org.At.tairPATH2TAIR {org.At.tair.db}R Documentation

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

Description

org.At.tairPATH2TAIR is an R object that provides mappings between KEGG identifiers and TAIR identifiers.

Details

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

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

    # Convert the object to a list
    xx <- as.list(org.At.tairPATH2TAIR)
    # Remove pathway identifiers that do not map to any tair id
    xx <- xx[!is.na(xx)]
    if(length(xx) > 0){
        # The tair identifiers for the first two elements of XX
        xx[1:2]
        # Get the first one
        xx[[1]]
    } 

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