\HeaderA{cdfMergeAlleles}{Function to join CDF allele A and allele B groups strand by strand}{cdfMergeAlleles}
\keyword{programming}{cdfMergeAlleles}
\keyword{internal}{cdfMergeAlleles}
\begin{Description}\relax
Function to join CDF allele A and allele B groups strand by strand.

This \code{\LinkA{function}{function}} is design to be used with \code{\LinkA{applyCdfGroups}{applyCdfGroups}}()
on an Affymetrix Mapping (SNP) CDF \code{\LinkA{list}{list}} structure.
\end{Description}
\begin{Usage}
\begin{verbatim}cdfMergeAlleles(groups, compReverseBases=FALSE, collapse="", ...)\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{groups}] A \code{\LinkA{list}{list}} structure with groups.
\item[\code{compReverseBases}] If \code{\LinkA{TRUE}{TRUE}}, the group names, which typically are
names for bases, are turned into their complementary bases for the
reverse strand.
\item[\code{collapse}] The \code{\LinkA{character}{character}} string used to collapse the allele A
and the allele B group names.
\item[\code{...}] Not used.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Allele A and allele B are merged into a \code{\LinkA{matrix}{matrix}} where first row
hold the elements for allele A and the second elements for allele B.
\end{Details}
\begin{Value}
Returns a \code{\LinkA{list}{list}} structure with the two groups \code{forward}
and \code{reverse}, if the latter exists.
\end{Value}
\begin{Author}\relax
Henrik Bengtsson (\url{http://www.braju.com/R/})
\end{Author}
\begin{References}\relax
[1] Affymetrix, \emph{Understanding Genotyping Probe Set Structure}, 2005.
\url{http://www.affymetrix.com/support/developer/whitepapers/genotyping_probe_set_structure.affx}\\
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{applyCdfGroups}{applyCdfGroups}}().
\end{SeeAlso}

