list.organisms {KEGGSOAP} | R Documentation |
These functions provides an R interface to allow users to get the names/ids of organisms, databases, pathways that are available through KEGG SOAP services.
list.organisms() list.pathways(org) list.databases()
org |
org a character string for the id used by KEGG for
organisms. The organism ids are normally three-letter codes with the
first letter being the first letter of the genus name and the rest
being the first two letters of the species name of the scientic name
of the organism of concern |
Some queries agsinst the KEGG databases require abbreviations of
organisms supported by KEGG. Although the abbreviations normally
consist of three letters by truncating the first letter of the genus
name and the first two letters of the species name (e. g. hsp for Homo
sapiens), list.organisms
obtains the abbreviations using
the service provided by KEGG SOAP to make sure the abbreviations are
correct and the organisms are indeed supported by KEGG databases.
list.organisms
returns a named vector with names of the
vector being the scientific names and the values of the vector being the
abbreviations used by KEGG for the organisms supported by the
databases.
list.pathways
returns a named vector with names of the
vector being textual descriptions of KEGG pathways and the values of
the vector being the ids used by KEGG to represent pathways.
list.databases
returns
Jianhua Zhang
http://www.genome.jp/kegg/soap/doc/keggapi_manual.html
if(require("SSOAP") && require("XML")){ list.organisms() }