crosstalk: Perform crosstalk analysis of enriched pathways

In mw201608/GOtest: Gene Ontology and Set Enrichment Test

Perform crosstalk analysis of enriched pathways

Description

Pathway Crosstalk

Usage

crosstalk(x, col.signature, col.pathway='MSigDB', col.overlap.size='Overlap.Size',
	col.adj.p='P.adj', col.elements='Overlap.Items', sep=';',
	adj.p.cutoff=0.05, min.size=5, min.common=3, ...)

Arguments

x	a data.frame as generated from msigdb.gsea.
col.signature	id of the column containing the query signatures.
col.pathway	id of the column containing the pathway gene sets.
col.overlap.size	id of the column containing the overlap size.
col.adj.p	id of the column containing the adjusted P value.
col.elements	id of the column containing the overlap elements which are concatenated with character sepcified by sep.
sep	a character string to concatenate the elements.
adj.p.cutoff	cutoff of adjusted P value to select significant pathways.
min.size	minimum number of elements required for a pathway to be selected.
min.common	minimum number of common elements required between a crosstalk pair.
...	additional parameters. Not used currently.

Details

See Jia et al (BMC Syst Biol. 2011, 5:S12) for a description of the pathway crosstalk analysis.

Examples

#example usage

mw201608/GOtest documentation built on May 3, 2023, 11:49 a.m.