translateKEGGID2GeneID: Translate between KEGGID and Entrez Gene ID

Description Usage Arguments Details Value Note Author(s) Examples

View source: R/annotation.R

Description

translateKEGGID2GeneID translates KEGGID to NCBI Entrez Gene ID, and translateGeneID2KEGGID translates Entrez Gene ID back to KEGGID.

Usage

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translateKEGGID2GeneID(x, organism="hsa")
translateGeneID2KEGGID(x, organism="hsa")

Arguments

x

KEGGID, e.g. 'hsa:1432', or Entrez Gene ID, e.g. '1432'

organism

Three alphabet code for organisms. The mapping between the orgniams and codes can be found at http://www.genome.jp/kegg/kegg3.html

Details

The KEGGID are unique identifiers used by KEGG PATHWAY to identify gene products. After parsing the KEGG pathway into graph, the graph use KEGGID as its nodes' names.

translateKEGGID2GeneID converts KEGGIDs into entrez GeneID, which can be translated to other types of identifiers, for example with biomaRt package or organism-specific annotation packages. See vignette for examples.

translateKEGG2GeneID is maintained for back-compatibility and wrapps translateKEGGID2GeneID.

Value

Entrez GeneID of the given KEGG ID(s)

Note

This function works so far only with human KEGGIDs, since for them the Entrez GeneID can be derived easily with removing the organism prefix.

The complete functional function will be implemented in the later release of the package.

Author(s)

Jitao David Zhang

Examples

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egNodes <- c("hsa:1432", "hsa:11072")
translateKEGGID2GeneID(egNodes)
translateGeneID2KEGGID("1432")

KEGGgraph documentation built on Nov. 17, 2017, 9:01 a.m.