getGeneSets: Generate genesets from an annotated network.

In ahmohamed/NetPathMiner: NetPathMiner for Biological Network Construction, Path Mining and Visualization

Generate genesets from an annotated network.

Description

This function generates genesets based on a given netowrk, by grouping vertices sharing common attributes (in the same pathway or compartment). Genes associated with each vertex can be specified through gene.attr argument.

Usage

getGeneSets(graph, use.attr = "pathway", gene.attr = "genes", gmt.file)

Arguments

graph	An annotated igraph object..
use.attr	The attribute by which vertices are grouped (tepically pathway, or GO)
gene.attr	The attribute listing genes annotated with each vertex (ex: miriam.ncbigene, miriam.uniprot, ...)
gmt.file	Optinal. If provided, Results are exported to a GMT file. GMT files are readily used by most gene set analysis packages.

Value

A list of genesets or written to gmt file if provided.

Author(s)

Ahmed Mohamed

See Also

getGeneSetNetworks

Examples

 data(ex_kgml_sig)	# Ras and chemokine signaling pathways in human
 genesets <- getGeneSets(ex_kgml_sig, use.attr="pathway", gene.attr="miriam.ncbigene")


	# Write the genesets in a GMT file, and read it using GSEABase package.
 getGeneSets(ex_kgml_sig, use.attr="pathway", gene.attr="miriam.ncbigene", gmt.file="kgml.gmt")
 ## Not run: 
	if(requireNamespace("GSEABase"))
		toGmt("kgml.gmt")
	
## End(Not run)

	# Create genesets using compartment information
	data(ex_sbml) # bipartite metabolic network of Carbohydrate metabolism.
	genesets <- getGeneSets(ex_sbml, use.attr="compartment.name", gene.attr="miriam.uniprot")

ahmohamed/NetPathMiner documentation built on Nov. 30, 2024, 1:18 a.m.