\HeaderA{states.hmm.func}{A function to fit unsupervised Hidden Markov model}{states.hmm.func}
\keyword{models}{states.hmm.func}
\begin{Description}\relax
This function is a workhorse of \code{\LinkA{find.hmm.states}{find.hmm.states}}. It
operates on the individual chromosomes/samples and is not called
directly by users.
\end{Description}
\begin{Usage}
\begin{verbatim}
states.hmm.func(sample, chrom, dat, datainfo = clones.info, vr = 0.01,
                maxiter = 100, aic = FALSE, bic = TRUE, delta = 1,
                nlists = 1, eps = .01, print.info = FALSE,
                diag.prob = .99)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{sample}] ~~Describe \code{sample} here~~ 
\item[\code{chrom}] ~~Describe \code{chrom} here~~ 
\item[\code{dat}] ~~Describe \code{dat} here~~ 
\item[\code{datainfo}] ~~Describe \code{datainfo} here~~ 
\item[\code{vr}] ~~Describe \code{vr} here~~ 
\item[\code{maxiter}] ~~Describe \code{maxiter} here~~ 
\item[\code{aic}] ~~Describe \code{aic} here~~ 
\item[\code{bic}] ~~Describe \code{bic} here~~ 
\item[\code{delta}] ~~Describe \code{delta} here~~ 
\item[\code{nlists}] ~~Describe \code{nlists} here~~ 
\item[\code{eps}] parameter controlling the convergence of the EM
algorithm. 
\item[\code{print.info}] print.info = T allows diagnostic information to be
printed on the screen. 
\item[\code{diag.prob}] parameter controlling the construction of the
initial transition probability matrix. 
\end{ldescription}
\end{Arguments}
\begin{SeeAlso}\relax
\code{\LinkA{aCGH}{aCGH}}
\end{SeeAlso}

