
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/THCA-TP/2403702/0.GDAC_MethylationPreprocess.Finished/THCA-TP.meth.for_correlation.filtered_data.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/THCA-TP/2332309/1.GDAC_clinicalDataPicker.Finished/THCA-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=215, in expression file=379, common to both=195
Number of genes in original expression dataset=17081
[1] "ALL"
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "HISTOLOGICALTYPE"                      
[10] "RADIATIONS.RADIATION.REGIMENINDICATION"
[11] "RADIATIONEXPOSURE"                     
[12] "BATCHNUMBER"                           

Input Data has 12 rows and 195 columns.

[1] "Batch" "12"   
[1] "Last Follow UP"
TCGA-BJ-A0Z3 TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC 
         182          197          251          264          122          183 
TCGA-BJ-A0ZE TCGA-BJ-A0ZF TCGA-BJ-A0ZG TCGA-BJ-A0ZH TCGA-BJ-A0ZJ TCGA-BJ-A18Y 
         237          210          230           22          152           85 
TCGA-BJ-A190 TCGA-BJ-A192 TCGA-BJ-A28R TCGA-BJ-A28T TCGA-BJ-A28V TCGA-BJ-A3PR 
          13          246          148           84          155          244 
TCGA-BJ-A3PT TCGA-CE-A13K TCGA-CE-A27D TCGA-CE-A3MD TCGA-CE-A3ME TCGA-DE-A0XZ 
         367           16            3            6            7          402 
TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DE-A3KN TCGA-DJ-A13M TCGA-DJ-A13O 
         231          952          161          286          274          215 
TCGA-DJ-A13P TCGA-DJ-A13R TCGA-DJ-A13T TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W 
        4199           92          758          393          362          454 
TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH 
         243          334         3041          549          212          243 
TCGA-DJ-A1QI TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN TCGA-DJ-A1QO TCGA-DJ-A1QQ 
         151          212           30          273           31          181 
TCGA-DJ-A2PN TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PQ TCGA-DJ-A2PR TCGA-DJ-A2PS 
         304          242          152          623          318           59 
TCGA-DJ-A2PU TCGA-DJ-A2PV TCGA-DJ-A2PW TCGA-DJ-A2PX TCGA-DJ-A2PY TCGA-DJ-A2PZ 
         312          242          234          153          267          256 
TCGA-DJ-A2Q0 TCGA-DJ-A2Q1 TCGA-DJ-A2Q2 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 
         247          284          206          280          287          301 
TCGA-DJ-A2Q6 TCGA-DJ-A2Q7 TCGA-DJ-A2Q9 TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC 
         262          291          315          378          330          304 
TCGA-DJ-A3UN TCGA-DJ-A3US TCGA-DJ-A3UY TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-E3-A3DY 
         380          630          405         1225           93          945 
TCGA-E3-A3DZ TCGA-E3-A3E0 TCGA-E3-A3E1 TCGA-E3-A3E2 TCGA-E3-A3E3 TCGA-E3-A3E5 
         365         1544         1222         1421          635          427 
TCGA-E8-A242 TCGA-E8-A2JQ TCGA-E8-A3X7 TCGA-E8-A413 TCGA-E8-A414 TCGA-E8-A415 
          34           NA           45           10            7            5 
TCGA-E8-A416 TCGA-E8-A417 TCGA-E8-A418 TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU 
          22            8           45          580          153          214 
TCGA-EM-A1CV TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB TCGA-EM-A1YC TCGA-EM-A1YD 
          NA          245          217          284         1421         1209 
TCGA-EM-A1YE TCGA-EM-A22I TCGA-EM-A22J TCGA-EM-A22K TCGA-EM-A22L TCGA-EM-A22N 
         650           81          207          202          138          209 
TCGA-EM-A22P TCGA-EM-A2CK TCGA-EM-A2CL TCGA-EM-A2CM TCGA-EM-A2CN TCGA-EM-A2CO 
         174          249          209          357          344          183 
TCGA-EM-A2CP TCGA-EM-A2CQ TCGA-EM-A2CS TCGA-EM-A2CT TCGA-ET-A25G TCGA-ET-A25I 
          90          199          284          319         1088           10 
TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M TCGA-ET-A25N TCGA-ET-A25O 
         903          589          450          375           75          135 
TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MY TCGA-ET-A2MZ TCGA-ET-A2N0 TCGA-ET-A2N4 
          15          621          579          373         1049           43 
TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39L TCGA-ET-A39N TCGA-ET-A39O TCGA-ET-A39P 
           9          362           59         2535         1309          406 
TCGA-ET-A39R TCGA-ET-A39S TCGA-ET-A39T TCGA-ET-A3BN TCGA-ET-A3BO TCGA-ET-A3BP 
        1413           20          237           51          177          127 
TCGA-ET-A3BQ TCGA-ET-A3BS TCGA-ET-A3BT TCGA-ET-A3BU TCGA-ET-A3BW TCGA-ET-A3BX 
          74          168          752           39           72          137 
TCGA-ET-A3DO TCGA-ET-A3DP TCGA-ET-A3DQ TCGA-ET-A3DR TCGA-ET-A3DS TCGA-ET-A3DV 
        2095         1536         1366           65            9         3424 
TCGA-ET-A3DW TCGA-FE-A22Z TCGA-FE-A230 TCGA-FE-A231 TCGA-FE-A233 TCGA-FE-A234 
         751         1565         1442          374          751         1333 
TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 TCGA-FE-A23A TCGA-FE-A3PA 
        2031         2292         1215           NA         1907         2872 
TCGA-FE-A3PB TCGA-FE-A3PC TCGA-FE-A3PD TCGA-FY-A2QD TCGA-FY-A3BL TCGA-FY-A3I5 
        2589         1868         1913           38           35           50 
TCGA-FY-A3NM TCGA-FY-A3NN TCGA-FY-A3NP TCGA-FY-A3ON TCGA-FY-A3R6 TCGA-FY-A3R7 
          30           NA           18           46           23            1 
TCGA-FY-A3R9 TCGA-FY-A3RA TCGA-GE-A2C6 TCGA-H2-A26U TCGA-H2-A2K9 TCGA-H2-A3RH 
          66          278          206          106          145          148 
TCGA-H2-A3RI TCGA-IM-A3EB TCGA-IM-A3ED TCGA-IM-A3U2 TCGA-IM-A3U3 TCGA-J8-A3NZ 
          90         1070          939           80           99           68 
TCGA-J8-A3O0 TCGA-J8-A3O1 TCGA-J8-A3O2 
         392          415           41 
Variable 1:'AGE':	nDistinctValues=65,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=168,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=TRUE.
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=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'HISTOLOGICAL.TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RADIATIONEXPOSURE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'BATCH.NUMBER':	nDistinctValues=19,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "GENDER"                                
[3] "HISTOLOGICAL.TYPE"                     
[4] "RADIATIONS.RADIATION.REGIMENINDICATION"
[5] "RADIATIONEXPOSURE"                     
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 195 columns, 1 survival variables, and 5 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
[1] "Survival variable Time to Death has too few event occurrence, nEvent=1"
AGE, nv=65, binary=FALSE, numeric=TRUE
C7ORF13 
   2325 
GENDER, nv=2, binary=FALSE, numeric=FALSE
UTP14C 
 15975 
HISTOLOGICAL.TYPE, nv=4, binary=FALSE, numeric=FALSE
EMP1 
4839 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
KIF15 
 7807 
RADIATIONEXPOSURE, nv=2, binary=FALSE, numeric=FALSE
ATL2 
1013 
> q(save="no")
