hsahomologyDATA {hsahomology}R Documentation

Maps Homo sapiens HomoloGeneIDs to homology data of other organisms that have homology relationships with genes represented by the HomoloGeneIDs

Description

Genes that share an arbitrary threshold level of similarity determined by alignment of matching bases are termed homologous. homologyDATA contains mappings between Homo sapiens internal HomoloGeneIDs (used by NCBI to represent sequences of an organism) and the data concerning genes in other organisms that have been identified to have homology relationships with genes represented by the HomoloGeneIDs

Details

homologyDATA is an environment object with key and value pairs. Keys are HomoloGeneIDs and values are lists of sublists for other organisms that have been identified to have homology relationships with the genes represented by the HomoloGeneIDs. The list for a given internal HomoloGeneID may have one to many sublists depending on whether homology relationships have been identified in only one or more other organisms.

A sublist has the following elements:

homoOrg - a named vector of a single character string whose value is the scientific name of the organism and name the numeric code used by NCBI for the organism.

homoHGID - an integer for internal HomoloGeneID.

homoType - a single letter for the type of similarity measurement between the homologous genes. homoType can be either B (reciprocal best best between three or more organisms), b (reciprocal best match between two organisms), or c (curated homology relationship between two organisms).

homoPS - a percentage value measured as the percent of identity of base pair alignment between the homologous sequences.

homoURL - a url to the source if the homology relationship is a curated orthology.

HomoData objects with homoType = B or b will not have any value for homoURL and objects with homoType = c will not have any value for homoPS.

The value of a given slot of a homoData object can be accessed by using homoOrg(xxx) for the homoOrg slot of the homoData object xxx, for example.

Mappings contained in homologyDATA 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

ftp://ftp.ncbi.nih.gov/pub/HomoloGene/hmlg.ftp

Examples

    require("annotate") || stop("annotate unavailable")
    # Convert homologyDATA to a list
    xx <- as.list(hsahomologyDATA)

    if(length(xx) > 0){
        # Gets the homology data for the first key of hsahomologyDATA
        homodata <- xx[[1]]
        # Gets the organism name, LocusLink id, internal HomoloGene id,
        # GenBank accession number, type of similarity, percent
        # similarity, and URL for percent similarity for the first
        # homoData object in the list obtained previously
        homodata[[1]][["homoOrg"]]
        homodata[[1]][["homoHGID"]]
        homodata[[1]][["homoType"]]
        homodata[[1]][["homoPS"]]
        homodata[[1]][["homoURL"]]
        # Gets the values for more than one keys
        xx[1:3]
    }

[Package hsahomology version 1.6.5 Index]