\HeaderA{breaks}{Identify breakpoints from the hidden Markov model predictions}{breaks}
\keyword{manip}{breaks}
\begin{Description}\relax
Identify breakpoints: physical position of breaks, number of SNPs in
region, and the called hidden state.
\end{Description}
\begin{Usage}
\begin{verbatim}
breaks(x, states, position, chromosome, sampleNames, chromosomeAnnotation = NULL, verbose = FALSE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] Locus X sample matrix of hidden states where the hidden
states are represented as integers
\item[\code{states}] Labels for the hidden states
\item[\code{position}] Physical position of loci
\item[\code{chromosome}] integer indicating chromosome (23=X)
\item[\code{sampleNames}] sample labels
\item[\code{chromosomeAnnotation}] chromosome annotation. see details
\item[\code{verbose}] verbose output
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
One may provide their own chromosome annotation with centromere start
and stop sites.  The format must be the same as the
chromosomeAnnotation dataset in the R package SNPchip.
\end{Details}
\begin{Value}
data.frame

\begin{ldescription}
\item[\code{sample}] sample label
\item[\code{chr}] chromosome (23 = X)
\item[\code{start}] starting physical position of segment
\item[\code{end}] last physical position of segment
\item[\code{nbases}] number of bases in segment
\item[\code{nprobes}] number of probes in segment
\item[\code{state}] label for the state of the segment
\end{ldescription}
\end{Value}
\begin{Author}\relax
R. Scharpf
\end{Author}
\begin{Examples}
\begin{ExampleCode}
x <- matrix(rep(c(1, 2, 3, 1, 2), each=50), ncol=1)
breaks(x, states=c("0", "1", "2"), position=1:nrow(x), chromosome=1,
       sampleNames="A")
\end{ExampleCode}
\end{Examples}

