
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/169412/KIRP.medianexp.clinical.results.txt", "-iI=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/169412/KIRP.medianexp.analysis.results.RData", "-rN=10", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/169412/KIRP.medianexp.exprdata.gct", "-iC=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/169412/KIRP.clin.merged.picked.clindata.txt", "-cP=1", "-cQ=0.05", "-nV=Nozzle.R1", "-OP=MRNA_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] "AGE"
[1] "GENDER"
[1] "PATHOLOGY.T"
[1] "TUMOR.STAGE"
[1] 6
            Clinical feature Statistical test            Significant genes
AGE         "AGE"            "Spearman correlation test" "N=0"            
GENDER      "GENDER"         "t test"                    "N=2"            
PATHOLOGY.T "PATHOLOGY T"    "Spearman correlation test" "N=1"            
TUMOR.STAGE "TUMOR STAGE"    "Spearman correlation test" "N=0"            
            Associated with
AGE         " "            
GENDER      "male"         
PATHOLOGY.T "higher pT"    
TUMOR.STAGE " "            
            &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
AGE         " "                                                                                       
GENDER      "N=1"                                                                                     
PATHOLOGY.T "N=0"                                                                                     
TUMOR.STAGE " "                                                                                       
            Associated with      
AGE         " "             " "  
GENDER      "female"        "N=1"
PATHOLOGY.T "lower pT"      "N=1"
TUMOR.STAGE " "             " "  
> q(save="no")
