KEGGpathway2Graph: Parses KEGGpathway to graph

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

Parses KEGGpathway to graph

Description

The function parses an object of KEGGPathway-class into graph.

Usage

KEGGpathway2Graph(pathway, genesOnly = TRUE, expandGenes = TRUE)

Arguments

pathway	An instance of KEGGPathway-class
genesOnly	logical, should only the genes are maintained and other types of nodes (compounds, etc) neglected? TRUE by default
expandGenes	logical, should homologue proteins expanded? TRUE by default

Details

When 'expandGenes=TRUE', the nodes have unique names of KEGGID (in the form of 'org:xxxx', for example 'hsa:1432'), otherwise an auto-increment index given by KEGG is used as node names. In the latter case, the node names are duplicated and graphs cannot be simply merged before the nodes are unique.

KEGG node and edge data is stored in 'nodeData' and 'edgeData' slots respectively, which can be extracted by getKEGGnodeData and getKEGGedgeData.

Value

A directed graph.

Author(s)

Jitao David Zhang mailto:[e-mail]

See Also

parseKGML2Graph

Examples

sfile <- system.file("extdata/hsa04010.xml",package="KEGGgraph")
kegg.pathway <- parseKGML(sfile)
gR.compact<- KEGGpathway2Graph(kegg.pathway,expandGenes=FALSE)

Accio/KEGGgraph documentation built on Jan. 13, 2023, 1:03 p.m.