parse_XMLfile

Description

The function parses KEGG XML (KGML) files

Usage

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

Arguments

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"))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(KEGGprofile)

KEGG.db contains mappings based on older data because the original
  resource was removed from the the public domain before the most
  recent update was produced. This package should now be considered
  deprecated and future versions of Bioconductor may not have it
  available.  Users who want more current data are encouraged to look
  at the KEGGREST or reactome.db packages

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/KEGGprofile/parse_XMLfile.Rd_%03d_medium.png", width=480, height=480)
> ### Name: parse_XMLfile
> ### Title: parse_XMLfile
> ### Aliases: parse_XMLfile
> 
> ### ** Examples
> 
> XML2database<-parse_XMLfile(pathway_id="04110",species="hsa",database_dir=system.file("extdata",package="KEGGprofile"))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>