parseKGML2Graph: Parse KGML files into KEGG graph

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

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:[e-mail]

Examples

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

Example output

Attaching package: 'KEGGgraph'

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

    plot

A graphNEL graph with directed edges
Number of Nodes = 265 
Number of Edges = 876 

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