comparison egsea.R @ 1:73281fbdf6c1 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 225518a08941e7ef8e5c402e3696ec5fa6e592a0

0:a8a083193440

    make_option(c("-genes", "--genes"), type="character", help="Path to genes file"),
    make_option(c("-species", "--species"), type="character"),
    make_option(c("-base_methods", "--base_methods"), type="character", help="Gene set testing methods"),
    make_option(c("-msigdb", "--msigdb"), type="character", help="MSigDB Gene Set Collections"),
    make_option(c("-keggdb", "--keggdb"), type="character", help="KEGG Pathways"),
    make_option(c("-gsdb", "--gsdb"), type="character", help = "GeneSetDB Gene Sets"),
    make_option(c("-display_top", "--display_top"), type="integer", help = "Number of top Gene Sets to display"),
    make_option(c("-min_size", "--min_size"), type="integer", help = "Minimum Size of Gene Set"),
    make_option(c("-fdr_cutoff", "--fdr_cutoff"), type="double", help = "FDR cutoff"),
    make_option(c("-combine_method", "--combine_method"), type="character", help="Method to use to combine the p-values"),
    make_option(c("-sort_method", "--sort_method"), type="character", help="Method to sort the results"),
    make_option(c("-rdata", "--rdaOpt"), type="character", help="Output RData file")
    )

parser <- OptionParser(usage = "%prog [options] file", option_list=option_list)
args = parse_args(parser)

    gsdb <- unlist(strsplit(args$gsdb, ","))
} else {
    gsdb <- "none"
}


## Index gene sets

gs.annots <- buildIdx(entrezIDs=rownames(counts), species=args$species, msigdb.gsets=msigdb, gsdb.gsets=gsdb, kegg.exclude=kegg_exclude)


## Run egsea.cnt

gsa <- egsea.cnt(counts=counts, group=group, design=design, contrasts=contrasts, gs.annots=gs.annots, symbolsMap=genes, baseGSEAs=base_methods, minSize=args$min_size, display.top=args$display_top, combineMethod=args$combine_method, sort.by=args$sort_method, report.dir='./report_dir', fdr.cutoff=args$fdr_cutoff, num.threads=args$threads, report=TRUE)


## Output RData file

if (!is.null(args$rdata)) {
  save.image(file = "EGSEA_analysis.RData")
}

1:73281fbdf6c1

    make_option(c("-genes", "--genes"), type="character", help="Path to genes file"),
    make_option(c("-species", "--species"), type="character"),
    make_option(c("-base_methods", "--base_methods"), type="character", help="Gene set testing methods"),
    make_option(c("-msigdb", "--msigdb"), type="character", help="MSigDB Gene Set Collections"),
    make_option(c("-keggdb", "--keggdb"), type="character", help="KEGG Pathways"),
    make_option(c("-keggupdated", "--keggupdated"), type="logical", help="Use updated KEGG"),
    make_option(c("-gsdb", "--gsdb"), type="character", help = "GeneSetDB Gene Sets"),
    make_option(c("-display_top", "--display_top"), type="integer", help = "Number of top Gene Sets to display"),
    make_option(c("-min_size", "--min_size"), type="integer", help = "Minimum Size of Gene Set"),
    make_option(c("-fdr_cutoff", "--fdr_cutoff"), type="double", help = "FDR cutoff"),
    make_option(c("-combine_method", "--combine_method"), type="character", help="Method to use to combine the p-values"),
    make_option(c("-sort_method", "--sort_method"), type="character", help="Method to sort the results"),
    make_option(c("-rdaOpt", "--rdaOpt"), type="character", help="Output RData file")
    )

parser <- OptionParser(usage = "%prog [options] file", option_list=option_list)
args = parse_args(parser)

    gsdb <- unlist(strsplit(args$gsdb, ","))
} else {
    gsdb <- "none"
}

## Index gene sets

gs.annots <- buildIdx(entrezIDs=rownames(counts), species=args$species, msigdb.gsets=msigdb, gsdb.gsets=gsdb, kegg.exclude=kegg_exclude, kegg.updated=args$keggupdated)


## Run egsea.cnt

gsa <- egsea.cnt(counts=counts, group=group, design=design, contrasts=contrasts, gs.annots=gs.annots, symbolsMap=genes, baseGSEAs=base_methods, minSize=args$min_size, display.top=args$display_top, combineMethod=args$combine_method, sort.by=args$sort_method, report.dir='./report_dir', fdr.cutoff=args$fdr_cutoff, num.threads=args$threads, report=TRUE)


## Output RData file

if (!is.null(args$rdaOpt)) {
  save.image(file = "EGSEA_analysis.RData")
}