getGeneSets {NetPathMiner} | R Documentation

## 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")

[Package NetPathMiner version 1.20.0 Index]