[1] "input.genenames.file:  /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSig_2CV/COAD-TP/22506528/sig_genes.txt"
[1] "option:  MutSig2CV"
[1] "gs.db:  /xchip/cga/reference/MSigDB/c2.cp.v4.0.symbols.gmt"
[1] "R version 3.0.1 (2013-05-16)"
[1] "# read input.genenames.file..."
[1] "parsing a gene list file from [  MutSig2CV  ] to extract gene name only...(using genes only q<0.3)"
[1] "R version 3.0.1 (2013-05-16)"
[1] "generated gene name list in input.genenames.txt"
[1] "# read gene set(pathway as default) database..."
[1] "# Hypergeometric test..."
[1] "# save all results in results_sorted.all.txt..."
[1] "# Filtering step: leave only meaningful genesets"
[1] "there are  1084 meaningful genesets (num.found>=1 & FDR<0.05) genesets out of  1320 genesets"
[1] "nozzle will present only top 20 significant meaningful gene sets in termse of FDR value"
[1] "# save results_sorted.sig.overlaps in results_sorted.sig.overlaps.txt..."
[1] "# save gene lists of each sig overlapping gene.sets..."
[1] "Number of Genes in Gene Universe: " "45956"                             
[1] "Original number of Gene Sets: " "1320"                          
[1] "Number of Gene Sets in (FDR adjusted P.value <0.05) & (overlaps >= 1): "
[2] "20"                                                                     
[1] "# generates basic_data_info file..."
[1] "# END!"
