        96.89        84.20         0.85 
TCGA-AR-A24T TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       76.01        85.35        50.96       128.65        20.25        62.86 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QM 
        7.36        40.04        38.17        39.39        40.54        54.74 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0IH TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IP 
       16.04        20.45       112.37        18.77       126.12       110.93 
TCGA-B6-A0RM TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RV TCGA-B6-A0X0 TCGA-B6-A1KI 
       78.02       102.77       140.48       157.41       129.70        73.51 
TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A40C TCGA-BH-A0BA TCGA-BH-A0BD TCGA-BH-A0BJ 
      170.17        85.35        55.00        37.22        18.21        21.70 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0DE TCGA-BH-A0DG 
       61.68        35.67        49.05        44.02        31.17        23.44 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0E2 
       22.13        13.91        17.26        38.47        45.17        14.30 
TCGA-BH-A0E9 TCGA-BH-A0EI TCGA-BH-A0H3 TCGA-BH-A0HF TCGA-BH-A0HK TCGA-BH-A0HP 
       46.19        24.43        37.78        23.90         5.85        13.61 
TCGA-BH-A0HY TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A18M TCGA-BH-A1EU TCGA-BH-A1EX 
       50.79        24.95        42.35        72.56        42.28        49.58 
TCGA-BH-A1FB TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A201 
      120.62        74.73       122.89        36.92        63.35         6.90 
TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
      130.16        10.65         6.44        20.12         0.99       109.28 
TCGA-BH-A42V TCGA-C8-A137 TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Z TCGA-C8-A273 
        8.94         3.85         0.30         0.23         8.28         9.67 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1JB TCGA-D8-A1JH 
        0.03         0.23        13.48        21.14        18.71        14.01 
TCGA-D8-A1JU TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XJ TCGA-D8-A1XL 
       14.70        16.73        25.74        23.90        21.83        19.92 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XY TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27G 
       17.69         7.96        16.54        14.24        17.42        13.45 
TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T 
       14.43         9.44        16.41         4.80         0.76        13.08 
TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A107 TCGA-E2-A14Q 
       12.26        14.50        18.51         7.33        34.42        38.24 
TCGA-E2-A14U TCGA-E2-A15E TCGA-E2-A15L TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1IF 
       43.33        20.71        20.58        53.03        29.95        37.41 
TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IN TCGA-E2-A1L6 TCGA-E2-A2P5 
       33.73        28.44        22.65        22.19        54.18        16.93 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A572 TCGA-E2-A576 TCGA-E9-A1N4 
        5.52        15.72         7.20        27.32        19.00        19.20 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R3 TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RI 
       11.90        14.30         2.10        20.81         0.66        35.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A22A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT 
       34.13         0.79        39.09         0.72        17.75         0.76 
TCGA-E9-A3X8 TCGA-E9-A5FK TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IX TCGA-EW-A1J2 
       15.72        14.70        14.40        15.39        39.72        13.25 
TCGA-EW-A1PA TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A3E8 
       18.90        13.94        10.52        14.43        34.55        21.27 
TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DC TCGA-GM-A2DI TCGA-GM-A2DK 
       10.59         7.40        59.57        53.52        61.91        62.33 
TCGA-GM-A2DL TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
       90.84        77.33        53.36       110.50        38.20        43.73 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YX TCGA-LD-A66U 
       66.38        72.03        13.55        18.12        11.57        21.24 
TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A50Y 
        6.67         4.08         4.60         8.75         9.53         7.59 
TCGA-LL-A5YM TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A740 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
       15.32        11.57         2.63         4.50         7.36        27.91 
TCGA-MS-A51U TCGA-OL-A5D6 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX 
        2.79        12.66        58.62        27.65        34.92        16.87 
TCGA-OL-A5RY TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66O 
       24.72        26.70        65.62        33.57        31.07         7.23 
TCGA-OL-A6VQ TCGA-PL-A8LY TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA11 TCGA-S3-AA14 
       19.73         0.26         6.81         8.65         5.56         7.17 
TCGA-W8-A86G TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
        5.29         9.60         9.14       100.01 

$subtype4
TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SH TCGA-A1-A0SN TCGA-A2-A04V TCGA-A2-A0CQ 
       43.43        48.10        47.24        39.32        63.12        88.60 
TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0D3 TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0SY 
       75.55        63.45        28.77        89.36        80.28        44.28 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A7-A0CJ TCGA-A7-A13G TCGA-A8-A06Y 
       17.46        18.90        20.75        30.61        23.61        26.01 
TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A092 
       19.99        18.97        18.97        93.04        40.01        30.97 
TCGA-A8-A093 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09E 
       17.95         9.99         9.99        12.00         1.02        49.05 
TCGA-A8-A09N TCGA-A8-A09T TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0AB TCGA-AC-A23E 
        1.02        19.04        19.04        13.02        17.03         2.37 
TCGA-AC-A3YJ TCGA-AC-A6NO TCGA-AN-A03Y TCGA-AN-A0AS TCGA-AN-A0FD TCGA-AN-A0XL 
       24.79         1.68         0.33         0.33         6.44         0.33 
TCGA-AN-A0XO TCGA-AN-A0XS TCGA-AN-A0XW TCGA-AO-A03N TCGA-AO-A0J8 TCGA-AO-A0J9 
       12.33         0.33         5.59        66.77        22.36        53.03 
TCGA-AO-A125 TCGA-AO-A12A TCGA-AR-A0U3 TCGA-AR-A1AP TCGA-AR-A1AV TCGA-AR-A24H 
       99.25        90.58       114.02        39.98        61.28       109.58 
TCGA-AR-A24N TCGA-AR-A24X TCGA-AR-A255 TCGA-AR-A2LK TCGA-B6-A0I5 TCGA-B6-A0RH 
       78.51        83.77        58.92        42.87       149.59       189.01 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A1KN TCGA-B6-A408 
      172.96       162.05        79.63        17.98       139.17        49.94 
TCGA-B6-A40B TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B5 TCGA-BH-A0BF TCGA-BH-A0BQ 
      103.63        46.95        40.83        48.36        25.71        27.19 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0EA TCGA-BH-A0HN 
       53.69        53.95        15.65         2.56        32.65        16.96 
TCGA-BH-A0HQ TCGA-BH-A0W7 TCGA-BH-A18F TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K 
       36.85        44.81         8.81         7.23        20.12        90.84 
TCGA-BH-A18P TCGA-BH-A1EY TCGA-BH-A1FL TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A138 
       30.28        17.69        55.00        11.77        12.66         3.75 
TCGA-C8-A1HE TCGA-D8-A1JS TCGA-D8-A1XB TCGA-D8-A1XS TCGA-D8-A1Y1 TCGA-E2-A10B 
       12.33        12.20        18.15        16.31         3.81        37.51 
TCGA-E2-A10F TCGA-E2-A14V TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A15D TCGA-E2-A15G 
       28.87        34.26        23.24        19.43        17.29        18.21 
TCGA-E2-A15J TCGA-E2-A15O TCGA-E2-A1BD TCGA-E2-A1IL TCGA-E2-A1IU TCGA-E2-A1L8 
       19.40        13.02        17.10         3.88        11.08        39.62 
TCGA-E2-A1L9 TCGA-E2-A570 TCGA-E9-A1N5 TCGA-E9-A1NI TCGA-E9-A1RA TCGA-E9-A1RC 
       19.66        30.61        36.82         9.86        32.09        40.24 
TCGA-E9-A249 TCGA-EW-A1IW TCGA-EW-A1IY TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1P3 
