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

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> source("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ClinicalAnalysisAllGenes_new.14.3949/ClinicalAnalysisAllGenes.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ClinicalAnalysisAllGenes_new.14.3949/", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MethylationPreprocess/UCEC-TP/4429434/UCEC-TP.meth.by_min_expr_corr.data.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/UCEC-TP/4435033/UCEC-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=954, in expression file=396, common to both=362
Number of genes in original expression dataset=20206
[1] "ALL"
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "HISTOLOGICALTYPE"                      
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "COMPLETENESS.OF.RESECTION"             
[18] "BATCHNUMBER"                           

Input Data has 18 rows and 362 columns.

[1] "Batch" "18"   
[1] "Last Follow UP"
TCGA-A5-A0GG TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0VO TCGA-A5-A1OF TCGA-A5-A1OG 
        2656         1167         1120          364          241          348 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 
        1104          292          243         2768         1409           NA 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N 
         161          156          223          455           31           33 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO 
          60           12          602           31           61           91 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BH TCGA-AJ-A3BI TCGA-AJ-A3BK 
          15           34           31           NA           61           51 
TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA 
          NA           64           65           50           39           28 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ 
         210           78           41           52           23           59 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A059 TCGA-AP-A05O 
         142           57           56           51          250          371 
TCGA-AP-A0LF TCGA-AP-A0LM TCGA-AP-A0LS TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
         103          825         1918         2180         1836         1700 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
         952           NA         1275         1495          204          940 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A06D 
         317          847          494          555           17           NA 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A1C4 
         833         1844         1065         1333         1219          404 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC 
         584          515          412          464          617          378 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
         610         2337         2207         1645         2052          764 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 
        1107          337           NA           NA         2167         1020 
TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
        1861         2090         1016         1232          489          660 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
         539          831           NA           NA         1176            7 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 
           3           10            4            6           NA            1 
TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
           4           NA            7           36          254          440 
TCGA-AX-A3GI TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JX TCGA-B5-A0K8 TCGA-B5-A0KB 
           4         1312         1483         1360          542          124 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
         265         5650         3447         2687         2303         1656 
TCGA-B5-A11L TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q 
        1396         1361         1337         1245         1120          975 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
        1019          831          509          594          592          595 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU 
         559          528          504         5835           NA           NA 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 
         438          447          355           NA          465          389 
TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-BG-A0MA TCGA-BG-A0MH TCGA-BG-A0MK TCGA-BG-A0VT 
        1890          152           NA         1341           NA          224 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
         260          131          490          868          907         1151 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
         451          382          419          448          426          470 
TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
         470          434           55          291           NA           16 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0CA TCGA-BK-A0CC TCGA-BK-A139 
         177          344          207         1064          311          309 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BS-A0T9 
         966          760          734          211          200           NA 
TCGA-BS-A0U5 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UL TCGA-BS-A0V4 TCGA-BS-A0V6 
        2935         2044         2686         2481         1810         1910 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO 
        1934         1507         1921         2021          512          602 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
         911          260           17          147          872          728 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
         685           53          135          669         1201          915 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A162 TCGA-D1-A163 
         909           NA          112          892         1145          991 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
          20          478         1098         1135         1106         1141 
TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
        1119           80           NA           NA          909          945 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X 
        1022          324           21          568           43          111 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 
         532          594          202          917          548          206 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
          48          212           30          926           39          852 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
         854          802          311           46           54           NA 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW 
         739           70          697           43          402           22 
TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 
         555          513          548           63          458           32 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
          NA          107         1260           NA         1365            8 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
         130          125          495         1195         1114          739 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX 
        1076           NA           NA           NA         2797          711 
TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
        1471          518           NA          202          487          223 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
         510          332          243          328          972         1066 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH 
        1004          825          981          761          974           NA 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AY TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC 
        1046          589          392           NA           NA          138 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
         248          741          826          709          709          727 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ 
         693          424          209          586          573          544 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW 
         536          459          490          378          481          260 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 
         197          588          383          109          438          574 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 
         694          409         1392          943          884          258 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A 
         421          196          544           65          212          113 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 
        1217         1064         1034         1095           NA           NA 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 
         273         2953         1795          276           NA          880 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 
         761          791           NA           53          203           73 
TCGA-PG-A5BC TCGA-A5-A0G1 
         329           NA 
Variable 1:'AGE':	nDistinctValues=58,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=38,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=291,	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=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'BATCH.NUMBER':	nDistinctValues=24,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "HISTOLOGICAL.TYPE"                     
[3] "RADIATIONS.RADIATION.REGIMENINDICATION"
[4] "COMPLETENESS.OF.RESECTION"             
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 362 columns, 1 survival variables, and 4 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
IFITM2 
  8209 
AGE, nv=58, binary=FALSE, numeric=TRUE
ANGPT4 
   644 
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
APBB1IP 
    822 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
MAP2K2 
 10391 
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
MYRIP 
11417 
> q(save="no")
