\HeaderA{LL2homology}{Functions that find the homology data for a given set of
LocusLink ids or HomoloGeneIDs}{LL2homology}
\aliasA{ACC2homology}{LL2homology}{ACC2homology}
\aliasA{HGID2homology}{LL2homology}{HGID2homology}
\keyword{misc}{LL2homology}
\begin{Description}\relax
Given a set of LocusLink ids or NCBI HomoloGeneIDs, the functions obtain the
homology data and represent them as a list of sub-lists using the
homology data package for the organism of interest. A sub-list can be of
length 1 or greater depending on whether a LocusLink id can be mapped
to one or more HomoloGeneIDs.
\end{Description}
\begin{Usage}
\begin{verbatim}
LL2homology(homoPkg, llids)
HGID2homology(hgid, homoPkg)
ACC2homology(accs, homoPkg)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{llids}] \code{llids} a vector of character strings or numberic
numbers for a set of LocusLink ids whose homologous genes in other
organisms are to be found
\item[\code{hgid}] \code{hgid} a named vector of character strings or numberic
numbers for a set of HomoloGeneIDs whose homologous genes in other
organisms are to be found. Names of the vector give the code used by
NCBI for organisms
\item[\code{accs}] \code{accs} a vector of character strings for a set of
GenBank Accession numbers
\item[\code{homoPkg}] \code{homoPkg} a character string for the name of the
homology data package for a given organism, which is a short version
of the scientific name of the organism plus homology (e. g. hsahomology)
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The homology data package has to be installed before executing any of
the two functions.

Each sub-list  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.

homoLL - an integer for LocusLink id.

homoHGID - an integer for internal HomoloGeneID.

homoACC - a character string for GenBank accession number of the
best matching sequence of the organism.

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.

Sub-lists with homoType = B or b will not have any value
for homoURL and objects with homoType = c will not have any value
for homoPS.
\end{Details}
\begin{Value}
Both functions returns a list of sub-lists containing data for
homologous genes in other organisms.
\end{Value}
\begin{Author}\relax
Jianhua Zhang
\end{Author}
\begin{References}\relax
\url{http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?=homologene}
\end{References}
\begin{Examples}
\begin{ExampleCode}
  if(require("hsahomology")){
      llids <- ls(env = hsahomologyLL2HGID)[2:5]
      LL2homology("hsahomology", llids)
  }
\end{ExampleCode}
\end{Examples}

