
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/ClinicalAnalysisAllGenesReport_nozzle.29.3859/ClinicalAnalysisAllGenesReport_nozzle.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ClinicalAnalysisAllGenesReport_nozzle.29.3859/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iR=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/395497/LIHC-TP.miRseq_RPKM_log2.clinical.results.txt", "-iI=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/395497/LIHC-TP.miRseq_RPKM_log2.analysis.results.RData", "-rN=10", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/395497/LIHC-TP.miRseq_RPKM_log2.exprdata.gct", "-iC=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/395497/LIHC-TP.clin.merged.picked.clindata.txt", "-cP=1", "-cQ=0.05", "-nV=Nozzle.R1", "-OP=MIRNASEQ_EXPR", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "dx"   "-iX="
[1] "dx" " " 
[1] "dx" " " 
[1] "Time to Death"
[1] "AGE"
[1] "GENDER"
[1] "COMPLETENESS.OF.RESECTION"
[1] 6
                          Clinical feature           
Time to Death             "Time to Death"            
AGE                       "AGE"                      
GENDER                    "GENDER"                   
COMPLETENESS.OF.RESECTION "COMPLETENESS OF RESECTION"
                          Statistical test            Significant genes
Time to Death             "Cox regression test"       "N=0"            
AGE                       "Spearman correlation test" "N=0"            
GENDER                    "t test"                    "N=0"            
COMPLETENESS.OF.RESECTION "ANOVA test"                "N=0"            
                          Associated with
Time to Death             " "            
AGE                       " "            
GENDER                    " "            
COMPLETENESS.OF.RESECTION " "            
                          &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
Time to Death             " "                                                                                       
AGE                       " "                                                                                       
GENDER                    " "                                                                                       
COMPLETENESS.OF.RESECTION " "                                                                                       
                          Associated with    
Time to Death             " "             " "
AGE                       " "             " "
GENDER                    " "             " "
COMPLETENESS.OF.RESECTION " "             " "
> q(save="no")
