[1] "libdir: /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/ClinicalAnalysisAllGenes_new/broadinstitute.org/cancer.genome.analysis/00333/60/"
[1] "terrence_modification_tag: TRUE"
[1] "op: MUTATION_RATE"
[1] "dfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun_HM/BRCA-TP/10796107/iteration1/BRCA-TP.patients.counts_and_rates.txt"
[1] "cfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/BRCA-TP/11541508/BRCA-TP.merged_data.txt"
[1] "gv: ALL"
[1] "gfn: "
[1] "sfn: "
[1] "fv: ALL"
[1] "ofn: "
[1] "dx: "
[1] "cfn"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/BRCA-TP/11541508/BRCA-TP.merged_data.txt"
[1] "ok3"

nSamples in clinical file=1043, in expression file=976, common to both=959
Number of genes in original expression dataset=2
[1] "ALL"
[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 959 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
         259          437         1321         1463          434         1437 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP 
         635          416           NA          242         1196          584 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T 
         554         3188           NA         1276         2499         2246 
TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK 
         671           NA         1948         1686         1099         4159 
TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
        1964           NA         3409         2813         2695         3283 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX 
        2298         2289           NA         1930         1948         1728 
TCGA-A2-A0CZ TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 
        1616          643         1051         1027          875          767 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER 
        3094         2718         2442         3273         2426         2263 
TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
        1127         1066         1043          968          905          752 
TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX 
         735         3017         1662           NA           NA         1534 
TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 
        1347          533          521           NA          569          624 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE 
         531          575          631          990          769          554 
TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK 
         469          666          659          441          566          588 
TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX 
        1474          965           NA          714          528         1119 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
         683          616          584          595          501         1596 
TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
        3276          496          523          552         2796          322 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV 
         635         1206           NA         2525           NA          996 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW 
        1505         1168         1064          973         1167          222 
TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 
         742          648          706          820          643          666 
TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 
        1165         1074         1043         1079          931         1139 
TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G 
        1085         1007          965          326          387          718 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I 
         899          954          738          722          724          661 
TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
         627          679          345          322          313          343 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SC 
         408          447          364          454          418          446 
TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW 
         441          644          545          448          368          326 
TCGA-A7-A5ZX TCGA-A8-A06N TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R 
         336           NA          396          396           31          547 
TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 
        1614           NA           NA          791           31          518 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07C TCGA-A8-A07E TCGA-A8-A07F 
        1642          274         1308         1034          608          577 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P 
         577          426          365          518          304          334 
TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A081 TCGA-A8-A082 
         273          760          304          853           NA          549 
TCGA-A8-A083 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B 
          NA          458         1124          396           30         1156 
TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08H TCGA-A8-A08I TCGA-A8-A08J 
         881         1004          607           NA          365           NA 
TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T 
          NA          943          943           30         1004         2830 
TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A090 TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 
        1308         1217           NA         1004          942          546 
TCGA-A8-A094 TCGA-A8-A095 TCGA-A8-A096 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A 
          NA         1277           NA          365          304          304 
TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09G TCGA-A8-A09I 
         365           31         1522         1492           NA         1371 
TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T 
         912         1006           31          761          273          579 
TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A09Z TCGA-A8-A0A1 TCGA-A8-A0A2 
         457           30           NA           NA          365          579 
TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD 
         396          640           30          396          518         1157 
TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK 
          29           72          330           81           45         1172 
TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM 
        1162         1234         1686         1125         1180           NA 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN 
        1542           31           28           69           30           21 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI 
         451          675           34          504          602          707 
TCGA-AC-A3YJ TCGA-AC-A5XS TCGA-AC-A62X TCGA-AC-A62Y TCGA-AN-A03X TCGA-AN-A03Y 
         754           47           34           55           10           10 
TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D 
           7           10           19           90           54           52 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS 
         244          224          198            5           10           10 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL 
          10          196          141          242          213          231 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX 
         218          191          183           10           11           10 
TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0G0 TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO 
          10           10           16           10           10          375 
TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV 
           9           10           10           10           10          162 
TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P 
         170         2442         1455         2031           NA         2576 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 
        2091         1456           NA          886          997          651 
TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 
        1587          735         1140          618          680         1613 
TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF 
         655         1542         1547         2190         2335          650 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 
        1528         1887         1683         2184         3120         3019 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D 
        3307         3248         2923         2755         2359         1948 
TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
        1743         1471         1266          863          448         2513 
TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
        2141           16          541          754          819         3957 
TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0TS 
          NA          475          989           78         1001         2275 
TCGA-AR-A0TU TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 
         360         1972           NA         1988         3101           NA 
TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL 
        3468         2298         1881         1605         1559         1485 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR 
        1903         1330         1325         1216         1310           NA 
TCGA-AR-A1AS TCGA-AR-A1AT TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX 
        1150           NA         2318         1864         1935         1890 
TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
         615         3333         1548         2221         2947         2388 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T 
        2561           26         3088         2653           NA         2312 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 
        1623         2596         1550         2548         2403         1708 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE 
        2387         2226         2213         1792           NA         3913 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN 
          NA         1912         1304          224         1218         1161 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP 
        1198         1233          620         1665          488          622 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I6 TCGA-B6-A0I8 
          NA           NA         4361         4550           NA           NA 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG 
          NA         6719           NA           NA           NA           NA 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO 
          NA         5383           NA         3836           NA         3350 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
        3374         4285         6435         2082         5749         7126 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RU 
        5261         4929           NA           NA         2721         3991 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX 
        4788           NA         5739           NA          547           NA 
TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
          NA         3941           NA         5672           NA           NA 
TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU 
          NA         1326         3088         2236         4233         5176 
TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
        2596         1651         1519         3152         1673          746 
TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B1 
        1180          622          777          867         1428         1148 
TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B8 
        1203         1191         1471         1732         1733         1569 
TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG 
        1572         1132          974          554          782          756 
TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ 
         660         1340         1876         1085         1481          827 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ 
        1633         1641         1386         1519          355         1492 
TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE 
        1270         1339         1464         1305         1394          948 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO 
         713         1156          673          423         1467          525 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
         476           98           78         1170         1374         1442 
TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 
         495          134          477          435          293         1363 
TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY 
        1405           NA          745          943          743          923 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 
         328          461         1149         1080          747          702 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HF TCGA-BH-A0HI TCGA-BH-A0HK 
        1247         1611          806          727          620          178 
TCGA-BH-A0HL TCGA-BH-A0HN TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU 
          72          516           76          414         1121          392 
TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 
        1561          829         1545          170          728          759 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18H 
        1288         1363          701          268           61           NA 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N 
         220           NA           NA           NA           NA           NA 
TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 
          NA           NA          210           22           NA           NA 
TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T 
          NA           NA          324          196          612           30 
TCGA-BH-A42U TCGA-BH-A42V TCGA-C8-A12K TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N 
        3324          272           NA          363          358          358 
TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12T TCGA-C8-A12U TCGA-C8-A12V 
         385          358            2           NA          385          385 
TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 
         385          385           NA           NA           95           54 
TCGA-C8-A132 TCGA-C8-A133 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 
          44           NA           21           19          117          114 
TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK 
         375          332          345          345            5          366 
TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W 
         317           70           99           NA            9            7 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
          11           13          252          294            1            1 
TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-D8-A13Y 
           1          371           30            1            7          362 
TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 
         635          403          626          425          431          410 
TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
         643          584          431          532          502          569 
TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH 
         480          552          575          366          366          426 
TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN 
         577          611          612          611          590          620 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 
         639          371          405          447          565          541 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC 
         509          783          727          839          552           81 
TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM 
         463          448          664          441          606          538 
TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU 
         242          499          482          496          193          395 
TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 
         461          385          503          466          472          116 
TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H 
         433          430          530          488          409          397 
TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P 
         439          287          499          410          146           23 
TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 
         307          398          381          373          441          563 
TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A 
         223         1308         1047          837         1417         1229 
TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O 
        1141         1220          865          878         1434         1359 
TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U 
        1246         1163         1174         1009         1013         1318 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 
        1042          974          972          870          518          773 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 
         825          707          591          640          726          450 
TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F 
         762          710          694          526          630          658 
TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
         554          393          530          590          275          626 
TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
         235          396          595          519          428          456 
TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
        2329         1631         1613          911          984          867 
TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
         501          520         1165         1138          997         1026 
TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO 
        1025          865          689          118          675          638 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA 
         337         1648          834         1205          598          748 
TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK 
        1231           NA          574         3247         3121           NA 
TCGA-E2-A1LL TCGA-E2-A1LS TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z 
        1309          470          515          168          478          219 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 
         931         1062          605           NA          584         1120 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE 
         365          399         1112         1203          383         1088 
TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 
         610          656           NA          300          362          435 
TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 
          19           64          186           42           84          645 
TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF 
         976          633         1224           20         1054          200 
TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 
         647         1052         1084         1038           24          381 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G 
         405         1189          692           NA          392          715 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A245 TCGA-E9-A247 TCGA-E9-A248 
         733          519           21           26          828           59 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO 
          29          747           22          540           23          793 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK 
         560           19          478          375            7          447 
TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
           8          420          438          371         1208          258 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 
         554          575          403          504          477          875 
TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 
         789          911          908         1229         1251         1210 
TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 
        1611          907          703          562          915           NA 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PG 
         575          608          187          424          320         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-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
         532          309          225         3342           NA         5909 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI 
        1616         1628         1309         1299         1286         1883 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
        1896         2763         2331         2352         1623         3361 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV 
        1162         1330         2108         2019         2191          412 
TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A50Y 
         551          360          352          290          348          231 
TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LQ-A4E4 
         519          466          447          440          450          849 
TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA 
          85           64          385         1416          973         1783 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
         841         1062         1106          513          752          679 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K 
         620          812          714         1996         1021 
Variable 1:'AGE':	nDistinctValues=64,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=112,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=634,	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=12,	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=6,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=26,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=29,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'BATCH.NUMBER':	nDistinctValues=50,	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 959 columns, 1 survival variables, and 11 non-survival variables.
[1] "changed to 12 non-survival variables adding another age variable for linear regression analysis on mutaion rate."
                              D                 
            "D" "Time to Death"         "Month" 
AGE, nv=64, binary=FALSE, numeric=TRUE
AGE_mutation.rate, nv=64, binary=FALSE, numeric=TRUE
$MUTATIONRATE_NONSYNONYMOUS

