hgu95av2PATH2PROBE {hgu95av2}R Documentation

Annotation of KEGG pathway identifiers by probe identifiers

Description

hgu95av2PATH2PROBE mappes KEGG pathway ids to probe ids

Details

This is an environment object with key and value pairs. Keys are KEGG pathway ids and values are the corresponding probe ids representing genes that are involved in the the pathways defined by the ids. Values are vectors of length 1 or greater depending on whether a given pathway id can be mapped to only one or more probe ids. Pathway ids can not be mapped to a probe identifier are assigned a value NA.

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.

Mappings were based on data provided by:

KEGG built: Release 29.0 (January 2004).ftp://ftp.genome.ad.jp/pub/kegg/pathways

LocusLink built: March 3, 2004. ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.ga

Package built Wed Mar 3 16:27:29 2004

References

http://www.genome.ad.jp/kegg/ and http://www.ncbi.nlm.nih.gov

Examples

    # Convert the environment to a list
    xx <- as.list(hgu95av2PATH2PROBE)
    # Remove patheay 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 hgu95av2 version 1.5.1 Index]