hgu95av2PATH {hgu95av2.db}R Documentation

Mappings between probe identifiers and KEGG pathway identifiers

Description

KEGG (Kyoto Encyclopedia of Genes and Genomes) maintains pathway data for various organisms.

hgu95av2PATH maps probe identifiers to the identifiers used by KEGG for pathways in which the genes represented by the probe identifiers are involved

hgu95av2PATH2PROBE is an R object that provides mappings between KEGG identifiers and manufacturer identifiers.

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: KEGG GENOME ftp://ftp.genome.jp/pub/kegg/genomes With a date stamp from the source of: 2011-Mar15

References

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

Examples

    x <- hgu95av2PATH
    # Get the probe identifiers that are mapped to a KEGG pathway ID
    mapped_probes <- mappedkeys(x)
    # Convert to a list
    xx <- as.list(x[mapped_probes])
    if(length(xx) > 0) {
      # Get the PATH for the first five probes
      xx[1:5]
      # Get the first one
      xx[[1]]
    }

    # Now convert the hgu95av2PATH2PROBE object to a list
    xx <- as.list(hgu95av2PATH2PROBE)
    if(length(xx) > 0){
        # Get the probe identifiers for the first two pathway identifiers
        xx[1:2]
        # Get the first one
        xx[[1]]
    } 

[Package hgu95av2.db version 2.10.1 Index]