\HeaderA{ggahomologyDATA}{Genes that are Homologous to Gallus gallus}{ggahomologyDATA}
\keyword{datasets}{ggahomologyDATA}
\begin{Description}\relax
This data set gives mappings between Gallus gallus genes and other
species based on homology. Genes that share an arbitrary threshold
level of similarity determined by alignment of matching bases are termed
homologous. The format is an R environment that maps HomoloGeneIds
(which are used by NCBI to represent sequences of an organism) to a
list of organisms that have homologous sequences.
\end{Description}
\begin{Details}\relax
Each HomoloGeneId is mapped to a list of lists. The names of the outer
list are the numeric code used for that organism by the NCBI. This is
included for convenience when processing the list using \code{lapply}.

Each inner list consists of five named elements; homoORG, homoType,
homoPS, homoHGID, and homoURL.

The homoORG element indicates the organism for which there is a
homologous gene. This will be an abbreviation of the first letter of
the genus and the first two letters of the species. For instance, Homo
sapiens is abbreviated \emph{hsa}.

The homoType element indicates the type of similarity
measurement. This can be either \emph{B}, indicating a reciprocal best
best match between three or more organisms, \emph{b}, indicating a
reciprocal best match between two organisms, or \emph{c}, indicating a
curated homology relationship between two organisms.

The homoPS element gives the percentage of identical base pair
alignments between the homologous genes.

The homoHGID element gives the internal HomoloGeneId.

The homoURL element gives a url to the source for a curated homology.

Note that there will not be a value for homoURL if the homoType is B
or b, and there will not be a value for homoPS if the homoType is c.

Mappings contained in homologyDATA were based on data provided
by HomoloGene.

HomoloGene:\bsl{}url{ ftp://ftp.ncbi.nih.gov/pub/HomoloGene/old/hmlg.ftp}. Built: HomoloGene built date not available

Packagebuilt Fri Mar 16 11:04:57 2007
\end{Details}
\begin{References}\relax
\url{ftp://ftp.ncbi.nih.gov/pub/HomoloGene/hmlg.ftp}
\end{References}
\begin{Examples}
\begin{ExampleCode}
    require("annotate") || stop("annotate unavailable")
    # Convert homologyDATA to a list
    xx <- as.list(ggahomologyDATA)

    if(length(xx) > 0){
        # Gets the homology data for the first key of ggahomologyDATA
        homodata <- xx[[1]]
        # Gets the organism name, Entrez Gene identifier. internal HomoloGene identifier,
        # 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]
    }
\end{ExampleCode}
\end{Examples}

