agPATH {ag}R Documentation

Mappings between probe identifiers and KEGG pathway identifiers

Description

KEGG (Kyoto Encyclopedia of Genes and Genomes) maintains pathway data for various organisms. agPATH maps probe identifiers to the identifiers used by KEGG for pathways in which the genes represented by the probe identifiers are involved

Details

Each KEGG pathway has a name and identifier. Pathway name for a given pathway identifier 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} by using pathway identifiers as keys.

Mappings were based on data provided by:

Tair: ftp://ftp.arabidopsis.org/home/tair//ath/ath_gene_map.tab Built: N/A

Tair: ftp://ftp.arabidopsis.org/home/tair/Microarrays/Affymetrix/affy_AG_array_elements-2006-07-14.txt Tair: ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR_sequenced_genes Tair: ftp://ftp.arabidopsis.org/home/tair/User_Requests/LocusPublished.02022007 Built: N/A

Package built Fri Aug 24 17:42:16 2007

References

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

Examples

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

[Package ag version 2.2.0 Index]