parse_XMLfile: parse_XMLfile

Description Usage Arguments Details Value Examples

View source: R/KEGG_function.R

Description

The function parses KEGG XML (KGML) files

Usage

1
parse_XMLfile(pathway_id, species, database_dir = getwd())

Arguments

pathway_id

the KEGG pathway id, such as '00010'

species

the species id in KEGG database, 'hsa' means human, 'mmu' means mouse, 'rno' means rat, etc

database_dir

the directory where the XML files and png files are located

Details

This function will parse the KEGG XML (KGML) file. Then a matrix with genes in this pathway and related infomations will be returned. This matrix can be used for plot the expression profiles on the pathway figure.

Value

a matrix containing genes in this pathway, and their names, locations etc, which could be used in the function plot_profile as param KEGG_database

Examples

1
XML2database<-parse_XMLfile(pathway_id="04110",species="hsa",database_dir=system.file("extdata",package="KEGGprofile"))

KEGGprofile documentation built on Nov. 17, 2017, 12:28 p.m.