getGeneSetNetworks {NetPathMiner} | R Documentation

## 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)

[Package NetPathMiner version 1.20.0 Index]