parse_XMLfile {KEGGprofile} | R Documentation |
The function parses KEGG XML (KGML) files
parse_XMLfile(pathway_id, species, database_dir = getwd())
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 |
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.
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
XML2database<-parse_XMLfile(pathway_id="04110",species="hsa", database_dir=system.file("extdata",package="KEGGprofile"))