Call:
lm(formula = as.numeric(i) ~ vv)

Residuals:
       Min         1Q     Median         3Q        Max 
-3.263e-06 -1.559e-06 -9.120e-07 -1.420e-07  1.369e-04 

Coefficients:
              Estimate Std. Error t value Pr(>|t|)   
(Intercept) -1.038e-06  1.022e-06  -1.016  0.31007   
vv           5.375e-08  1.700e-08   3.163  0.00161 **
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 

Residual standard error: 6.856e-06 on 944 degrees of freedom
  (13 observations deleted due to missingness)
Multiple R-squared: 0.01049,	Adjusted R-squared: 0.009438 
F-statistic:    10 on 1 and 944 DF,  p-value: 0.001612 


$MUTATIONRATE_SILENT

Call:
lm(formula = as.numeric(i) ~ vv)

Residuals:
       Min         1Q     Median         3Q        Max 
-8.750e-07 -4.315e-07 -2.492e-07 -2.350e-08  3.045e-05 

Coefficients:
              Estimate Std. Error t value Pr(>|t|)   
(Intercept) -3.027e-07  2.721e-07  -1.112  0.26629   
vv           1.463e-08  4.522e-09   3.234  0.00126 **
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 

Residual standard error: 1.824e-06 on 944 degrees of freedom
  (13 observations deleted due to missingness)
Multiple R-squared: 0.01096,	Adjusted R-squared: 0.00991 
F-statistic: 10.46 on 1 and 944 DF,  p-value: 0.001263 


NEOPLASM.DISEASESTAGE, nv=13, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "PATHOLOGY.T.STAGE"
[1] "num to class table"
vv1
  1   2   3   4 
256 553 113  35 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "PATHOLOGY.N.STAGE"
[1] "num to class table"
vv1
  0   1   2   3 
456 317 105  66 
PATHOLOGY.M.STAGE, nv=4, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=7, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=29, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE
[1] "saved param, results, example.expr in analysis.result.Rdata "
