
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

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> source("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ClinicalAnalysisAllGenes_new.13.3873/ClinicalAnalysisAllGenes.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ClinicalAnalysisAllGenes_new.13.3873/", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_RPPA_preprocess/BRCA-TP/2330201/0.GDAC_RPPA_preprocess.Finished/BRCA-TP.rppa.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/BRCA-TP/2330060/1.GDAC_clinicalDataPicker.Finished/BRCA-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=866, in expression file=408, common to both=408
Number of genes in original expression dataset=165
[1] "ALL"
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "DAYSTOLASTKNOWNALIVE"                  
[10] "RADIATIONS.RADIATION.REGIMENINDICATION"
[11] "BATCHNUMBER"                           

Input Data has 11 rows and 408 columns.

[1] "Batch" "11"   
[1] "Last Follow UP"
TCGA-A1-A0SH TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A2-A04N TCGA-A2-A04P 
        1437          426           NA          852         3153           NA 
TCGA-A2-A04Q TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04Y 
        1275         1950          670           NA         1918          763 
TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CS TCGA-A2-A0CT 
        1827           NA         2495         2392         2298         1917 
TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0CY TCGA-A2-A0CZ 
          NA         1870         1750         1303         1288         1338 
TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EO 
         643          786          761          736          496         2181 
TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW 
        2053         1902         1001          733          545          770 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW 
         549          485         1643         1351           NA           NA 
TCGA-A2-A0SX TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 
        1288          337          322           NA          456          395 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE 
         321          344          397          643          550          252 
TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK 
         289          404          379          358          326          334 
TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG 
         268          661           NA          170          253          166 
TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D 
         161          188          159          373          140          267 
TCGA-A7-A13E TCGA-A7-A13F TCGA-A8-A06N TCGA-A8-A06P TCGA-A8-A06R TCGA-A8-A06U 
         287          196           NA          396          546           NA 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 
          NA          791           31          517         1641          274 
TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R 
         608          576          426          304          334          273 
TCGA-A8-A07S TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A081 TCGA-A8-A082 TCGA-A8-A083 
         242          304          853           NA          549           NA 
TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08G TCGA-A8-A08H 
         458         1124          396           30          606           NA 
TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08T TCGA-A8-A08X 
          NA           NA          942          942         2830         1034 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A094 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A 
        1217          580           NA         1276          304          304 
TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09G TCGA-A8-A09I TCGA-A8-A09K 
         365           31          942           NA         1006          911 
TCGA-A8-A09M TCGA-A8-A09R TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A09Z TCGA-A8-A0A4 
         457          273           30           NA           NA          396 
TCGA-A8-A0A7 TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ 
          30            7           19           89           52          243 
TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT 
         223          197            5            9            9           10 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FS 
         195          140          241          212          230          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-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XS TCGA-AN-A0XT 
          16           10          375            9           10           10 
TCGA-AN-A0XU TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O 
          10          170         2442         1455         1645           NA 
TCGA-AO-A03P TCGA-AO-A03U TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J6 
        2576           NA          585          302          735          775 
TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD 
         260          277         1255         1150         1547         1813 
TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL 
        1965          354          449         1172         1512         1319 
TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A 
        1826         3119         2850         2877         2923         2754 
TCGA-AO-A12B TCGA-AO-A12C TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G 
        2359         1993         1948         1742         1471         1265 
TCGA-AO-A12H TCGA-AQ-A04L TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS 
         862         3344         2392         1500           NA         1138 
TCGA-AR-A0TT TCGA-AR-A0TU TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
        1679          360          904          739           15           NA 
TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 
        1313            8          185           NA         2263         1627 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AO 
        2298         1881         1604         1558         1485         1324 
TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AT TCGA-AR-A1AU TCGA-AR-A1AV 
        1215         1309         1242           NA         1409         1295 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-B6-A0I2 TCGA-B6-A0I6 TCGA-B6-A0I8 
        1072         1103          614         3826           NA           NA 
TCGA-B6-A0I9 TCGA-B6-A0IB TCGA-B6-A0IG TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IO 
          NA           NA           NA         5383           NA         3350 
TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN 
        3871         2082         5748           NA           NA         5261 
TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV 
        4928           NA           NA         2721         3991         4788 
TCGA-B6-A0WX TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AY 
          NA           NA         5671          746         1180          777 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B1 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 
         867         1427         1148         1203         1191         1471 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BF TCGA-BH-A0BJ 
        1733         1572         1132          974          781          660 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
        1117         1085         1481          826         1632         1640 
TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 
        1386         1519          355         1492         1270         1338 
TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI 
        1464         1305         1393          713         1156          673 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
         423         1467          476           77         1170         1374 
TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 
         133          477          376          292         1362         1405 
TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0H5 
          NA          745          943          743          917         1080 
TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HK TCGA-BH-A0HL 
         747          701         1247          856          178           72 
TCGA-BH-A0HN TCGA-BH-A0HP TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY 
         516          414          392         1560          829          867 
TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18H 
         170          175          543          268           61           NA 
TCGA-BH-A18J TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q 
          NA           NA           NA           NA           NA           NA 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-C8-A12K 
          NA           NA           NA           NA           NA           NA 
TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q 
          NA           NA           NA           NA           NA           NA 
TCGA-C8-A12T TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y 
          NA           NA           NA           NA           NA           NA 
TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A133 TCGA-C8-A134 
          NA           NA           NA           NA           NA           NA 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 
          NA            3            7          264          210           27 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-E2-A107 
          61          172           49          344            2          763 
TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E 
         124         1172          352          748          853          418 
TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14V 
        1172          487          974          834          890          748 
TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 
         833          692          688          518          591          588 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 
         586          325          553          481          450          515 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G 
         502          496          315          517          468          315 
TCGA-E2-A15H TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O 
          42          463           34          331          234          395 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 
         315          330          274          267         1964         1271 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD 
        1361          911          774          338          297          317 
Variable 1:'AGE':	nDistinctValues=60,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=44,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=285,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'BATCH.NUMBER':	nDistinctValues=19,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "GENDER"                                
[3] "RADIATIONS.RADIATION.REGIMENINDICATION"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 408 columns, 1 survival variables, and 3 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
PIK3CA |PI3K-P110-ALPHA-R-C 
                         97 
AGE, nv=60, binary=FALSE, numeric=TRUE
ESR1|ER-ALPHA-R-V 
               55 
GENDER, nv=2, binary=FALSE, numeric=FALSE
AKT1 AKT2 AKT3|AKT_PT308-R-V 
                          18 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
RAD50|RAD50-M-C 
            110 
> q(save="no")
