
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/2666753/0.GDAC_MethylationPreprocess.Finished/UCEC-TP.meth.for_correlation.filtered_data.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/UCEC-TP/2589075/1.GDAC_clinicalDataPicker.Finished/UCEC-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=452, in expression file=258, common to both=256
Number of genes in original expression dataset=17621
[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] "COMPLETENESS.OF.RESECTION"             
[14] "BATCHNUMBER"                           

Input Data has 14 rows and 256 columns.

[1] "Batch" "14"   
[1] "Last Follow UP"
TCGA-A5-A0GG TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0VO TCGA-A5-A1OF TCGA-A5-A1OG 
        2516         1167          780          128          241          348 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
         292          243           31           60           12           49 
TCGA-AJ-A2QN TCGA-AP-A059 TCGA-AP-A05O TCGA-AP-A0LF TCGA-AP-A0LM TCGA-AP-A0LS 
          61          250          371          103          825         1668 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ 
        1816         1650         1329          952           NA         1184 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
        1131          204          691          317          523          267 
TCGA-AW-A1PO TCGA-AX-A06D TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ 
          17           NA          833         1479         1065         1333 
TCGA-AX-A0J0 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
        1219          404          584          515          412          464 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
         617          378          610         2337         2207         1645 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H5 
        2052          764         1107          337           NA         2167 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
        1020         1861         2090         1016         1232          489 
TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IO TCGA-B5-A0JT TCGA-B5-A0JU 
         660          831           NA         1176         1312         1483 
TCGA-B5-A0JX TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
        1360          542          124          265         5279         3076 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11M TCGA-B5-A11N 
        2317         2038         1291         1396         1117         1147 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
        1034         1120          702          650          271          231 
TCGA-B5-A11W TCGA-B5-A11X TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
         339          337          315          291          259         5690 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 
          NA          380          174           NA          465          389 
TCGA-BG-A0MA TCGA-BG-A0MH TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
          NA         1341          224          260          131          490 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
         868          907         1151          279          186          230 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 
         231          252          155          169          220           46 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BK-A0CA TCGA-BK-A139 
          14           NA           16          177          371          239 
TCGA-BK-A13C TCGA-BK-A26L TCGA-BS-A0T9 TCGA-BS-A0U5 TCGA-BS-A0U9 TCGA-BS-A0UA 
         202          233           NA         2204         1749         2540 
TCGA-BS-A0UL TCGA-BS-A0V6 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
          36         1650         1507         1661         1207          512 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
          69          690            8           17          147          578 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
         350          377           53           43          480         1012 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A162 
         915          909           NA          112          892          976 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
         938           20          478          913          905          744 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
         908          909           80           NA           NA          742 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V 
         640          864          221           21          238           43 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
         111          532          324          202          506          347 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
         206           19          212            1          160           39 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
         454          429          459          311           46           54 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
          NA          326           70          396           43          311 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
          22          399          396            8            2          377 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-DI-A0WH 
          32           NA         1260           NA         1365          405 
TCGA-DI-A1BY TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ 
        1114          943           NA           NA          711         1289 
TCGA-E6-A1M0 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y8 
         427           NA           66           46          332          328 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EY-A1G7 
         972         1066         1004          672           NA           NA 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
          NA          138          248          552          532          527 
TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GM TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS 
         506          503          209          340          344          284 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1H0 TCGA-EY-A212 
         300          259          257          260          339          109 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 
         252          391          235         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=53,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=21,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=212,	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=3,	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:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'BATCH.NUMBER':	nDistinctValues=16,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "HISTOLOGICAL.TYPE"                     
[3] "TUMOR.GRADE"                           
[4] "RADIATIONS.RADIATION.REGIMENINDICATION"
[5] "COMPLETENESS.OF.RESECTION"             
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE" "3"           
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 256 columns, 1 survival variables, and 4 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
TMEM84 
 15664 
AGE, nv=53, binary=FALSE, numeric=TRUE
SLFN14 
 14221 
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
CARD11 
  2675 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
GRIK3 
 6603 
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
DNASE1L2 
    4553 
> q(save="no")