        0.95        12.20         8.48        16.57        15.68        52.96 
TCGA-EW-A1P6 TCGA-S3-A6ZF TCGA-S3-AA17 TCGA-Z7-A8R6 
       18.48        16.50         3.91       105.04 

$subtype5
TCGA-A1-A0SG TCGA-A1-A0SQ TCGA-A2-A04R TCGA-A2-A0D4 TCGA-A2-A0ET TCGA-A2-A0YF 
       14.27        18.21        82.16        25.22        35.05        15.42 
TCGA-A2-A1G4 TCGA-A7-A0CD TCGA-A7-A3IY TCGA-A8-A06P TCGA-A8-A06T TCGA-A8-A06Z 
       19.56        38.30        11.34        13.02        53.06         1.02 
TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07Z TCGA-A8-A085 TCGA-A8-A086 
       17.03        10.98         7.99        28.04        36.95        13.02 
TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A091 TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A0A9 
       19.96        12.00        33.01        25.02         8.98        13.02 
TCGA-A8-A0AD TCGA-AC-A8OR TCGA-AN-A041 TCGA-AN-A0FK TCGA-AN-A0XP TCGA-AN-A0XR 
       38.04         1.32         0.23         7.00         0.30         0.33 
TCGA-AO-A12B TCGA-AO-A12H TCGA-AO-A1KQ TCGA-AQ-A04H TCGA-AQ-A54O TCGA-AR-A0TV 
       77.56        28.37        61.87        24.79        32.91        29.75 
TCGA-AR-A24R TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0RI TCGA-B6-A0WT TCGA-B6-A0X5 
       87.22       220.90        50.70       234.28       188.68        68.94 
TCGA-BH-A0C0 TCGA-BH-A0DH TCGA-BH-A0DQ TCGA-BH-A0E1 TCGA-BH-A0E7 TCGA-BH-A0H6 
       41.75        38.01         3.22        15.68        44.81        24.56 
TCGA-BH-A0HO TCGA-BH-A0HW TCGA-BH-A0W3 TCGA-BH-A18N TCGA-BH-A18S TCGA-BH-A1F5 
        2.50        51.32        23.93        37.74        66.05        89.16 
TCGA-C8-A12X TCGA-C8-A1HL TCGA-D8-A1JE TCGA-D8-A1JI TCGA-D8-A1JT TCGA-D8-A1X6 
       12.66        10.42        18.90        18.97        13.32        17.79 
TCGA-D8-A1XR TCGA-E2-A106 TCGA-E2-A10A TCGA-E2-A14S TCGA-E2-A156 TCGA-E2-A1BC 
       15.85        59.41        40.41        33.17        23.87        16.47 
TCGA-E9-A1R7 TCGA-E9-A24A TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5UO TCGA-EW-A1J1 
       21.21        24.56        12.33         0.23        13.81        18.90 
TCGA-EW-A1OX TCGA-EW-A1P0 TCGA-EW-A1P5 TCGA-EW-A2FW TCGA-GM-A2DM TCGA-LL-A442 
       29.95        41.13        23.11        22.09        76.64        10.95 
TCGA-PL-A8LX TCGA-S3-AA12 
        0.16         8.52 

$subtype6
TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A0CM TCGA-A2-A0D0 
       28.01        19.20        73.84        22.06        24.79        21.14 
TCGA-A2-A0SX TCGA-A2-A0YM TCGA-A2-A25F TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XX 
       50.43        31.73        10.59        83.01        29.98        38.40 
TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RX TCGA-A7-A0CE TCGA-A7-A0DA TCGA-A7-A13D 
       34.98        38.37        24.39        35.31        35.67        31.73 
TCGA-A7-A13E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A4SE TCGA-A7-A5ZV TCGA-A7-A6VV 
       10.72        24.26        23.74        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        33.99         9.99         8.98        24.99 
TCGA-A8-A08R TCGA-AC-A2BK TCGA-AC-A62X TCGA-AC-A6IW TCGA-AC-A8OQ TCGA-AN-A0FJ 
        0.99        38.53         1.12         0.69         1.12         7.96 
TCGA-AN-A0FL TCGA-AN-A0FX TCGA-AN-A0XU TCGA-AO-A03U TCGA-AO-A0J4 TCGA-AO-A0J6 
        7.59         0.33         0.33        59.05        52.18        37.48 
TCGA-AO-A0JL TCGA-AO-A129 TCGA-AO-A12F TCGA-AO-A1KR TCGA-AQ-A04J TCGA-AQ-A54N 
       55.33        96.10        48.36        70.39        26.93         2.56 
TCGA-AR-A0TP TCGA-AR-A0TS TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ 
      111.32        74.79        85.97        75.55        61.84        52.77 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AY TCGA-AR-A24Q TCGA-AR-A256 TCGA-AR-A2LR 
       43.07        17.23        20.22       101.52        93.83        20.38 
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-A0X7 TCGA-B6-A1KF TCGA-B6-A402 
       89.46       131.21        21.47        58.88       101.52        54.28 
TCGA-BH-A0AV TCGA-BH-A0B9 TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0WA TCGA-BH-A18G 
       38.79        51.68         4.41         9.63        23.05         2.01 
TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A1F6 TCGA-BH-A1FC TCGA-C8-A12V TCGA-C8-A134 
       55.63         7.36        97.48       114.15        12.66         0.69 
TCGA-C8-A1HJ TCGA-C8-A27B TCGA-D8-A147 TCGA-D8-A1JL TCGA-D8-A1XK TCGA-D8-A1XQ 
        0.16         0.99        19.20        20.09        14.50        16.41 
TCGA-D8-A1XW TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27M TCGA-E2-A14N TCGA-E2-A14R 
       12.66        16.04        13.05        13.48        47.15        38.60 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A158 TCGA-E2-A1AZ TCGA-E2-A1B6 TCGA-E2-A1II 
       31.96        28.60        14.79        60.53        28.50        33.70 
TCGA-E2-A1LG TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A573 TCGA-E9-A1N8 TCGA-E9-A1ND 
       18.87       102.61         8.75        34.92        12.00        12.59 
TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A3QA TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P8 
       23.51         0.69         0.62        22.82        29.82         7.86 
TCGA-EW-A1PB TCGA-EW-A3U0 TCGA-GI-A2C9 TCGA-GM-A2DF TCGA-GM-A3XL TCGA-LL-A441 
       19.99        17.49       109.87        42.71        69.30        11.44 
TCGA-LL-A6FR TCGA-OL-A5D7 TCGA-OL-A5S0 TCGA-OL-A66I TCGA-OL-A6VO TCGA-PL-A8LV 
        3.88        46.55        20.38        23.47        28.21         0.23 
TCGA-PL-A8LZ TCGA-S3-AA0Z TCGA-S3-AA10 
        3.95        10.59         7.92 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.03     0.03     0.03     0.33     0.16     0.16 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  146.50   194.27   170.17   189.01   234.28   211.56 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  23.275   20.040   21.190   24.200   22.600   24.390 
[1] "0.0 - 146.5 (23.3)" "0.0 - 194.3 (20.0)" "0.0 - 170.2 (21.2)"
[4] "0.3 - 189.0 (24.2)" "0.2 - 234.3 (22.6)" "0.2 - 211.6 (24.4)"
D10V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1      14       16        2        0        73        52         0
  subtype2      13        9        1        2        53        33         0
  subtype3      25       29        5        3        78        78         1
  subtype4      17        9        1        0        45        23         1
  subtype5       7        6        1        0        30        21         0
  subtype6       7       13        0        0        63        26         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
  subtype1         42          7         14        5         1       5
  subtype2         20          3         11        6         0       1
  subtype3         44          6         28        1         0       1
  subtype4         11          5          5        3         0       6
  subtype5         13          5          0        1         0       1
  subtype6         10          2          4        1         0       3
D10V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I          14       13       25       17        7        7
  STAGE IA         16        9       29        9        6       13
  STAGE IB          2        1        5        1        1        0
  STAGE II          0        2        3        0        0        0
  STAGE IIA        73       53       78       45       30       63
  STAGE IIB        52       33       78       23       21       26
  STAGE III         0        0        1        1        0        0
  STAGE IIIA       42       20       44       11       13       10
  STAGE IIIB        7        3        6        5        5        2
  STAGE IIIC       14       11       28        5        0        4
  STAGE IV          5        6        1        3        1        1
  STAGE TIS         1        0        0        0        0        0
  STAGE X           5        1        1        6        1        3
[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  52 139  29  10
  subtype2  40  95  13   4
  subtype3  92 147  54   5
  subtype4  35  74   7  10
  subtype5  24  46   9   6
  subtype6  27  88  10   4
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1       52       40       92       35       24       27
  T2      139       95      147       74       46       88
  T3       29       13       54        7        9       10
  T4       10        4        5       10        6        4
