\HeaderA{scaleTransitionProbability}{Scales the probability of transitioning between two states in the
Viterbi algorithm}{scaleTransitionProbability}
\keyword{manip}{scaleTransitionProbability}
\begin{Description}\relax
Function only returns a matrix of 1's (by default, no scaling of the
transition probabilities).  This may be changed in future releases.
\end{Description}
\begin{Usage}
\begin{verbatim}
scaleTransitionProbability(states, SCALE = 2, normalLabel = "N")
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{states}] character string of hidden states
\item[\code{SCALE}] Numeric. See details.
\item[\code{normalLabel}] Character: label used for the baseline state.
\end{ldescription}
\end{Arguments}
\begin{Value}
A matrix of dimension S x S, where S is the number of states.  The
diagonal should always be 1 (we do not scale the probability of
remaining in the same state).  A slot for storing this matrix is
provided in the \code{HmmParameter} class.
\end{Value}
\begin{Author}\relax
RS
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{genomicDistance}{genomicDistance}}, \code{\LinkA{transitionScale}{transitionScale}}, \code{\LinkA{HmmParameter-class}{HmmParameter.Rdash.class}}
\end{SeeAlso}

