get.ko.by.gene: Client-side interfaces to obtain the KEGG ko ids for a...

In kozo2/keggapi: Client-side REST access KEGG

Description

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

Usage

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)

Arguments

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

Value

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

Author(s)

Kozo Nishida

References

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

See Also

list.pathways

Examples

  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")

kozo2/keggapi documentation built on May 20, 2019, 1:11 p.m.