NetPathMiner (version 1.8.0)

getGeneSetNetworks: Generate geneset networks from an annotated network.

Description

This function generates geneset networks based on a given netowrk, by grouping vertices sharing common attributes (in the same pathway or compartment).

Usage

getGeneSetNetworks(graph, use.attr = "pathway", format = c("list", "pathway-class"))

Arguments

graph

An annotated igraph object..

use.attr

The attribute by which vertices are grouped (tepically pathway, or GO)

format

The output format. If "list" is specified, a list of subgraphs are returned (default). If "pathway-class" is specified, a list of pathway-class objects are returned. Pathway-class is used by graphite package to run several methods of topology-based enrichment analyses.

Value

A list of geneset networks as igraph or Pathway-class objects.

See Also

getGeneSets

Examples

data(ex_kgml_sig)	# Ras and chemokine signaling pathways in human
 genesetnets <- getGeneSetNetworks(ex_kgml_sig, use.attr="pathway")

 # Integration with graphite package
 ## Not run: 
#  if(require(graphite) & require(clipper) & require(ALL)){
# 		genesetnets <- getGeneSetNetworks(ex_kgml_sig,
# 						use.attr="pathway", format="pathway-class")
# 		path <- convertIdentifiers(genesetnets$`Chemokine signaling pathway`,
# 						"entrez")
# 		genes <- nodes(path)
# 		data(ALL)
# 		all <- as.matrix(exprs(ALL[1:length(genes),1:20]))
# 		classes <- c(rep(1,10), rep(2,10))
# 		rownames(all) <- genes
# 
# 		runClipper(path, all, classes, "mean", pathThr=0.1)
#  }
#  ## End(Not run)