
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/PRAD-TP/2403442/0.GDAC_MethylationPreprocess.Finished/PRAD-TP.meth.for_correlation.filtered_data.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/PRAD-TP/2331893/1.GDAC_clinicalDataPicker.Finished/PRAD-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=145, in expression file=140, common to both=114
Number of genes in original expression dataset=17323
[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] "RADIATIONS.RADIATION.REGIMENINDICATION"
[12] "BATCHNUMBER"                           

Input Data has 12 rows and 114 columns.

[1] "Batch" "12"   
[1] "Last Follow UP"
TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
          31          395           60          731           31          395 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5763 
        1065          942           31           62         1339          365 
TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
          31          700           31          458          731           62 
TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 
         395          485          820          303          974         1004 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
          91          881          378          605          594          396 
TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5507 
         536          532          729          229          447          182 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
         907         1096          737          788          782          724 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
        1061          783          849         1195         1153          842 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
        1403          834          790          567          397         1272 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7314 TCGA-EJ-7315 
         724          910          519          821          295          289 
TCGA-EJ-7317 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
         285          233          175          170          191            9 
TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
         169           64          131          167          258           79 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
          52           70          217          526           43          284 
TCGA-EJ-7797 TCGA-FC-7708 TCGA-G9-6332 TCGA-G9-6336 TCGA-G9-6348 TCGA-G9-6356 
         187           32         2328         1669         1144         1000 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6378 
         841          804          101          846          505          664 
TCGA-G9-6384 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
         390         1442         1014          674          457          486 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 TCGA-HC-7078 TCGA-HC-7211 
         451          324          512           31          162           30 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7736 TCGA-HC-7744 TCGA-HC-7747 
          60           51           72           30           51           57 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7171 TCGA-J4-8198 
          61           34         2315         1949           NA           98 
Variable 1:'AGE':	nDistinctValues=27,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=100,	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=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'BATCH.NUMBER':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "RADIATIONS.RADIATION.REGIMENINDICATION"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 114 columns, 1 survival variables, and 2 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
[1] "Survival variable Time to Death has too few event occurrence, nEvent=1"
AGE, nv=27, binary=FALSE, numeric=TRUE
CACNA1B 
   2514 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NAA20 
 9918 
> q(save="no")
