KEGGgraph (version 1.30.0)

getKGMLurl: Get KGML file (url) with KEGG PATHWAY ID and (optional) organism

Description

The function simply returns the KGML file url given KEGG PATHWAY ID. If the KEGG PATHWAY ID contains no organism prefix, user can specify the 'organism' parameter. Otherwise the 'organism' option is ignored.

retrieveKGML is a simple wrapper to getKGMLurl, which downloads the KGML file with download.file in utils package.

Usage

getKGMLurl(pathwayid, organism = "hsa")
retrieveKGML(pathwayid, organism, destfile,method="wget", ...)
kgmlNonmetabolicName2MetabolicName(destfile)
getCategoryIndepKGMLurl(pathwayid, organism="hsa", method="wget", ...)

Arguments

pathwayid

KEGG PATHWAY ID, e.g. 'hsa00020'

organism

three-alphabet organism code, if pathwayid contains the ocde this option is ignored

destfile

Destination file, to which the remote KGML file should be saved

method

Method to be used for downloading files, passed to download.file function. Currently supports "internal", "wget" and "lynx"

...

Parameters passed to download.file

Value

KGML File URL of the given pathway.

Details

The function getKGMLurl takes the pathway identifier (can be in the form of 'hsa00020' or with 'pathway' prefix, for example 'path:hsa00020'), and returns the url to download KGML file.

The mapping between pathway identifier and pathway name can be found by KEGGPATHNAME2ID (or reversed mappings) in KEGG.db package. See vignette for example. retrieveKGML calls download.file to download the KGML file from KEGG FTP remotely. Since July 2011 the KGML is downloaded directly from the HTTP main page of each pathway, instead of from the FTP server. The FTP server is only open to subscribers. Commercial and other users should consider support the KEGG database by subscribing to the FTP service. See the references section below.

References

Plea from KEGG (available as of Aug 2011) http://www.genome.jp/kegg/docs/plea.html

Examples

getKGMLurl("hsa00020")
getKGMLurl("path:hsa00020")
getKGMLurl("00020",organism="hsa")
getKGMLurl(c("00460", "hsa:00461", "path:hsa00453", "path:00453"))

## NOT RUN
tmp <- tempfile()
retrieveKGML(pathwayid='00010', organism='cel', destfile=tmp, method="wget")