org.At.tairPATH {org.At.tair.db}R Documentation

Mappings between TAIR identifiers and KEGG pathway identifiers

Description

KEGG (Kyoto Encyclopedia of Genes and Genomes) maintains pathway data for various organisms. org.At.tairPATH maps TAIR identifiers to the identifiers used by KEGG for pathways in which the genes represented by the TAIR 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 GENOME ftp://ftp.genome.jp/pub/kegg/genomes With a date stamp from the source of: 2011-Mar15

References

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

Examples

        x <- org.At.tairPATH
        # Get the TAIR 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]]
        }

[Package org.At.tair.db version 2.6.4 Index]