\HeaderA{findBreaks}{Identify breakpoints from the hidden Markov model predictions}{findBreaks}
\keyword{manip}{findBreaks}
\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}
findBreaks(x, states, position, chromosome, sample, lik1, lik2)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] matrix of predicted hidden states (integer)
\item[\code{states}] character string giving the hidden states
\item[\code{position}] physical position of the SNPs
\item[\code{chromosome}] chromosome number
\item[\code{sample}] sample name
\item[\code{lik1}] likelihood under alternative model
\item[\code{lik2}] likelihood under NULL model
\end{ldescription}
\end{Arguments}
\begin{Value}
\begin{ldescription}
\item[\code{data.frame}] data.frame describing regions of normal and altered states
\end{ldescription}
\end{Value}

