
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/1841599/0.GDAC_MethylationPreprocess.Finished/THCA.meth.for_correlation.filtered_data.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/THCA/1709390/1.GDAC_clinicalDataPicker.Finished/THCA.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=194, in expression file=158, common to both=114
Number of genes in original expression dataset=17057
[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] "NEOADJUVANTTHERAPY"                    
[12] "BATCHNUMBER"                           

Input Data has 12 rows and 114 columns.

[1] "Batch" "12"   
[1] "Last Follow UP"
TCGA-BJ-A0Z5 TCGA-BJ-A0Z9 TCGA-BJ-A0ZA TCGA-BJ-A0ZB TCGA-BJ-A0ZC TCGA-BJ-A0ZE 
         197          251          264          122          183          237 
TCGA-BJ-A0ZJ TCGA-BJ-A190 TCGA-BJ-A28R TCGA-BJ-A28V TCGA-CE-A13K TCGA-CE-A27D 
         152           13          148          155           16            3 
TCGA-DE-A0Y2 TCGA-DE-A0Y3 TCGA-DE-A2OL TCGA-DJ-A13M TCGA-DJ-A13P TCGA-DJ-A13T 
         231          952          161          274         4199          758 
TCGA-DJ-A13U TCGA-DJ-A13V TCGA-DJ-A13W TCGA-DJ-A13X TCGA-DJ-A1QD TCGA-DJ-A1QE 
         393          362          454          243          334         3041 
TCGA-DJ-A1QF TCGA-DJ-A1QG TCGA-DJ-A1QH TCGA-DJ-A1QL TCGA-DJ-A1QM TCGA-DJ-A1QN 
         549          212          243          212           30          273 
TCGA-DJ-A1QO TCGA-DJ-A1QQ TCGA-DJ-A2PO TCGA-DJ-A2PP TCGA-DJ-A2PR TCGA-DJ-A2PS 
          31          181          242          152          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-A2Q1 TCGA-DJ-A2Q3 TCGA-DJ-A2Q4 TCGA-DJ-A2Q5 TCGA-DJ-A2Q7 TCGA-DJ-A2Q9 
         284          280          287          301          291          315 
TCGA-DJ-A2QA TCGA-DJ-A2QB TCGA-DJ-A2QC TCGA-DO-A1JZ TCGA-DO-A1K0 TCGA-E8-A242 
         378          330          304         1225           93           34 
TCGA-EM-A1CS TCGA-EM-A1CT TCGA-EM-A1CU TCGA-EM-A1CW TCGA-EM-A1YA TCGA-EM-A1YB 
         580          153          214          245          217          284 
TCGA-EM-A1YC TCGA-EM-A1YD TCGA-EM-A1YE TCGA-EM-A22P TCGA-EM-A2CN TCGA-EM-A2CO 
        1421         1209          650          174          344          183 
TCGA-ET-A25G TCGA-ET-A25I TCGA-ET-A25J TCGA-ET-A25K TCGA-ET-A25L TCGA-ET-A25M 
        1088           10          903          589          450          375 
TCGA-ET-A25N TCGA-ET-A25O TCGA-ET-A25P TCGA-ET-A25R TCGA-ET-A2MY TCGA-ET-A2N0 
          75          135           15          621          579         1049 
TCGA-ET-A2N4 TCGA-ET-A39I TCGA-ET-A39J TCGA-ET-A39L TCGA-ET-A39N TCGA-ET-A39O 
          43            9          362           59         2535         1309 
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-A3DS TCGA-ET-A3DV TCGA-ET-A3DW TCGA-FE-A22Z TCGA-FE-A230 
        2095            9         3424          751         1565         1442 
TCGA-FE-A231 TCGA-FE-A233 TCGA-FE-A236 TCGA-FE-A237 TCGA-FE-A238 TCGA-FE-A239 
         374          751         2031         2292         1215           NA 
TCGA-FE-A23A TCGA-FY-A2QD TCGA-FY-A3BL TCGA-H2-A26U TCGA-IM-A3EB TCGA-IM-A3ED 
        1907           38           35          106         1070          939 
Variable 1:'AGE':	nDistinctValues=56,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=101,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=TRUE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=3,	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=11,	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:'NEOADJUVANT.THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'BATCH.NUMBER':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "GENDER"                                
[3] "HISTOLOGICAL.TYPE"                     
[4] "RADIATIONS.RADIATION.REGIMENINDICATION"
[5] "NEOADJUVANT.THERAPY"                   
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 114 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=56, binary=FALSE, numeric=TRUE
 INA 
7255 
GENDER, nv=2, binary=FALSE, numeric=FALSE
KIF4B 
 7810 
HISTOLOGICAL.TYPE, nv=4, binary=FALSE, numeric=FALSE
KLK2 
7904 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
MAP3K3 
  8952 
NEOADJUVANT.THERAPY, nv=2, binary=FALSE, numeric=FALSE
PTGS2 
11905 
> q(save="no")
