pwKEGGxml {PathWave} | R Documentation |
Reads and parses KEGG xml files. Extracts gene IDs, reaction IDs, compound IDs and internal KEGG IDs for every pathway.
pwKEGGxml(url = "ftp://ftp.genome.jp/pub/kegg/xml/organisms/hsa/")
url |
Url or directory containing the xml files that should be parsed (default "ftp://ftp.genome.jp/pub/kegg/xml/organisms/hsa/"). See details. |
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. |
Gunnar Schramm
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 as pwAdjMatrices
kegg.ftp="ftp://ftp.genome.jp/pub/kegg/xml/organisms/hsa/" keggXml=pwKEGGxml(kegg.ftp)