subGraphByNodeType: Subset KEGG graph by node types

In KEGGgraph: KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor

Description

The function subsets KEGG graph by node types, mostly used in extracting gene networks.

Usage

subGraphByNodeType(graph, type = "gene", kegg=TRUE)

Arguments

graph	A KEGG graph object produced by calling parseKGML2Graph
type	node type, see KEGGNodeType for details
kegg	logical, should the KEGG Node and Edge attributes be maintained during the subsetting? By default set to 'TRUE'

Value

A subgraph of the original graph

Author(s)

Jitao David Zhang mailto:[e-mail]

Examples

sfile <- system.file("extdata/hsa04010.xml",package="KEGGgraph")
sGraph <- parseKGML2Graph(sfile,expandGenes=TRUE, genesOnly=FALSE)
sGraphGene <- subGraphByNodeType(sGraph, type="gene")

Example output

Attaching package: 'KEGGgraph'

The following object is masked from 'package:graphics':

    plot

KEGGgraph documentation built on Nov. 8, 2020, 5:42 p.m.