
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/GDAC_geneListPathwayEnrichment.29.3502/geneListPathwayEnrichment.R")
Loading required package: AnnotationDbi
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: DBI
> result <- main("-pw/xchip/cga/reference/MSigDB/c2.cp.v3.0-2.symbols.gmt", "-gi/xchip/cga/reference/hg18_refseq_download.txt", "-el/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_ConsensusClusteringPipeline/LGG-TP/2401725/3.GDAC_selectBestcluster.Finished/LGG-TP.subclassmarkers.txt", "-al/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Pipeline/LGG-TP/2374593/1.Gistic2_Analysis.Finished/amp_genes.conf_99.txt", "-dl/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Pipeline/LGG-TP/2374593/1.Gistic2_Analysis.Finished/del_genes.conf_99.txt", "-cl/xchip/cga/gdac-prod/tcga-gdac/jobResults/getCopyNumberExpCor/LGG-TP/2401742/1.getCNExpCorrelation.Finished/LGG-TP.CORS.tsv", "-ml/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/LGG-TP/2403996/0.MutSigRun.Finished/LGG-TP.sig_genes.txt", "-ofpathwayEnrich")
> q(save="no")
