translateKEGGID2GeneID {KEGGgraph} | R Documentation

## Translate between KEGGID and Entrez Gene ID

### Description

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

### Usage

    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

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

[Package KEGGgraph version 1.1.0 Index]