
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.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/2285050/0.GDAC_MethylationPreprocess.Finished/UCEC-TP.meth.for_correlation.filtered_data.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/UCEC-TP/2174329/1.GDAC_clinicalDataPicker.Finished/UCEC-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=448, in expression file=221, common to both=220
Number of genes in original expression dataset=17586
[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] "HISTOLOGICALTYPE"                      
[11] "TUMORGRADE"                            
[12] "RADIATIONS.RADIATION.REGIMENINDICATION"
[13] "BATCHNUMBER"                           

Input Data has 13 rows and 220 columns.

[1] "Batch" "13"   
[1] "Last Follow UP"
TCGA-A5-A0GG TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OK 
        2516         1167          780          241          348          243 
TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AP-A059 TCGA-AP-A05O TCGA-AP-A0LF TCGA-AP-A0LM 
          31           60          250          371          103          825 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DQ TCGA-AP-A1DR 
        1816         1650         1329          952         1184         1131 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AW-A1PO 
         204          691          317          523          267           17 
TCGA-AX-A06D TCGA-AX-A06H TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A1C4 
          NA          833         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-A2H5 TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
        1107          337         2167         1016         1232          489 
TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-B5-A0JT TCGA-B5-A0JX TCGA-B5-A0K8 
         660          831           NA         1312         1360          542 
TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
         124          265         5279         3076         2317         2038 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P 
        1291         1396         1117         1147         1034         1120 
TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11X 
         702          650          271          231          339          337 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MX 
         315          291          259         5690           NA          174 
TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-BG-A0MA TCGA-BG-A0MH TCGA-BG-A0VT TCGA-BG-A0VV 
          NA          389           NA         1341          224          260 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
         131          490          868          907         1151          279 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
         186          230          231          252          155          169 
TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BK-A0CA 
         220           46           14           NA           16          371 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BK-A26L TCGA-BS-A0T9 TCGA-BS-A0U5 TCGA-BS-A0U9 
         239          202          233           NA         2204         1749 
TCGA-BS-A0UA TCGA-BS-A0UL TCGA-BS-A0V6 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ 
        2540           36         1650         1507         1661         1207 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
         512           69          690            8           17          147 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
         578          350          377           53           43          480 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
        1012          915          909           NA          112          892 
TCGA-D1-A162 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
         976          938           20          478          913          905 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I 
         744          908          909           80           NA           NA 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
         742          640          864          221           21          238 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
          43          111          532          324          202          506 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
         347          206           19          212            1          160 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
          39          454          429          459          311           46 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU 
          54           NA          326           70          396          311 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1O0 TCGA-D1-A1O8 TCGA-D1-A2G6 
          22          399          396            2           NA           NA 
TCGA-DI-A0WH TCGA-DI-A1BY TCGA-DI-A1NN TCGA-DI-A1NO TCGA-E6-A1LX TCGA-E6-A1LZ 
         405         1114          943           NA          711         1289 
TCGA-E6-A1M0 TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1G7 
         427           66           46          332          328           NA 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GK TCGA-EY-A1GM 
          NA          138          248          552          503          209 
TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
         340          344          284          300          259          257 
TCGA-EY-A1GW TCGA-EY-A1H0 TCGA-EY-A212 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 
         260          339          109         1217         1064         1034 
TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW 
        1095           NA           NA          273         2557         1795 
TCGA-FI-A2EX TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 
         276          880          761          791 
Variable 1:'AGE':	nDistinctValues=52,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=187,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'HISTOLOGICAL.TYPE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'TUMOR.GRADE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'BATCH.NUMBER':	nDistinctValues=17,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "HISTOLOGICAL.TYPE"                     
[3] "TUMOR.GRADE"                           
[4] "RADIATIONS.RADIATION.REGIMENINDICATION"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE" "3"           
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 220 columns, 1 survival variables, and 3 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
TMEM84 
 15632 
AGE, nv=52, binary=FALSE, numeric=TRUE
SLFN14 
 14193 
HISTOLOGICAL.TYPE, nv=6, binary=FALSE, numeric=FALSE
ARL13B 
   882 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
C12ORF35 
    1596 
> q(save="no")
