hgfocusPATH {hgfocus} | R Documentation

## Mappings between probe identifiers and KEGG pathway identifiers

### Description

KEGG (Kyoto Encyclopedia of Genes and Genomes) maintains pathway data for various organisms. hgfocusPATH maps probe identifiers to the identifiers used by KEGG for pathways in which the genes represented by the probe identifiers are involved

### Details

Each KEGG pathway has a name and id. 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.

Graphic presentations of pathways are searchable at url{http://www.genome.ad.jp/kegg/pathway.html} by using pathway ids as keys.

Mappings were based on data provided by:

KEGG:ftp://ftp.genome.ad.jp/pub/kegg/tarfiles/pathway.tar.gz. Built: Release 37.0, January 4, 2006

Entrez Gene:ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/. Built: Source data downloaded from Entrez Gene on Sat Mar 25 22:06:31 2006

Package built Sat Mar 25 22:23:22 2006

### References

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

### Examples

        # Convert the environment to a list
        xx <- as.list(hgfocusPATH)
        # 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 hgfocus version 1.12.0 Index]