hu6800PATH {hu6800}R Documentation

Annotation of probe identifiers by KEGG pathway identifiers

Description

hu6800PATH mappes probe ids to ids of KEGG pathways in which the genes represented by the probe ids are involved

Details

This is an environment object with key and value pairs. Keys are probe ids and values are the corresponding KEGG pathway ids. Values are vectors of length 1 or greater depending on whether a given probe identifier can be associated with only one or more pathways. NA is assigned to probe ids that can not be associated with any pathway at this time.

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(hu6800PATH)
    # Remove probe ids that do not map to any pathway id
    xx <- xx[!is.na(xx)]
    if(length(xx) > 0){
        # The pathway ids for the first two elements of XX
        xx[1:2]
        # Get the first one
        xx[[1]]
    } 

[Package hu6800 version 1.5.1 Index]