[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  90  83  33  18
  subtype2  73  43  21  12
  subtype3 129 107  30  29
  subtype4  68  37  10   9
  subtype5  38  36   9   0
  subtype6  85  32   8   4
D10V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0       90       73      129       68       38       85
  N1       83       43      107       37       36       32
  N2       33       21       30       10        9        8
  N3       18       12       29        9        0        4
[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        1 203   6  21
  subtype2        1 126   6  19
  subtype3        1 231   1  66
  subtype4        2 107   3  14
  subtype5        0  73   1  11
  subtype6        0 112   1  17
D10V6, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  CM0 (I+)        1        1        1        2        0        0
  M0            203      126      231      107       73      112
  M1              6        6        1        3        1        1
  MX             21       19       66       14       11       17
[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"
D10V7, binary
          cls
clus         0   1
  subtype1 229   2
  subtype2 149   3
  subtype3 298   1
  subtype4 124   2
  subtype5  82   3
  subtype6 130   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  229    2
  subtype2  149    3
  subtype3  298    1
  subtype4  124    2
  subtype5   82    3
  subtype6  130    0
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE      229      149      298      124       82      130
  MALE          2        3        1        2        3        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                          0                           198
  subtype2                          0                           133
  subtype3                          0                           148
  subtype4                          0                            94
  subtype5                          0                            67
  subtype6                          1                           114
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                             12                   0
  subtype2                              9                   0
  subtype3                            130                   1
  subtype4                             21                   0
  subtype5                              1                   0
  subtype6                              1                   5
          vv
clus       MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                                6                  5             10
  subtype2                                1                  0              9
  subtype3                                9                  3              8
  subtype4                                7                  0              4
  subtype5                                4                  7              6
  subtype6                                1                  0              7
D10V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  INFILTRATING CARCINOMA NOS              0        0        0        0        0
  INFILTRATING DUCTAL CARCINOMA         198      133      148       94       67
  INFILTRATING LOBULAR CARCINOMA         12        9      130       21        1
  MEDULLARY CARCINOMA                     0        0        1        0        0
  MIXED HISTOLOGY (PLEASE SPECIFY)        6        1        9        7        4
  MUCINOUS CARCINOMA                      5        0        3        0        7
  OTHER  SPECIFY                         10        9        8        4        6
                                  clus
vv                                 subtype6
  INFILTRATING CARCINOMA NOS              1
  INFILTRATING DUCTAL CARCINOMA         114
  INFILTRATING LOBULAR CARCINOMA          1
  MEDULLARY CARCINOMA                     5
  MIXED HISTOLOGY (PLEASE SPECIFY)        1
  MUCINOUS CARCINOMA                      0
  OTHER  SPECIFY                          7
[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"
D10V9, binary
          cls
clus         0   1
  subtype1  82 149
  subtype2  47 105
  subtype3  55 244
  subtype4  33  93
  subtype5  24  61
  subtype6  37  93
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   82  149
  subtype2   47  105
  subtype3   55  244
  subtype4   33   93
  subtype5   24   61
  subtype6   37   93
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO        82       47       55       33       24       37
  YES      149      105      244       93       61       93
[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"
D10V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1    18                        22
  subtype2                                0    11                        22
  subtype3                                0    13                        45
  subtype4                                0     6                        12
  subtype5                                0     4                         9
  subtype6                                0     5                        49
          vv
clus       WHITE
  subtype1   170
  subtype2   104
  subtype3   235
  subtype4    89
  subtype5    50
  subtype6    70
D10V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0        0        0
  ASIAN                                  18       11       13        6        4
  BLACK OR AFRICAN AMERICAN              22       22       45       12        9
  WHITE                                 170      104      235       89       50
                                  clus
vv                                 subtype6
  AMERICAN INDIAN OR ALASKA NATIVE        0
  ASIAN                                   5
  BLACK OR AFRICAN AMERICAN              49
  WHITE                                  70
[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"
D10V12, binary
          cls
clus         0   1
  subtype1   5 183
  subtype2   5 125
  subtype3  13 260
  subtype4   5  94
  subtype5   5  50
  subtype6   3 113
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5  183
  subtype2    5  125
  subtype3   13  260
  subtype4    5   94
  subtype5    5   50
  subtype6    3  113
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            5        5       13        5        5        3
  NOT HISPANIC OR LATINO      183      125      260       94       50      113
[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(11) Variable = MIRSEQ_MATURE_CNMF
D11V1, survival
          sevent
clus2        0   1
  subtype1 149  24
  subtype2 113  16
  subtype3  80   3
  subtype4  88  13
  subtype5 111   8
subtype1 subtype2 subtype3 subtype4 subtype5 
     173      129       83      101      119 
subtype1 subtype2 subtype3 subtype4 subtype5 
      24       16        3       13        8 
$subtype1
TCGA-A1-A0SN TCGA-A2-A0CS TCGA-A2-A0D3 TCGA-A2-A0T3 TCGA-A2-A1FW TCGA-A2-A1FZ 
       39.32        75.55        28.77        18.71        17.36        22.45 
TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A25B TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A3J0 
       20.25        19.56        16.31        12.72        23.61        10.29 
TCGA-A7-A3RF TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23H TCGA-AO-A03V TCGA-AO-A12A 
       13.41         0.95         2.37         2.66        29.13        90.58 
TCGA-AO-A12H TCGA-AO-A1KP TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A1H2 TCGA-AR-A0TY 
       28.37        82.62         0.53        17.79        15.62        55.86 
TCGA-AR-A1AK TCGA-AR-A1AP TCGA-AR-A1AT TCGA-AR-A1AV TCGA-AR-A24H TCGA-AR-A24L 
       51.25        39.98        41.82        61.28       109.58        73.02 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24R TCGA-AR-A24V TCGA-AR-A24X TCGA-AR-A24Z 
       96.89        78.51        87.22        85.35        83.77        79.00 
TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A255 TCGA-B6-A0RH TCGA-B6-A1KN TCGA-BH-A0AU 
       56.15        73.18        58.92       189.01       139.17        24.53 
TCGA-BH-A0B7 TCGA-BH-A0BP TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0DD 
       56.98        48.69        53.69        53.95        45.57        45.83 
TCGA-BH-A0DG TCGA-BH-A0H5 TCGA-BH-A0HA TCGA-BH-A0HN TCGA-BH-A18I TCGA-BH-A18K 
       23.44        35.51        52.96        16.96         7.23        90.84 
TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18S TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1EV 
       26.66        37.74        66.05        69.93       113.82        12.00 
TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F5 TCGA-BH-A1F8 TCGA-BH-A1FL TCGA-BH-A1FM 
       49.58        17.69        89.16        24.66        55.00        45.63 
TCGA-BH-A1FR TCGA-BH-A202 TCGA-BH-A204 TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12Q 
      144.59         0.72        83.31        11.77        12.66         0.07 
TCGA-C8-A12U TCGA-C8-A12X TCGA-C8-A132 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF 
       12.66        12.66         1.45         3.75        12.33        10.92 
TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN 
       11.34        11.34        12.03        10.42         2.30         3.25 
TCGA-C8-A27A TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A1J8 TCGA-D8-A1J9 
       12.20        11.90        13.25        20.58        14.17        17.49 
TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JP 
       15.78        18.15        18.90        18.97        20.09        21.01 
TCGA-D8-A1JS TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1XA TCGA-D8-A1XC 
       12.20        18.58        17.79        16.73        27.58         2.66 
TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XU 
       17.16        15.22         7.96        15.85        16.31        12.99 
TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A27V TCGA-E2-A10A 
       15.16        16.54        15.52         3.81        12.53        40.41 
TCGA-E2-A14O TCGA-E2-A14T TCGA-E2-A14W TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A15C 
       44.68        33.30        32.02        27.12        19.43        22.82 
TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15K TCGA-E2-A15O TCGA-E2-A15R 
       18.21        12.92        17.42         9.04        13.02        17.06 
TCGA-E2-A15T TCGA-E2-A1B5 TCGA-E2-A1IE TCGA-E2-A1IG TCGA-E2-A1IL TCGA-E2-A1IN 
       14.99        32.35        38.30        32.78         3.88        22.19 
TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E9-A1N6 
       20.98        11.08        39.62        19.66        40.47        13.48 
TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R5 
       35.77        20.05        21.57         0.62         6.12         1.38 
TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RF 
        2.76        21.21        32.09        40.24        34.65         6.58 
TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22B TCGA-E9-A22E 
       21.27        35.64        12.53        13.32        22.75        12.89 
TCGA-E9-A22H TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A24A TCGA-EW-A1IY TCGA-EW-A1J1 
       24.10        27.22         0.95        24.56         8.48        18.90 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OY TCGA-EW-A1OZ 
       16.57        15.68        28.77        25.94        29.85        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P6 TCGA-EW-A2FS TCGA-EW-A2FW TCGA-OL-A5RZ 
       41.13        18.48        52.73        22.09        22.32 

$subtype2
TCGA-A2-A04U TCGA-A2-A0CL TCGA-A2-A1G1 TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU 
       22.06        64.57        19.20        33.93        83.01        29.98 
TCGA-A2-A3XX TCGA-A2-A3Y0 TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A7-A0DA TCGA-A7-A13D 
       38.40        38.37        24.39        26.96        35.67        31.73 
TCGA-A7-A13E TCGA-A7-A26I TCGA-A7-A4SD TCGA-A7-A5ZV TCGA-A7-A6VV TCGA-A7-A6VW 
       10.72        21.73        14.50        12.10        10.29         9.37 
TCGA-A7-A6VY TCGA-AC-A2BK TCGA-AC-A3W5 TCGA-AC-A62X TCGA-AC-A6IW TCGA-AC-A8OQ 
        8.75        38.53        16.57         1.12         0.69         1.12 
TCGA-AN-A0AT TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AR-A0TS TCGA-AR-A1AH 
        0.33        48.36        61.87        70.39        74.79        75.55 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AW TCGA-AR-A1AY 
       61.84        52.77        43.07        17.23        63.62        20.22 
TCGA-AR-A24Q TCGA-AR-A24U TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A5QQ 
      101.52        53.36        78.48        72.76        93.83        10.59 
TCGA-B6-A0I1 TCGA-B6-A1KF TCGA-B6-A402 TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BW 
       77.62       101.52        54.28        24.85        44.05        11.67 
TCGA-BH-A0DL TCGA-BH-A18R TCGA-BH-A18V TCGA-BH-A1F0 TCGA-BH-A1F6 TCGA-BH-A1FN 
       48.23        37.55        51.16        25.81        97.48        72.07 
TCGA-BH-A209 TCGA-C8-A12L TCGA-C8-A12V TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A135 
      130.16        11.93        12.66         1.78         0.69         0.62 
TCGA-C8-A1HJ TCGA-C8-A278 TCGA-C8-A27B TCGA-D8-A143 TCGA-D8-A147 TCGA-D8-A1JG 
        0.16         0.03         0.99        14.17        19.20        12.03 
TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1XK TCGA-D8-A1XQ TCGA-D8-A1XT TCGA-D8-A1XW 
       20.12        20.09        14.50        16.41         6.35        12.66 
TCGA-D8-A1XZ TCGA-D8-A1Y3 TCGA-D8-A27F TCGA-D8-A27M TCGA-E2-A14N TCGA-E2-A14P 
       15.32        14.14        16.04        13.48        47.15        40.96 
TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A159 TCGA-E2-A15M 
       38.60        31.96        28.60        25.41        25.05         7.73 
TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B6 TCGA-E2-A1II TCGA-E2-A1L7 TCGA-E2-A1LA 
       60.53        53.62        28.50        33.70        27.42        24.59 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LS TCGA-E2-A573 TCGA-E2-A574 
      106.75       102.61         8.75        15.45        34.92        19.89 
TCGA-E2-A9RU TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1ND TCGA-E9-A1RH TCGA-E9-A22G 
        9.21        12.00        13.12        12.59        34.59        23.51 
TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A3QA TCGA-EW-A1IZ TCGA-EW-A1OW TCGA-EW-A1P4 
        0.69         1.94         0.62        18.21        22.82        29.82 
TCGA-EW-A1P7 TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A3U0 TCGA-GI-A2C9 TCGA-GM-A2DF 
       30.08        19.99         6.15        17.49       109.87        42.71 
TCGA-GM-A3XL TCGA-LL-A441 TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y 
       69.30        11.44        14.47        14.79         3.88         4.14 
TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-OL-A66I TCGA-OL-A66P TCGA-OL-A6VO TCGA-PL-A8LV 
       36.36        20.38        23.47        14.07        28.21         0.23 
TCGA-PL-A8LZ TCGA-S3-AA0Z TCGA-S3-AA10 
        3.95        10.59         7.92 

$subtype3
TCGA-5T-A9QA TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 
        0.39        23.47        36.79         7.30        21.30        23.21 
TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SC 
       21.14        21.90        14.70        14.93        13.74        14.66 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZX TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y 
       17.92        14.73        11.05         1.55         0.07         1.81 
TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AQ-A54O TCGA-AR-A5QM TCGA-AR-A5QN 
        1.68         1.74         1.32        32.91        54.74        16.04 
TCGA-AR-A5QP TCGA-B6-A408 TCGA-BH-A0DO TCGA-BH-A0HL TCGA-BH-A42T TCGA-BH-A42U 
       20.45        49.94        17.26         2.37         0.99       109.28 
TCGA-BH-A42V TCGA-D8-A3Z5 TCGA-D8-A4Z1 TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A15F 
        8.94        14.50         7.33        38.24        33.17        21.63 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A572 TCGA-E2-A576 TCGA-E9-A54Y TCGA-E9-A5FK 
        7.20        30.61        27.32        19.00         0.23        14.70 
TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A3E8 TCGA-EW-A424 TCGA-GM-A3XG 
       13.81        14.40        15.39        21.27        10.59        43.73 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-LD-A66U TCGA-LD-A7W6 TCGA-LL-A442 
       72.03        13.55        18.12        21.24         4.60        10.95 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A6FP TCGA-LL-A6FQ 
        7.59        17.06        15.32        14.70        11.57         2.63 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 
        7.36        27.91         2.79         2.10        12.66        31.99 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A66H 
       58.62        27.65        34.92        16.87        24.72        26.70 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-PL-A8LX TCGA-S3-AA11 
       65.62        33.57        31.07        26.04         0.16         5.56 
