
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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/mRNAseq_preprocessor/STAD-TP/2844989/STAD-TP.mRNAseq_RPKM_log2.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/STAD-TP/2844303/1.GDAC_clinicalDataPicker.Finished/STAD-TP.clin.merged.picked.txt", "-fV=ALL", "-fG=", "-fS=", "-fF=ALL", "-OT=", "-iX=")
[1] "ok3"

nSamples in clinical file=178, in expression file=43, common to both=43
Number of genes in original expression dataset=19433
[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] "PATHOLOGICSPREAD(PT)"                  
[11] "PATHOLOGICSPREAD(PN)"                  
[12] "PATHOLOGICSPREAD(M)"                   
[13] "TUMORSTAGE"                            
[14] "RADIATIONS.RADIATION.REGIMENINDICATION"
[15] "COMPLETENESS.OF.RESECTION"             
[16] "NUMBER.OF.LYMPH.NODES"                 
[17] "BATCHNUMBER"                           

Input Data has 17 rows and 43 columns.

[1] "Batch" "17"   
[1] "Last Follow UP"
TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-4292 TCGA-BR-4294 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4357 TCGA-BR-4361 TCGA-BR-4362 TCGA-BR-4363 TCGA-BR-4366 TCGA-BR-4367 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4368 TCGA-BR-4369 TCGA-BR-4370 TCGA-BR-4371 TCGA-CG-4301 TCGA-CG-4304 
          NA           NA           NA           NA           92          822 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4442 
         485           31         1611         1644          122           NA 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
         912         1431          580          669           31          273 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4475 TCGA-CG-4476 
         576          215          365           31           NA           NA 
TCGA-CG-4477 
          31 
Variable 1:'AGE':	nDistinctValues=27,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=16,	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:'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=6,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'HISTOLOGICAL.TYPE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'PATHOLOGY.T':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'PATHOLOGY.N':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'PATHOLOGICSPREAD(M)':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'TUMOR.STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'BATCH.NUMBER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                       "GENDER"                   
[3] "HISTOLOGICAL.TYPE"         "PATHOLOGY.T"              
[5] "PATHOLOGY.N"               "PATHOLOGICSPREAD(M)"      
[7] "TUMOR.STAGE"               "COMPLETENESS.OF.RESECTION"
[9] "NUMBER.OF.LYMPH.NODES"    
[1] "TUMOR.?STAGE" "7"           
[1] "stage2"
vv
 1  2  3  4 
 7  4  6 11 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "4"          
[1] "PATHOLOGY.N" "5"          
Output Data has 43 columns, 1 survival variables, and 9 non-survival variables.
                              D                 
            "D" "Time to Death"         "Month" 
RNF145|153830_CALCULATED 
                   15039 
AGE, nv=27, binary=FALSE, numeric=TRUE
ADIPOQ|9370_CALCULATED 
                 12583 
GENDER, nv=2, binary=FALSE, numeric=FALSE
XIST|7503_CALCULATED 
               19374 
HISTOLOGICAL.TYPE, nv=5, binary=FALSE, numeric=FALSE
SEL1L|6400_CALCULATED 
                 5715 
PATHOLOGY.T, nv=4, binary=FALSE, numeric=TRUE
IRS1|3667_CALCULATED 
               10654 
[1] "PATHOLOGY.T"
[1] "num to class table"
vv1
T1 T2 T3 T4 
 2 14  9  9 
PATHOLOGY.N, nv=4, binary=FALSE, numeric=TRUE
NKX2-2|4821_CALCULATED 
                 11630 
[1] "PATHOLOGY.N"
[1] "num to class table"
vv1
N0 N1 N2 N3 
 8 14  5  5 
PATHOLOGICSPREAD(M), nv=3, binary=FALSE, numeric=FALSE
DBR1|51163_CALCULATED 
                12822 
TUMOR.STAGE, nv=4, binary=FALSE, numeric=TRUE
MARCH4|57574_CALCULATED 
                  10772 
[1] "TUMOR.STAGE"
[1] "num to class table"
vv1
Stage 1 Stage 2 Stage 3 Stage 4 
      7       4       6      11 
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
ZNF673|55634_CALCULATED 
                  19405 
NUMBER.OF.LYMPH.NODES, nv=6, binary=FALSE, numeric=TRUE
GPATCH2|55105_CALCULATED 
                     732 
> q(save="no")
