import.gsea.compare.runs: Import the output produced by gsea.compare.runs.sh

In drmjc/metaGSEA: Meta-analysis of GSEA analyses, including intra- and inter-experiment comparisons

Description

Import the output produced by gsea.compare.runs.sh

Usage

import.gsea.compare.runs(xls, gmt = .GSEA.GMT.CATEGORIES)

Arguments

xls	an XLS file produced by running import.gsea.compare.runs.sh, or import.gsea.compare.runs.1gmt.sh
gmt	either an integer indicating which sheet of the xls to import, or the name of the gmt file. use the latter if gsea was run on all 15 of the gmt categories listed in .GSEA.GMT.CATEGORIES

Author(s)

Mark Cowley, 2009-03-23

Examples

## Not run: 
gseacmp <- import.gsea.compare.runs("GSEA/gsea.compare.runs.xls")
gseacmp <- import.gsea.compare.runs("GSEA/gsea.compare.runs.xls", c("c2_all"))
gseacmp <- import.gsea.compare.runs("GSEA/gsea.compare.runs.xls", c("c2_all", "c5_bp"))
gseacmp <- import.gsea.compare.runs("GSEA/gsea.compare.runs.xls", grep("all", .GSEA.GMT.CATEGORIES, value=TRUE))

## End(Not run)

drmjc/metaGSEA documentation built on Aug. 8, 2020, 1:53 p.m.