getGeneSetNetworks: Generate geneset networks from an annotated network.

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

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.

Author(s)

Ahmed Mohamed

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(requireNamespace("graphite") & requireNamespace("clipper") & requireNamespace("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)

ahmohamed/NetPathMiner documentation built on Oct. 31, 2024, 8:01 a.m.