rae230aPATH2PROBE {rae230a}R Documentation

Mappings between KEGG pathway identifiers and probe identifiers

Description

KEGG (Kyoto Encyclopedia of Genes and Genomes) maintains pathway data for various organisms. Each pathway has a name, pathway id, and graphical presentation of the pathway. rae230aPATH2PROBE maps KEGG pathway ids to probe identifiers representing genes whose products participate in the interactions of the pathway

Details

Pathway name for a given pathway id can be obtained using the KEGG data package that can either be built using AnnBuilder or downloaded from Bioconductor http://www.bioconductor.org.

Graphic presentations of pathways are searchable at url{http://www.genome.ad.jp/kegg/pathway.html} using pathway ids as keys.

Mappings were based on data provided by:

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

LocusLink:ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gz. Built: September 15, 2004

Package built Thu Sep 16 09:31:44 2004

References

http://www.genome.ad.jp/kegg/

Examples

    # Convert the environment to a list
    xx <- as.list(rae230aPATH2PROBE)
    # Remove pathway ids that do not map to any probe id
    xx <- xx[!is.na(xx)]
    if(length(xx) > 0){
        # The probe ids for the first two elements of XX
        xx[1:2]
        # Get the first one
        xx[[1]]
    } 

[Package rae230a version 1.6.5 Index]