TCGA-S3-AA12 TCGA-S3-AA17 TCGA-XX-A899 TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        8.52         3.91         9.60       100.01       105.04 

$subtype4
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SF TCGA-A1-A0SI TCGA-A2-A04W TCGA-A2-A0CV 
        8.52        14.37        48.10        20.88        64.04        63.45 
TCGA-A2-A0EP TCGA-A2-A0ES TCGA-A2-A1G6 TCGA-A7-A26E TCGA-A7-A26G TCGA-A7-A26J 
      107.61        37.05        16.47        31.36        23.74        20.61 
TCGA-A7-A3IY TCGA-A7-A4SE TCGA-A7-A5ZW TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2FF 
       11.34        21.17        10.72        10.85         1.48        55.43 
TCGA-AC-A2FG TCGA-AC-A2QJ TCGA-AC-A3YI TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AO-A1KO 
       36.99         2.27        23.24         1.18         0.43        14.73 
TCGA-AQ-A1H3 TCGA-AQ-A7U7 TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AU 
       32.52         9.99        48.82        43.73        43.56        76.21 
TCGA-AR-A24O TCGA-AR-A24P TCGA-B6-A0IH TCGA-B6-A0WS TCGA-B6-A1KI TCGA-BH-A0AZ 
       84.20         0.85       112.37        97.48        73.51        28.50 
TCGA-BH-A0B0 TCGA-BH-A0B5 TCGA-BH-A0BQ TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DE 
       46.95        48.36        27.19        48.13        42.90        31.17 
TCGA-BH-A0DI TCGA-BH-A0DT TCGA-BH-A0DX TCGA-BH-A0E9 TCGA-BH-A0EI TCGA-BH-A0H3 
       22.13        38.47        47.41        46.19        24.43        37.78 
TCGA-BH-A18F TCGA-BH-A18M TCGA-BH-A1EO TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1F2 
        8.81        72.56        91.99        42.28        55.69        31.53 
TCGA-BH-A1FB TCGA-BH-A1FE TCGA-BH-A1FH TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A208 
      120.62        74.73        36.92        72.07         6.90        57.83 
TCGA-BH-A28O TCGA-D8-A13Z TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1JB TCGA-D8-A1JH 
       10.65        20.88        13.48        21.14        18.71        14.01 
TCGA-D8-A1JU TCGA-D8-A1XB TCGA-E2-A14U TCGA-E2-A153 TCGA-E2-A15D TCGA-E2-A15E 
       14.70        18.15        43.33        23.24        17.29        20.71 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1IJ 
       53.03        29.95        16.47        17.10        33.73        28.44 
TCGA-E2-A1IK TCGA-E2-A1L6 TCGA-E2-A3DX TCGA-E9-A1QZ TCGA-E9-A227 TCGA-E9-A3X8 
       22.65        54.18        15.72        11.90         0.79        15.72 
TCGA-E9-A5FL TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1J2 TCGA-EW-A1P1 TCGA-EW-A1PD 
        0.26        12.20        39.72        13.25        39.78        13.94 
TCGA-EW-A1PG TCGA-EW-A2FR TCGA-GM-A3XN TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A740 
       34.55        55.00        66.38         8.75         9.53         4.50 
TCGA-PL-A8LY TCGA-S3-AA14 TCGA-S3-AA15 TCGA-W8-A86G TCGA-XX-A89A 
        0.26         7.17         6.87         5.29         9.14 

$subtype5
TCGA-A2-A0CK TCGA-A2-A0CO TCGA-A2-A0CR TCGA-A2-A0CW TCGA-A2-A25A TCGA-A2-A25D 
      136.73       112.08       107.93        64.04       107.70        18.15 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XY TCGA-A2-A3XZ 
       20.88        39.65        32.75        49.48        34.98        31.99 
TCGA-A7-A0DB TCGA-A7-A13H TCGA-A7-A26H TCGA-A7-A2KD TCGA-A7-A3IZ TCGA-A7-A3J1 
       33.11        29.56        23.80        22.32        10.59        11.28 
TCGA-A7-A6VX TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO 
       10.42        38.20        40.57        38.79        26.04        50.70 
TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
        1.02         0.92         0.99         0.69        14.83        22.19 
TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3YJ TCGA-AR-A1AM TCGA-AR-A2LH TCGA-AR-A2LJ 
        1.12        19.79        24.79        62.56        20.25        62.86 
TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       42.87         7.36        40.04        38.17        39.39        40.54 
TCGA-AR-A2LR TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0B6 
       20.38       170.17        85.35       103.63        55.00        56.94 
TCGA-BH-A0E2 TCGA-BH-A0W7 TCGA-BH-A203 TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-C8-A130 
       14.30        44.81        38.60         6.44        20.12         3.12 
TCGA-C8-A137 TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z 
        3.85         0.30         0.23         0.36         0.43         8.28 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A1X9 
        9.67         0.03         0.03         0.03         0.23        23.90 
TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       17.42        13.45        13.05        14.43         9.44        16.41 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27W TCGA-D8-A3Z6 
        4.80         0.76        10.09        13.08        12.26        18.51 
TCGA-E2-A15P TCGA-E2-A1LE TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E9-A1R0 TCGA-E9-A1RD 
       19.56        28.90        16.93         5.52        14.30         0.66 
TCGA-E9-A226 TCGA-E9-A22A TCGA-E9-A245 TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT 
       34.13        39.09         0.85         0.72        17.75         0.76 
TCGA-E9-A3Q9 TCGA-EW-A1PA TCGA-EW-A2FV TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA 
       18.41        18.90        25.91         7.40        59.57       194.27 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK 
       53.13        53.52        43.04        42.28        61.91        62.33 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY 
       90.84        76.64        77.33        53.36       110.50        38.20 
TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LL-A73Z TCGA-LL-A7SZ 
       11.84        11.57         6.67         4.08         4.50         5.59 
TCGA-LL-A7T0 TCGA-OL-A6VQ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH 
        3.22        19.73        16.50         6.81         8.65 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.07     0.03     0.07     0.26     0.03 
subtype1 subtype2 subtype3 subtype4 subtype5 
  189.01   130.16   109.28   120.62   194.27 
subtype1 subtype2 subtype3 subtype4 subtype5 
   20.25    22.06    15.32    23.74    19.73 
[1] "0.1 - 189.0 (20.2)" "0.0 - 130.2 (22.1)" "0.1 - 109.3 (15.3)"
[4] "0.3 - 120.6 (23.7)" "0.0 - 194.3 (19.7)"
D11V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1      20       17        1        1        64        39         0
  subtype2      10        7        0        0        64        25         0
  subtype3       5        8        4        1        20        19         0
  subtype4      15        8        0        0        27        27         0
  subtype5      11        6        0        3        32        35         2
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  subtype1         26          4          5        1       1
  subtype2         17          3          3        0       1
  subtype3         11          1         13        2       0
  subtype4         12          2          7        1       2
  subtype5         14          3         12        1       0
D11V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          20       10        5       15       11
  STAGE IA         17        7        8        8        6
  STAGE IB          1        0        4        0        0
  STAGE II          1        0        1        0        3
  STAGE IIA        64       64       20       27       32
  STAGE IIB        39       25       19       27       35
  STAGE III         0        0        0        0        2
  STAGE IIIA       26       17       11       12       14
  STAGE IIIB        4        3        1        2        3
  STAGE IIIC        5        3       13        7       12
  STAGE IV          1        0        2        1        1
  STAGE X           1        1        0        2        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  59 101  13   6
  subtype2  27  91   8   5
  subtype3  19  45  18   2
  subtype4  42  45  12   2
  subtype5  28  66  22   3
D11V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       59       27       19       42       28
  T2      101       91       45       45       66
  T3       13        8       18       12       22
  T4        6        5        2        2        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"
          vv
clus       N0 N1 N2 N3
  subtype1 85 66 19  6
  subtype2 79 33 16  3
  subtype3 33 29  6 13
