indacPATH {indac} | R Documentation

## Mappings between probe identifiers and KEGG pathway identifiers

### Description

KEGG (Kyoto Encyclopedia of Genes and Genomes) maintains pathway data for various organisms. indacPATH 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 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:ftp://ftp.genome.ad.jp/pub/kegg/tarfiles/pathway.tar.gz. Built: Release 41.1, February 1, 2007

Entrez Gene:ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/. Built: Source data downloaded from Entrez Gene on Fri Aug 24 00:35:59 2007

Package built Fri Aug 24 00:42:00 2007

### References

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

### Examples

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

[Package indac version 2.0.1 Index]