ggahomologyLL2HGID {ggahomology}R Documentation

Mappings between public database ids and NCBI's Internal HomoloGeneIDs for Gallus gallus

Description

R environments that provides mappings between public database ids and internal HomoloGeneIDs (HGID) used by NCBI to represent sequences for Gallus gallus. Public database ids include LocusLink ids (LL) and GenBank Accesion/RefSeq numbers (ACC).

Details

Each R environment provides mapping between either HomoloGeneIds and database ids, or the converse. The mapping direction is indicated by the name of the environment. For instance, ggahomologyACC2HGID provides mappings between GenBank accession numbers and HomoloGeneIds.

For each environment, a given id will map to a named vector of ids, the names of which are the NCBI code for that organism.

Mappings contained were based on data provided by HomoloGene.

HomoloGene: ftp://ftp.ncbi.nih.gov/pub/HomoloGene/old/hmlg.ftp. Built: HomoloGene built date not available

Packagebuilt Sun Mar 26 00:44:32 2006

References

http://www.ncbi.nih.gov/entrez/query.fcgi?db=homologene

Examples

    require("annotate") || stop("annotate unavailable")
    xx <- as.list(ggahomologyLL2HGID)
        if(length(xx) > 5){
                # Get the value of the first key
                xx[2]
                # Get the value for a few keys
                if(length(xx) >= 3){
                        xx[2:4]
                }
        }

[Package ggahomology version 1.12.0 Index]