pwKEGGxml {PathWave}R Documentation

PathWave parser for KEGG XML files

Description

Reads and parses KEGG xml files. Extracts gene IDs, reaction IDs, compound IDs and internal KEGG IDs for every pathway.

Usage

pwKEGGxml(url = "ftp://ftp.genome.jp/pub/kegg/xml/organisms/hsa/")

Arguments

url Url or directory containing the xml files that should be parsed (default "ftp://ftp.genome.jp/pub/kegg/xml/organisms/hsa/"). See details.

Details

url
Variable url can either be an url or a directory. The function searches for xml files in the given url.
IMPORTANT: reaction IDs are extracted for each pathway. To avoid mismatching similar reaction IDs of different pathways, pathway ID and reaction ID are concatenated, e.g. hsa00251:R00256 .

Value

A List is returned:

ids Internal KEGG IDs. Contains a list of pathway IDs. For every pathway ID a vector is stored with the internal KEGG IDs for every reaction ID.
genes Contains a list of pathway IDs. For every pathway ID a vector is stored with the entrez gene IDs for every reaction ID. Reaction IDs can occur more than once if more than one gene can be mapped on it.
reactions Contains a list of pathway IDs. For every pathway ID a vector is stored with reaction IDs (concatenated with the pathway ID).
compounds Contains a list of pathway IDs. For every pathway ID a list of the pathways reaction IDs is stored. These lists contain the compounds the specific reaction is connected with.

Author(s)

Gunnar Schramm

References

KEGG: Kanehisa, M., Araki, M., Goto, S., Hattori, M., Hirakawa, M., Itoh, M., Katayama, T., Kawashima, S., Okuda, S., Tokimatsu, T., and Yamanishi, Y.; KEGG for linking genomes to life and the environment. Nucleic Acids Res. 36, D480-D484 (2008).

See Also

See Also as pwAdjMatrices

Examples

kegg.ftp="ftp://ftp.genome.jp/pub/kegg/xml/organisms/hsa/"
keggXml=pwKEGGxml(kegg.ftp)

[Package PathWave version 1.0 Index]