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

Description Usage Arguments Details Value Note Author(s) Examples

View source: R/termSimilarity.R

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

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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

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 	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. 1, 2018, 2:26 a.m.