\HeaderA{snpm2mapLD}{prepare input to mapLD function for haplotype block identification}{snpm2mapLD}
\aliasA{smtest}{snpm2mapLD}{smtest}
\keyword{models}{snpm2mapLD}
\begin{Description}\relax
prepare input to mapLD function for haplotype block identification
\end{Description}
\begin{Usage}
\begin{verbatim}
snpm2mapLD(x, chrnum, runMAP=TRUE, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] snp.matrix instance
\item[\code{chrnum}] chromosome number
\item[\code{runMAP}] logical indicating whether or not to run mapLD
\item[\code{...}] additional arguments to mapLD
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
sets up a data frame suitable for mapLD, and will invoke with
appropriate arguments identifying columns for alleles and
other identifiers if runMAP is TRUE (default).

smtest is a small snp.matrix instance
\end{Details}
\begin{Value}
a list with element struc holding the data frame,
and mapLD output if requested.  Note that mapLD writes an eps
file to disk *sigh*.
\end{Value}
\begin{Author}\relax
Vince Carey <stvjc@channing.harvard.edu>
\end{Author}
\begin{Examples}
\begin{ExampleCode}
data(smtest)
ss = snpm2mapLD(smtest, chrnum=20, runMAP=FALSE)
ss
# you could run mapLD on ss[[1]]
\end{ExampleCode}
\end{Examples}

