import.gsea: Import the results from a GSEA or GseaPreRanked analysis.

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

Description

Import the output from a single GSEA PreRanked run, including: the toptable, the leading edge genes, the rnk file used, and the report which summarises the analysis settings used, and optionally, the edb file.

Usage

import.gsea(x, edb = FALSE)

Arguments

x	The path to the GSEA results to import. (1) a GSEA zip file; (2) a vector of multiple GSEA zip files; (3) a single directory containing GSEA results. There should be an index.html file in this directory; (4) a vector of multiple GSEA directories like in (3) (5) a directory which contains >=1 GSEA directories within it.
edb	logical: Import the edb file? See Details.

Details

A flexible function which takes a directory of GSEA results, or a GSEA zip file, and imports the ‘top table’, the leading edge genes, the pre-ranked file (if one was used) and the report file which describes the parameters used when the GSEA was run.

The top table is a combination of the up/down tables that GSEA makes, sorted by decreasing NES, with additional ‘LEADING.EDGE.SIZE’ and ‘DIRECTION’ columns.

The leading.edge is a named list, where the names are the geneset names, and each list element is a vector of gene symbols, sorted in decreasing significance (i.e. first gene is the most important gene for this geneset).

The edb file contains the machine readable output which the GSEA Desktop tool can read. You should import it if you plan on subsetting or merging GSEA results which are destined to be viewed in the Leading Edge Viewer tool. Otherwise it is quite large, so best avoided unless you really need it!

Value

A GSEA list, with the following elements:

tt	the combined (pos & neg) GSEA top table
leading.edge	a named list of leading edge genes
rnk	The pre-ranked file (if one was used)
rpt	The GSEA report, listing the parameter values used during the GSEA run
edb	[optional] The edb object, as an XML tree. See import.gsea.edb

Author(s)

Mark Cowley

See Also

import.gsea.topTable import.gsea.leadingedge import.gsea.rpt import.gsea.rnk import.gsea.edb

Examples

# not run
# import.gsea("./c2_all.Gsea.1252055214188")
# import.gsea("./c2_all.Gsea.1252055214188", edb=TRUE)
# import.gsea(c("./c1_all.Gsea.1252052322484", "./c2_all.Gsea.1252055214188", "./c3_all.Gsea.1252086970993"))
# import.gsea("/path/to/dir/containing/lots/of/GSEA/dirs")

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