hgu95aPATH2PROBE {hgu95a}R Documentation

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

Description

hgu95aPATH2PROBE 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:

KEGG:ftp://ftp.genome.ad.jp/pub/kegg/tarfiles/pathway.tar.gz. Built: Release 38.1, June 1, 2006

Entrez Gene:ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/. Built: Source data downloaded from Entrez Gene on Mon Sep 25 20:19:44 2006

Package built Mon Sep 25 20:43:03 2006

References

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

Examples

    # Convert the environment to a list
    xx <- as.list(hgu95aPATH2PROBE)
    # 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 hgu95a version 1.14.0 Index]