xlahomologyLL2HGID {xlahomology}R Documentation

Mappings between public database ids and NCBI's Internal HomoloGeneIDs for Xenopus laevis

Description

Provides mappings between public database ids and internal HomoloGeneIDs (HGID) used by NCBI to represent sequences for Xenopus laevis. Public database ids include LocusLink ids (LL) and GenBank Accesion/RefSeq numbers (ACC).

Details

Each object is an environment object with key and value pairs. Keys are ids specified by the abbreviation proceeding the number 2 of the name of an object (e.g. LL in xlahomologyLL2HGID) and values are ids specified by the abbreviation following the number 2 (e.g. HGID in xlahomologyLL2HGID). Values may be vectors of length 1 or greater depending on whether a key id can be mapped to only one or more other ids. Vector names are the code used by NCBI for various organism.

xlahomologyLL2HGID or xlahomologyACC2HGID can be used to find the HomoloGeneIDs for a give LocusLink id or GenBank/RefSeq accession number and then the data for homologous genes found in other organisms.

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 Wed Oct 20 16:32:42 2004

References

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

Examples

    require("annotate") || stop("annotate unavailable")
    xx <- as.list(xlahomologyLL2HGID)
        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 xlahomology version 1.6.5 Index]