  subtype4 43 42  8  7
  subtype5 53 41 11 13
D11V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       85       79       33       43       53
  N1       66       33       29       42       41
  N2       19       16        6        8       11
  N3        6        3       13        7       13
[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        1 157   1  20
  subtype2        0 106   0  25
  subtype3        1  44   2  37
  subtype4        3  77   1  20
  subtype5        0  97   1  21
D11V6, multiclass
          clus
vv         subtype1 subtype2 subtype3 subtype4 subtype5
  CM0 (I+)        1        0        1        3        0
  M0            157      106       44       77       97
  M1              1        0        2        1        1
  MX             20       25       37       20       21
[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"
D11V7, binary
          cls
clus         0   1
  subtype1 175   4
  subtype2 130   1
  subtype3  82   2
  subtype4 100   1
  subtype5 119   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  175    4
  subtype2  130    1
  subtype3   82    2
  subtype4  100    1
  subtype5  119    0
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE      175      130       82      100      119
  MALE          4        1        2        1        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                           146
  subtype2                          1                           118
  subtype3                          0                            35
  subtype4                          0                            62
  subtype5                          0                            59
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                             11                   0
  subtype2                              2                   5
  subtype3                             43                   0
  subtype4                             29                   0
  subtype5                             52                   0
          vv
clus       MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                               10                  6              6
  subtype2                                1                  0              4
  subtype3                                1                  4              1
  subtype4                                2                  1              7
  subtype5                                1                  2              5
D11V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  INFILTRATING CARCINOMA NOS              0        1        0        0        0
  INFILTRATING DUCTAL CARCINOMA         146      118       35       62       59
  INFILTRATING LOBULAR CARCINOMA         11        2       43       29       52
  MEDULLARY CARCINOMA                     0        5        0        0        0
  MIXED HISTOLOGY (PLEASE SPECIFY)       10        1        1        2        1
  MUCINOUS CARCINOMA                      6        0        4        1        2
  OTHER  SPECIFY                          6        4        1        7        5
[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"
D11V9, binary
          cls
clus         0   1
  subtype1  62 117
  subtype2  41  90
  subtype3   4  80
  subtype4  23  78
  subtype5  17 102
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   62  117
  subtype2   41   90
  subtype3    4   80
  subtype4   23   78
  subtype5   17  102
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        62       41        4       23       17
  YES      117       90       80       78      102
[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"
D11V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1    20                        10   149
  subtype2     9                        48    73
  subtype3     0                        32    51
  subtype4     3                        12    84
  subtype5    15                        20    82
D11V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                           20        9        0        3       15
  BLACK OR AFRICAN AMERICAN       10       48       32       12       20
  WHITE                          149       73       51       84       82
[1] 3 5
[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   8 164
  subtype2   3 122
  subtype3   2  76
  subtype4   7  87
  subtype5   6 111
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8  164
  subtype2    3  122
  subtype3    2   76
  subtype4    7   87
  subtype5    6  111
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            8        3        2        7        6
  NOT HISPANIC OR LATINO      164      122       76       87      111
[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(12) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D12V1, survival
          sevent
clus2        0   1
  subtype1 246  40
  subtype2 198  11
  subtype3  97  13
subtype1 subtype2 subtype3 
     286      209      110 
subtype1 subtype2 subtype3 
      40       11       13 
$subtype1
TCGA-5T-A9QA TCGA-A2-A04U TCGA-A2-A0CL TCGA-A2-A0T3 TCGA-A2-A1FV TCGA-A2-A1FW 
        0.39        22.06        64.57        18.71        23.47        17.36 
TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A25B TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU 
       19.20        19.56        16.31        33.93        83.01        29.98 
TCGA-A2-A3XV TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4S0 TCGA-A2-A4S1 
       32.75        38.40        34.98        38.37        23.21        26.96 
TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A26G 
       35.67        31.73        10.72        12.72        23.61        23.74 
TCGA-A7-A26I TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A5ZV 
       21.73        10.29        13.41        14.50        17.92        12.10 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A2BK 
       10.29         9.37         8.75         0.95         2.66        38.53 
TCGA-AC-A3YJ TCGA-AC-A62X TCGA-AC-A6IW TCGA-AC-A8OR TCGA-AN-A0AT TCGA-AO-A03V 
       24.79         1.12         0.69         1.32         0.33        29.13 
TCGA-AO-A12F TCGA-AO-A12H TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS 
       48.36        28.37        82.62        61.87        70.39         0.53 
TCGA-AQ-A1H2 TCGA-AR-A0TS TCGA-AR-A0TY TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ 
       15.62        74.79        55.86        75.55        61.84        52.77 
TCGA-AR-A1AK TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AT 
       51.25        43.56        39.98        43.07        17.23        41.82 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L 
       76.21        61.28        63.62        20.22       109.58        73.02 
TCGA-AR-A24O TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A24Z 
       84.20       101.52        87.22        53.36        83.77        79.00 
TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
       56.15        78.48        73.18        72.76        58.92        93.83 
TCGA-AR-A2LR TCGA-B6-A0I1 TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A402 TCGA-BH-A0AU 
       20.38        77.62       101.52       139.17        54.28        24.53 
TCGA-BH-A0B7 TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0BR TCGA-BH-A0BS 
       56.98        24.85        44.05        48.69        53.69        53.95 
TCGA-BH-A0BT TCGA-BH-A0BW TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DL 
       45.57        11.67        48.13        42.90        45.83        48.23 
TCGA-BH-A0H5 TCGA-BH-A0HA TCGA-BH-A0HL TCGA-BH-A0HN TCGA-BH-A18F TCGA-BH-A18K 
       35.51        52.96         2.37        16.96         8.81        90.84 
TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18V TCGA-BH-A1EN 
       26.66        37.74        37.55        66.05        51.16        69.93 
TCGA-BH-A1ES TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1F5 
      113.82        12.00        55.69        49.58        25.81        89.16 
TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR 
       97.48        24.66        55.00        45.63        72.07       144.59 
TCGA-BH-A1FU TCGA-BH-A202 TCGA-BH-A204 TCGA-BH-A209 TCGA-C8-A12L TCGA-C8-A12O 
       72.07         0.72        83.31       130.16        11.93        12.66 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A131 
        0.07        12.66        12.66        12.66         3.12         1.78 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG 
        1.45         0.69         0.62        12.33        10.92        11.34 
TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN 
