org.Sc.sgdPATH {org.Sc.sgd.db} | R Documentation

## Mappings between ORF identifiers and KEGG pathway identifiers

### Description

KEGG (Kyoto Encyclopedia of Genes and Genomes) maintains pathway data for various organisms. org.Sc.sgdPATH maps ORF identifiers to the identifiers used by KEGG for pathways. The reverse map org.Sc.sgdPATH2ORF maps back from KEGG pathway IDs to the ORF 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 ) on 2008-Apr1

### References

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

### Examples

        x <- org.Sc.sgdPATH
        # Get the ORF 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]]
        }
        # Convert the object to a list
        xx <- as.list(org.Sc.sgdPATH2ORF)
        # Remove pathway identifiers that do not map to any ORF id
        xx <- xx[!is.na(xx)]
        if(length(xx) > 0){
            # The ORF identifiers for the first two elements of XX
            xx[1:2]
            # Get the first one
            xx[[1]]
        }

[Package org.Sc.sgd.db version 2.2.0 Index]