\HeaderA{viterbi}{viterbi algorithm}{viterbi}
\keyword{models}{viterbi}
\begin{Description}\relax
The Viterbi algorithm for computing the most likely state sequence
given a model
\end{Description}
\begin{Usage}
\begin{verbatim}
viterbi(initialStateProbs, emission, tau, arm, tau.scale, verbose = TRUE, returnLikelihood = FALSE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{initialStateProbs}] initial state probabilities (log scale)
\item[\code{emission}] matrix of log emission probabilities (one sample is a matrix)
\item[\code{tau}] transition probabilities (original scale)
\item[\code{arm}] numeric or character string indicating chromosomal arm
\item[\code{tau.scale}] matrix to scale the probability of transitioning
between states.
\item[\code{verbose}] Logical
\item[\code{returnLikelihood}] whether to return the 'loglikelihood'
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The Viterbi algorithm is fit independently to each chromosomal arm if
arm is specified.

Argument \code{tau.scale} is a matrix that scales the probability of
transitioning from an altered state to a normal state to the
probability of transitioning between two altered states.  If missing,
tau.scale is 1 (no scaling)

returnLikelihood is experimental
\end{Details}
\begin{Value}
\begin{ldescription}
\item[\code{matrix}] predicted states
\end{ldescription}
\end{Value}
\begin{Author}\relax
R. Scharpf
\end{Author}

