parse_XMLfile: parse_XMLfile

In KEGGprofile: An annotation and visualization package for multi-types and multi-groups expression data in KEGG pathway

Description

The function parses KEGG XML (KGML) files

Usage

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

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

KEGGprofile documentation built on Nov. 8, 2020, 6:13 p.m.