hgfocusPATH2PROBE {hgfocus} | R Documentation

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

### Description

hgfocusPATH2PROBE is an R environment that provides mappings between KEGG ids and manufacturer ids.

### Details

Each KEGG id is mapped to a named vector of manufacturer ids. The name represents the KEGG id and the vector contains all manufacturer ids that are found in that particular pathway. An `NA` is reported for any KEGG id that cannot be mapped to any manufacturer ids.

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 http://www.genome.ad.jp/kegg/pathway.html 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(hgfocusPATH2PROBE)
        # Remove pathway 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 hgfocus version 1.12.0 Index]