agPATH2PROBE {ag}R Documentation

Map between Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway identifiers and Manufacturer Identifiers

Description

agPATH2PROBE is an R environment that provides mappings between KEGG identifiers and manufacturer identifiers.

Details

Each KEGG identifier is mapped to a named vector of manufacturer identifiers. The name represents the KEGG identifier and the vector contains all manufacturer identifiers that are found in that particular pathway. An NA is reported for any KEGG identifier that cannot be mapped to any manufacturer identifiers.

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 http://www.genome.ad.jp/kegg/pathway.html 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(agPATH2PROBE)
    # Remove pathway identifiers that do not map to any probe id
    xx <- xx[!is.na(xx)]
    if(length(xx) > 0){
        # The probe identifiers for the first two elements of XX
        xx[1:2]
        # Get the first one
        xx[[1]]
    } 

[Package ag version 2.2.0 Index]