KEGGPATHID2EXTID {KEGG}R Documentation

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

Description

KEGGPATHID2EXTID maps KEGG pathway ids to LocusLink (for human, mouse, and rat) or Open Reading Frame (for yeast) ids

Details

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

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(KEGGPATHID2EXTID)
        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]