
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/miRseq_preprocessor/CESC-TP/2282010/0.miRseq_preprocessor.Finished/CESC-TP.miRseq_RPKM_log2.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/CESC-TP/2172423/1.GDAC_clinicalDataPicker.Finished/CESC-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=32, in expression file=122, common to both=32
Number of genes in original expression dataset=564
[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] "NUMBERPACKYEARSSMOKED"                 
[12] "STOPPEDSMOKINGYEAR"                    
[13] "TOBACCOSMOKINGHISTORYINDICATOR"        
[14] "BATCHNUMBER"                           

Input Data has 14 rows and 32 columns.

[1] "Batch" "14"   
[1] "Last Follow UP"
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
        1505          925         2155         1289           NA           81 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1O9 TCGA-DS-A1OA TCGA-DS-A1OB TCGA-DS-A1OC 
        2127         2892           NA           NA           NA          376 
TCGA-DS-A1OD TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
        3096          183            8           53           40           25 
TCGA-EA-A3HT TCGA-EA-A3HU TCGA-EK-A2PI TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23K 
          19           81           NA          178          211           37 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
          37           30           66            2           31           44 
TCGA-HG-A2PA TCGA-HM-A3JK 
         773          168 
Variable 1:'AGE':	nDistinctValues=24,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=26,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=1,	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=10,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'HISTOLOGICAL.TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'NUMBERPACKYEARSSMOKED':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 12:'STOPPEDSMOKINGYEAR':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 13:'TOBACCOSMOKINGHISTORYINDICATOR':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'BATCH.NUMBER':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "RADIATIONS.RADIATION.REGIMENINDICATION"
[3] "NUMBERPACKYEARSSMOKED"                 
[4] "STOPPEDSMOKINGYEAR"                    
[5] "TOBACCOSMOKINGHISTORYINDICATOR"        
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 32 columns, 1 survival variables, and 5 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
HSA-MIR-939 
        555 
AGE, nv=24, binary=FALSE, numeric=TRUE
HSA-MIR-3690 
         333 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
HSA-MIR-338 
        283 
NUMBERPACKYEARSSMOKED, nv=5, binary=FALSE, numeric=TRUE
HSA-MIR-548E 
         456 
[1] "NUMBERPACKYEARSSMOKED"
[1] "num to class table"
vv1
 5 12 15 20 40 
 1  1  2  1  1 
STOPPEDSMOKINGYEAR, nv=4, binary=FALSE, numeric=TRUE
HSA-LET-7F-2 
           9 
[1] "STOPPEDSMOKINGYEAR"
[1] "num to class table"
vv1
1978 1995 2008 2011 
   1    1    1    1 
TOBACCOSMOKINGHISTORYINDICATOR, nv=4, binary=FALSE, numeric=TRUE
HSA-MIR-3158-2 
           243 
[1] "TOBACCOSMOKINGHISTORYINDICATOR"
[1] "num to class table"
vv1
 1  2  3  4 
14  8  1  6 
> q(save="no")
