
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/GDAC_RPPA_preprocess/SKCM-TM/2332880/0.GDAC_RPPA_preprocess.Finished/SKCM-TM.rppa.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/SKCM-TP/2332214/1.GDAC_clinicalDataPicker.Finished/SKCM-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=169, in expression file=143, common to both=97
Number of genes in original expression dataset=175
[1] "ALL"
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "GENDER"                                
 [7] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [8] "RADIATIONTHERAPY"                      
 [9] "RADIATIONS.RADIATION.REGIMENINDICATION"
[10] "BATCHNUMBER"                           

Input Data has 10 rows and 97 columns.

[1] "Batch" "10"   
[1] "Last Follow UP"
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-DA-A1HV TCGA-DA-A1HW 
        4511         1513           82          194         1487           NA 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA 
        3564           NA           NA         3265           NA           NA 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A185 
         713           NA           NA           NA           NA           NA 
TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
        2399         1455         1205          979           NA         1349 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
          NA         1716          440         1700        10523           NA 
TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GI 
          NA          743         1787         1315         5536          686 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
        1664         1673           NA          435         1691          595 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
        2042           NA         3931           NA           NA           NA 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
          NA           NA         4403         6175           NA           NA 
TCGA-EE-A2MP TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA 
        7562         3150         4150         1265         1620          129 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
        3733          786          112          813           NA          714 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A19O 
          NA           NA           NA           NA         1340           NA 
TCGA-ER-A1A1 TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZA 
        2433           NA           NA           NA           NA           NA 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-GN-A262 
        3080           NA           NA         1617           NA         3664 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
          NA         2577           NA           NA           NA           NA 
TCGA-GN-A26D 
        1204 
Variable 1:'AGE':	nDistinctValues=53,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=45,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=49,	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:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=23,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 8:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'BATCH.NUMBER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"    "GENDER"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 97 columns, 1 survival variables, and 2 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
GSK3A GSK3B|GSK3-ALPHA-BETA-M-V 
                             66 
AGE, nv=53, binary=FALSE, numeric=TRUE
MAPK9|JNK2-R-C 
            78 
GENDER, nv=2, binary=FALSE, numeric=FALSE
SRC|SRC-M-V 
        132 
> q(save="no")
