KEGGEXTID2PATHID {KEGG}R Documentation

An annotation data file that maps LocusLink or Open Reading Frame ids KEGG pathway ids

Description

KEGGEXTID2PATHID maps LocusLink (for human, mouse, and rat) and Open Reading Frame (for yeast) ids to KEGG pathway ids.

Details

This is an environment object containing key and value pairs. Keys are LocusLink ids for human, mouse, and rat and Open Reading Frame (ORF) ids for yeast and values are the corresponding KEGG pathway ids. Values are vectors of length 1 or greater depending on whether a given external id can be mapped to only one or more KEGG pathway ids. NAs are assigned to LocusLink or ORF ids that can not be mapped to any pathway id.

KEGG pathway ids are the identifiers used by KEGG for various pathways.

Mappings between KEGG pathway ids and pathway names can be obtained through another environment named PATHID2NAME.

Mappings were based on data provided by:

KEGG:ftp://ftp.genome.ad.jp/pub/kegg/pathways/map_title.tab. Built: Release 31.0 (July 2004)

Package built: Fri Sep 17 16:18:11 2004

References

ftp://ftp.genome.ad.jp/pub/kegg/pathways

Examples

        require("annotate") || stop("annotate unavailable")
        xx <- as.list(KEGGEXTID2PATHID)
        if(length(xx) > 0){
                # Get the value of the first key
                xx[[1]]
                # Get the values for multiget for a few keys
                if(length(xx) >= 3){
                        xx[1:3]
                }
        }

[Package KEGG version 1.6.5 Index]