       11.34         0.16        12.03        10.42         2.30         3.25 
TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A143 
        0.03        12.20         0.99        11.90        13.25        14.17 
TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JC TCGA-D8-A1JG TCGA-D8-A1JI 
       19.20        14.17        17.49        15.78        12.03        18.97 
TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JS TCGA-D8-A1X5 TCGA-D8-A1X6 
       20.09        20.12        20.09        12.20        18.58        17.79 
TCGA-D8-A1X7 TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XK 
       16.73        27.58         2.66        17.16        15.22        14.50 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XZ 
       16.41        15.85         6.35        15.16        12.66        15.32 
TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27V 
       15.52         3.81        14.14        17.42        16.04        12.53 
TCGA-E2-A10A TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T 
       40.41        47.15        40.96        38.60        33.17        33.30 
TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A159 
       32.02        31.96        28.60        25.41        27.12        25.05 
TCGA-E2-A15E TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15K TCGA-E2-A15M TCGA-E2-A15O 
       20.71        12.92        17.42         9.04         7.73        13.02 
TCGA-E2-A15R TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B5 TCGA-E2-A1B6 
       17.06        14.99        60.53        53.62        32.35        28.50 
TCGA-E2-A1IE TCGA-E2-A1IG TCGA-E2-A1II TCGA-E2-A1IL TCGA-E2-A1L7 TCGA-E2-A1L9 
       38.30        32.78        33.70         3.88        27.42        19.66 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LS 
       24.59        40.47       106.75       102.61         8.75        15.45 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1ND 
       34.92        19.89        13.48        12.00        13.12        12.59 
TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 
       35.77        20.05         0.62         6.12         1.38         2.76 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH 
       21.21        32.09        34.65         6.58        21.27        34.59 
TCGA-E9-A228 TCGA-E9-A22B TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A244 TCGA-E9-A245 
       12.53        22.75        23.51        24.10         0.69         0.85 
TCGA-E9-A247 TCGA-E9-A24A TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54Y TCGA-E9-A5UO 
       27.22        24.56        18.41         0.62         0.23        13.81 
TCGA-E9-A5UP TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 
       14.40        18.21        18.90        16.57        15.68        28.77 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P4 
       25.94        22.82        29.85        40.41        41.13        29.82 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A2FS TCGA-EW-A2FV 
       18.48        30.08        19.99         6.15        52.73        25.91 
TCGA-EW-A2FW TCGA-EW-A3U0 TCGA-GI-A2C9 TCGA-GM-A2DM TCGA-GM-A3XL TCGA-LL-A442 
       22.09        17.49       109.87        76.64        69.30        10.95 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A73Y TCGA-OL-A5RW TCGA-OL-A5RZ TCGA-OL-A5S0 
       14.47        14.79         4.14        36.36        22.32        20.38 
TCGA-OL-A66I TCGA-OL-A66P TCGA-OL-A6VO TCGA-PL-A8LV TCGA-PL-A8LX TCGA-PL-A8LZ 
       23.47        14.07        28.21         0.23         0.16         3.95 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA12 TCGA-S3-AA17 
       10.59         7.92         8.52         3.91 

$subtype2
TCGA-A2-A0CK TCGA-A2-A0CO TCGA-A2-A0CR TCGA-A2-A0CW TCGA-A2-A0EP TCGA-A2-A1FX 
      136.73       112.08       107.93        64.04       107.61        36.79 
TCGA-A2-A25A TCGA-A2-A25D TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XW TCGA-A2-A3XZ 
      107.70        18.15        20.88        39.65        49.48        31.99 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0DB 
        7.30        24.39        21.30        21.14        21.90        33.11 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IZ 
       29.56        31.36        23.80        20.61        22.32        10.59 
TCGA-A7-A3J1 TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SC TCGA-A7-A4SE 
       11.28        14.70        14.93        13.74        14.66        21.17 
TCGA-A7-A56D TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VX TCGA-AC-A23G TCGA-AC-A2BM 
       14.73        10.72        11.05        10.42        10.85        38.20 
TCGA-AC-A2FB TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI 
       40.57        38.79        26.04        50.70         1.02         0.92 
TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN 
        2.27         0.99         0.69        14.83        22.19         1.12 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y 
       16.57        19.79        23.24         1.55         0.07         1.81 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AQ-A54O TCGA-AQ-A7U7 
        0.43         1.68         1.74         1.12        32.91         9.99 
TCGA-AR-A1AM TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM 
       62.56        20.25        62.86        42.87         7.36        40.04 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP 
       38.17        39.39        40.54        54.74        16.04        20.45 
TCGA-AR-A5QQ TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C 
       10.59       170.17        85.35        49.94       103.63        55.00 
TCGA-BH-A0B6 TCGA-BH-A0DO TCGA-BH-A0E2 TCGA-BH-A203 TCGA-BH-A28O TCGA-BH-A28Q 
       56.94        17.26        14.30        38.60        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A137 TCGA-C8-A26V 
       20.12         0.99       109.28         8.94         3.85         0.30 
TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 
        0.23         0.36         0.43         8.28         9.67         0.03 
TCGA-C8-A275 TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A1X9 TCGA-D8-A27G TCGA-D8-A27H 
        0.03         0.03         0.23        23.90        13.45        13.05 
TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P 
       14.43         9.44        16.41        13.48         4.80         0.76 
TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 
       10.09        13.08        12.26        14.50        18.51         7.33 
TCGA-E2-A14O TCGA-E2-A14U TCGA-E2-A15F TCGA-E2-A1LE TCGA-E2-A2P5 TCGA-E2-A2P6 
       44.68        43.33        21.63        28.90        16.93         5.52 
TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A572 TCGA-E2-A576 TCGA-E2-A9RU 
       15.72         7.20        30.61        27.32        19.00         9.21 
TCGA-E9-A1R0 TCGA-E9-A1RD TCGA-E9-A226 TCGA-E9-A22A TCGA-E9-A295 TCGA-E9-A2JS 
       14.30         0.66        34.13        39.09         0.72        17.75 
TCGA-E9-A2JT TCGA-E9-A3X8 TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A6HE TCGA-EW-A1PA 
        0.76        15.72        14.70         0.26        15.39        18.90 
TCGA-EW-A2FR TCGA-EW-A3E8 TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA 
       55.00        21.27        10.59         7.40        59.57       194.27 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI 
       53.13        53.52        43.04        42.71        42.28        61.91 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY 
       62.33        90.84        77.33        53.36       110.50        38.20 
TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW 
       43.73        66.38        72.03        13.55        18.12        11.84 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF 
       11.57        21.24         6.67         4.08         4.60         8.75 
TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN 
        9.53        11.44         7.59        17.06        15.32        14.70 
TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ 
       11.57         2.63         3.88         4.50         4.50         5.59 
TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
        3.22         7.36        27.91         2.79         2.10        12.66 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY 
       31.99        58.62        27.65        34.92        16.87        24.72 
TCGA-OL-A66H TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A6VQ TCGA-PL-A8LY 
       26.70        33.57        31.07        26.04        19.73         0.26 
TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 
       16.50         6.81         8.65         5.56         7.17         6.87 
TCGA-W8-A86G TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
        5.29         9.60         9.14       100.01       105.04 

$subtype3
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SF TCGA-A1-A0SI TCGA-A1-A0SN TCGA-A2-A04W 
        8.52        14.37        48.10        20.88        39.32        64.04 
TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0D3 TCGA-A2-A0ES TCGA-A2-A1FZ TCGA-A2-A1G0 
       75.55        63.45        28.77        37.05        22.45        20.25 
TCGA-A2-A1G6 TCGA-A7-A3IY TCGA-AC-A23E TCGA-AC-A2B8 TCGA-AC-A2FF TCGA-AC-A2FG 
       16.47        11.34         2.37         1.48        55.43        36.99 
TCGA-AC-A6IV TCGA-AO-A12A TCGA-AO-A1KO TCGA-AO-A1KT TCGA-AQ-A1H3 TCGA-AR-A1AL 
        1.18        90.58        14.73        17.79        32.52        48.82 
TCGA-AR-A1AN TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24P TCGA-AR-A24V TCGA-B6-A0IH 
       43.73        96.89        78.51         0.85        85.35       112.37 
TCGA-B6-A0RH TCGA-B6-A0WS TCGA-B6-A1KI TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B5 
      189.01        97.48        73.51        28.50        46.95        48.36 
TCGA-BH-A0BQ TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DT TCGA-BH-A0DX 
       27.19        31.17        23.44        22.13        38.47        47.41 
TCGA-BH-A0E9 TCGA-BH-A0EI TCGA-BH-A0H3 TCGA-BH-A0W7 TCGA-BH-A18I TCGA-BH-A18M 
       46.19        24.43        37.78        44.81         7.23        72.56 
TCGA-BH-A1EO TCGA-BH-A1EU TCGA-BH-A1EY TCGA-BH-A1F2 TCGA-BH-A1FB TCGA-BH-A1FE 
       91.99        42.28        17.69        31.53       120.62        74.73 
TCGA-BH-A1FH TCGA-BH-A201 TCGA-BH-A208 TCGA-C8-A12N TCGA-C8-A138 TCGA-D8-A13Z 
       36.92         6.90        57.83        11.77         3.75        20.88 
TCGA-D8-A141 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JE 
       20.58        13.48        21.14        18.71        18.15        18.90 
TCGA-D8-A1JH TCGA-D8-A1JP TCGA-D8-A1JU TCGA-D8-A1XB TCGA-D8-A1XO TCGA-D8-A1XS 
       14.01        21.01        14.70        18.15         7.96        16.31 
TCGA-D8-A1XU TCGA-D8-A1XY TCGA-E2-A14Q TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A15C 
       12.99        16.54        38.24        23.24        19.43        22.82 
TCGA-E2-A15D TCGA-E2-A15G TCGA-E2-A15P TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1BC 
       17.29        18.21        19.56        53.03        29.95        16.47 
TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IN TCGA-E2-A1IO 
       17.10        33.73        28.44        22.65        22.19        20.98 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L8 TCGA-E9-A1NG TCGA-E9-A1QZ TCGA-E9-A1RC 
       11.08        54.18        39.62        21.57        11.90        40.24 
TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A229 TCGA-E9-A22E TCGA-E9-A248 TCGA-E9-A249 
       35.64         0.79        13.32        12.89         1.94         0.95 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1J2 TCGA-EW-A1P1 TCGA-EW-A1PD 
       12.20        39.72         8.48        13.25        39.78        13.94 
TCGA-EW-A1PG TCGA-OL-A66J 
       34.55        65.62 

subtype1 subtype2 subtype3 
    0.03     0.03     0.79 
subtype1 subtype2 subtype3 
  144.59   194.27   189.01 
subtype1 subtype2 subtype3 
  21.895   16.410   22.735 
[1] "0.0 - 144.6 (21.9)" "0.0 - 194.3 (16.4)" "0.8 - 189.0 (22.7)"
D12V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1      27       21        2        1       121        64         0
  subtype2      15       15        3        4        52        55         2
  subtype3      19       10        0        0        34        26         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE X
  subtype1         42          7          7        1       1
  subtype2         27          5         29        2       0
  subtype3         11          1          4        2       3
D12V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          27       15       19
  STAGE IA         21       15       10
  STAGE IB          2        3        0
  STAGE II          1        4        0
  STAGE IIA       121       52       34
  STAGE IIB        64       55       26
  STAGE III         0        2        0
  STAGE IIIA       42       27       11
  STAGE IIIB        7        5        1
  STAGE IIIC        7       29        4
  STAGE IV          1        2        2
  STAGE X           1        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  75 185  25  10
  subtype2  53 109  42   5
  subtype3  47  54   6   3
D12V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       75       53       47
  T2      185      109       54
  T3       25       42        6
  T4       10        5        3
[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 155  94  35   7
  subtype2  87  72  17  30
  subtype3  51  45   8   5
D12V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0      155       87       51
  N1       94       72       45
  N2       35       17        8
  N3        7       30        5
[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        1 251   1  42
  subtype2        2 140   2  65
  subtype3        2  90   2  16
D12V6, multiclass
          clus
vv         subtype1 subtype2 subtype3
  CM0 (I+)        1        2        2
  M0            251      140       90
  M1              1        2        2
  MX             42       65       16
[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"
D12V7, binary
          cls
clus         0   1
  subtype1 291   4
  subtype2 207   2
  subtype3 108   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  291    4
  subtype2  207    2
  subtype3  108    2
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      291      207      108
  MALE          4        2        2
[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                          1                           245
  subtype2                          0                            93
  subtype3                          0                            82
          vv
clus       INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  subtype1                             13                   5
  subtype2                            106                   0
  subtype3                             18                   0
          vv
clus       MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER  SPECIFY
  subtype1                                9                  9             13
  subtype2                                2                  3              5
  subtype3                                4                  1              5
D12V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  INFILTRATING CARCINOMA NOS              1        0        0
  INFILTRATING DUCTAL CARCINOMA         245       93       82
  INFILTRATING LOBULAR CARCINOMA         13      106       18
  MEDULLARY CARCINOMA                     5        0        0
  MIXED HISTOLOGY (PLEASE SPECIFY)        9        2        4
  MUCINOUS CARCINOMA                      9        3        1
  OTHER  SPECIFY                         13        5        5
[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"
D12V9, binary
          cls
clus         0   1
  subtype1  93 202
  subtype2  19 190
  subtype3  35  75
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   93  202
  subtype2   19  190
  subtype3   35   75
     clus
vv    subtype1 subtype2 subtype3
  NO        93       19       35
  YES      202      190       75
[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"
D12V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1    27                        57   210
  subtype2    14                        59   132
  subtype3     6                         6    97
D12V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                           27       14        6
  BLACK OR AFRICAN AMERICAN       57       59        6
  WHITE                          210      132       97
[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"
D12V12, binary
          cls
clus         0   1
  subtype1  13 268
  subtype2   7 194
  subtype3   6  98
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13  268
  subtype2    7  194
  subtype3    6   98
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           13        7        6
  NOT HISPANIC OR LATINO      268      194       98
[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"
