org.EcK12.egPATH {org.EcK12.eg.db} | R Documentation

## Mappings between Entrez Gene identifiers and KEGG pathway identifiers

### Description

KEGG (Kyoto Encyclopedia of Genes and Genomes) maintains pathway data for various organisms. org.EcK12.egPATH maps entrez gene identifiers to the identifiers used by KEGG for pathways

### 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 ) on 2008-Sep2

### References

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

### Examples

        x <- org.EcK12.egPATH
        # Get the entrez gene identifiers that are mapped to a KEGG pathway ID
        mapped_genes <- mappedkeys(x)
        # Convert to a list
        xx <- as.list(x[mapped_genes])
        if(length(xx) > 0) {
          # Get the PATH for the first five genes
          xx[1:5]
          # Get the first one
          xx[[1]]
        }

        # For the reverse map:
        # Convert the object to a list
        xx <- as.list(org.EcK12.egPATH2EG)
        # Remove pathway identifiers that do not map to any entrez gene id
        xx <- xx[!is.na(xx)]
        if(length(xx) > 0){
            # The entrez gene identifiers for the first two elements of XX
            xx[1:2]
            # Get the first one
            xx[[1]]
        }

[Package org.EcK12.eg.db version 2.2.6 Index]