parseKGML2Graph {KEGGgraph} | R Documentation

## Parse KGML files into KEGG graph

### Description

This function is a wrapper for parseKGML and KEGGpathway2Graph. It takes two actions: first it reads in the KGML file and parses it into an object of `KEGGPathway-class`, the second step it calls `KEGGpathway2Graph` function to return the graph model.

### Usage

    parseKGML2Graph(file, ...)

### Arguments

`file` | Name of KGML file
`...` | other parameters passed to KEGGpathway2Graph, see `KEGGpathway2Graph`

### Details

Note that groups of genes will be split into single genes by calling the `KEGGpathway2Graph` function. Edges that connected to groups will be duplicated to connect each member of the group.

### Value

A graph object.

### Author(s)

Jitao David Zhang mailto:jitao_david.zhang@roche.com

### Examples

    sfile <- system.file("extdata/hsa04010.xml",package="KEGGgraph")
    gR <- parseKGML2Graph(sfile,expandGenes=TRUE)
    gR

[Package KEGGgraph version 1.40.0 Index]