getGOGraph: (1) Get GO graph with specified GO terms at its leave; (2)...

In GOSim: Computation of functional similarities between GO terms and gene products; GO enrichment analysis

Description

The function getGOGraph returns a graphNEL object representing the GO graph with leaves specified in the argument. The function getGOGraphsGenes returns a set of graphNEL objects. The ith graph object is created by call to getGOGraph with the GO terms associated to gene i. It hence shows for each gene, where its GO terms are located within the GO structure.

Usage

getGOGraph(term, prune=Inf)

getGOGraphsGenes(genelist, prune=Inf)

Arguments

term	character vector of GO terms
genelist	character vector of Entrez gene IDs
prune	do not show the complete graph, but prune it after the specified number of ancestors

Details

The result is computed within the currently set ontology ("BP","MF","CC").

Value

graphNEL object(s)

Note

directly calls the function GOGraph in the "GOstats" library

Author(s)

Holger Froehlich

Examples

	
 	G=getGOGraph(c("GO:0006955","GO:0007584"))
 	if(require(igraph)){
 		g=igraph.from.graphNEL(G) 		 
 		plot(g, vertex.label=V(g)$name)
 		Gs = getGOGraphsGenes(c("207","7494"))
 		g = igraph.from.graphNEL(Gs[[1]])
 		plot(g, vertex.label=V(g)$name) # plot the first of both GO graphs
 	} 

GOSim documentation built on Nov. 8, 2020, 11:05 p.m.