
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/421018/KICH-TP.meth.by_min_expr_corr.data.clinical.results.txt", "-iI=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/421018/KICH-TP.meth.by_min_expr_corr.data.analysis.results.RData", "-rN=10", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/421018/KICH-TP.meth.by_min_expr_corr.data.exprdata.gct", "-iC=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/421018/KICH-TP.clin.merged.picked.clindata.txt", "-cP=1", "-cQ=0.05", "-nV=Nozzle.R1", "-OP=METHYLATION", "-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] "LYMPH.NODE.METASTASIS"
[1] "NEOPLASM.DISEASESTAGE"
[1] 6
                      Clinical feature        Statistical test           
AGE                   "AGE"                   "Spearman correlation test"
GENDER                "GENDER"                "t test"                   
LYMPH.NODE.METASTASIS "LYMPH NODE METASTASIS" "ANOVA test"               
NEOPLASM.DISEASESTAGE "NEOPLASM DISEASESTAGE" "ANOVA test"               
                      Significant genes Associated with
AGE                   "N=0"             " "            
GENDER                "N=0"             " "            
LYMPH.NODE.METASTASIS "N=768"           " "            
NEOPLASM.DISEASESTAGE "N=24"            " "            
                      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
AGE                   " "                                                                                       
GENDER                " "                                                                                       
LYMPH.NODE.METASTASIS " "                                                                                       
NEOPLASM.DISEASESTAGE " "                                                                                       
                      Associated with    
AGE                   " "             " "
GENDER                " "             " "
LYMPH.NODE.METASTASIS " "             " "
NEOPLASM.DISEASESTAGE " "             " "
> q(save="no")
