
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/mRNAseq_preprocessor/UCEC/1768877/0.mRNAseq_preprocessor.Finished/UCEC.mRNAseq_RPKM_log2.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/UCEC/1709392/1.GDAC_clinicalDataPicker.Finished/UCEC.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=451, in expression file=266, common to both=266
Number of genes in original expression dataset=18744
[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] "NEOADJUVANTTHERAPY"                    
[14] "BATCHNUMBER"                           

Input Data has 14 rows and 266 columns.

[1] "Batch" "14"   
[1] "Last Follow UP"
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G3 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
          NA         4053         1079          790         2165           NA 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI 
         275           97         2717         2516         1671         1750 
TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GR TCGA-A5-A0GU 
        1447         1448         1477         1087          780          495 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
         485          385          924          369           40          125 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OG TCGA-A5-A1OK 
         294          555          927          177          348          243 
TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
          31           60         2545           NA          181           NA 
TCGA-AP-A056 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
        2026         1198         1364          831          639          239 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
         371          260           NA         3443         2906         2986 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
         103         1921           NA         2602          965         2141 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LT TCGA-AP-A0LV 
         825         1992           NA         1875         1185          385 
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-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
         317          523          267           17           NA          603 
TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
         902         2191         1413         1075         1398         2024 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
        1064         1639           NA         1554          833          913 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
        1065          868         1148         1333         1219         2004 
TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
         584          412          464          617          378          610 
TCGA-AX-A1CF TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR 
        2337         1645         2052          764         1107          337 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
        1465         1241         1312         1125         1360          821 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
         689          679          746          682          700          466 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
         426          372          542          265         5279         3076 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11M TCGA-B5-A11N TCGA-B5-A11O 
        2317         2038         1291         1117         1147         1034 
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-A1MU TCGA-B5-A1MY TCGA-B5-A1N2 
         315          291          259           NA           NA          389 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
         194          252          237          316          742          480 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MC TCGA-BG-A0MG 
         241          698          690          765          827          896 
TCGA-BG-A0MH TCGA-BG-A0MI TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
        1341           NA         1021          761          553          240 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
         231          128          224          260          131          490 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
         868          907          279          230          231          252 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BK-A0C9 
         155          169          220           46           14          289 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C TCGA-BS-A0T9 
         371          188          211          239          202           NA 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
         714         2260         2002           NA         2034         1443 
TCGA-BS-A0TJ TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF 
        1514           NA         2606         1749         2540         1843 
TCGA-BS-A0UJ TCGA-BS-A0UM TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V8 TCGA-D1-A0ZN 
          27         2191          595          149         1507          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-A15V TCGA-D1-A15W TCGA-D1-A15X 
         350          377           53         1012          915          909 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A162 TCGA-D1-A163 TCGA-D1-A165 
          NA          112          892          976          938           20 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
         478          913          905          744          908          909 
TCGA-D1-A16F TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
          80           NA           NA          742          640          864 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
         221           21          238           43          111          532 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
         324          202          506          347          206           19 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
         212            1          160           39          454          429 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
         459          311           46           54           NA          326 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NW TCGA-DI-A0WH TCGA-DI-A1BY 
          70          396          311           22          405         1114 
TCGA-DI-A1NO TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EY-A1GM TCGA-EY-A1GS 
          NA         1289          332          328          209          284 
TCGA-EY-A1GV TCGA-EY-A212 
         257          109 
Variable 1:'AGE':	nDistinctValues=52,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=228,	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=16,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'HISTOLOGICAL.TYPE':	nDistinctValues=7,	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:'NEOADJUVANT.THERAPY':	nDistinctValues=2,	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] "NEOADJUVANT.THERAPY"                   
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE" "3"           
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 266 columns, 1 survival variables, and 4 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
KCNK10|54207 
        8279 
AGE, nv=52, binary=FALSE, numeric=TRUE
DIO2|1734 
     4666 
HISTOLOGICAL.TYPE, nv=7, binary=FALSE, numeric=FALSE
KIAA1324|57535 
          8451 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
F13A1|2162 
      5508 
NEOADJUVANT.THERAPY, nv=2, binary=FALSE, numeric=FALSE
RANGRF|29098 
       13356 
> q(save="no")
