KEGGpathway2Graph {KEGGgraph} | R Documentation

## 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:j.zhang@dkfz.de

### See Also

`parseKGML2Graph`

### Examples

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

[Package KEGGgraph version 1.1.0 Index]