\HeaderA{SMAPHMM}{Constructor for "SMAPHMM" objects}{SMAPHMM}
\keyword{classes}{SMAPHMM}
\begin{Description}\relax
A constructor for \code{\LinkA{SMAPHMM-class}{SMAPHMM.Rdash.class}} objects.
\end{Description}
\begin{Usage}
\begin{verbatim}
SMAPHMM(noStates, Phi, A=NULL,
        Pi=rep(1/noStates,noStates),
        initTrans=0.2/(noStates - 1))
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{noStates}] The number of hidden states in the HMM (numeric).
\item[\code{Phi}] A Gaussian distribution parameter matrix (numeric).
\item[\code{A}] A \code{noStates * noStates} matrix of transition
probabilities betweeen the hidden states (numeric).
\item[\code{Pi}] A vector of initial probabilities of starting in a certain
state (numeric).
\item[\code{initTrans}] Specifies the transition probability between
non-equal states (numeric).
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
\code{Phi} is a \code{noStates * 2} matrix that specifies the
paramaters of Gaussian distributions associated with each hidden
state.  The first column specifies standard deviations, the second
specifies means.

If \code{A == NULL}, \code{initTrans} specifies the transition
probability between states \code{i} and \code{j} in \code{1:noStates},
such that \code{i != j}. Only used if \code{A ==
        NULL}. \code{initTrans * noStates} must be smaller than (or equal
to) 1.
\end{Details}
\begin{Value}
An object of class \code{\LinkA{SMAPHMM-class}{SMAPHMM.Rdash.class}}.
\end{Value}
\begin{Author}\relax
Robin Andersson, \email{robin.andersson@lcb.uu.se}
\end{Author}
\begin{References}\relax
Andersson, R., Bruder, C. E. G., Piotrowski, A., Menzel, U., Nord, H.,
Sandgren, J., Hvidsten, T. R., Diaz de Stahl, T., Dumanski, J. P.,
Komorowski, J., A Segmental Maximum A Posteriori Approach to Array-CGH
Copy Number Profiling, submitted
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{smap}{smap}},
\code{\LinkA{SMAPHMM-class}{SMAPHMM.Rdash.class}},
\code{\LinkA{SMAPObservations-class}{SMAPObservations.Rdash.class}}
\end{SeeAlso}

