get.ko.by.gene: Client-side interfaces to obtain the KEGG ko ids for a...
In kozo2/keggapi: Client-side REST access KEGG

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/KEGGREST.R

Given a KEGG pathway ko identifier, the functions query the KEGG PATHWAY database for all the pathway id or vice versa.

get.ko.by.gene(genes.id)
get.ko.by.ko.class(ko.class.id)
get.genes.by.ko(ko.id, org)
get.kos.by.pathway(pathway.id)
get.pathways.by.kos(ko.id.list, org)

`genes.id`	a vector of gene IDs
`ko.id`	a vector of ko IDs
`ko.class.id`	a vector of ko class IDs
`pathway.id`	`pathway.id` a character string for a KEGG pathway id. KEGG pathway ids consist of the string path followed by a colon, a three-letter code for the organism of concern, and then a number (e. g. "path:eco00020"). The three-letter organism code consists of the first letter of the genus name and the first two letters of the species name of the scientific name of the organism of concern
`ko.id.list`	`pathway.id` a vector of KEGG ko IDs.
`org`	`pathway.id` a string containing the three letter KEGG prefix to use in looking up the IDs

The functions return a vector or a named list of values depending on what the function is supposed to retrieve.

Kozo Nishida

http://www.kegg.jp/kegg/docs/keggapi.html

list.pathways

  ko <- get.ko.by.gene("eco:b0002")
	ko <- get.ko.by.ko.class("00524")
	genes <- get.genes.by.ko("ko:K12524", "eco")
        kos <- get.kos.by.pathway("path:hsa00010")
        pathways <- get.pathways.by.kos(c("ko:K00016","ko:K00382"), "hsa")