\HeaderA{SMAPHMM-class}{Class "SMAPHMM": A class to manage HMMs for the SMAP package}{SMAPHMM.Rdash.class}
\aliasA{A}{SMAPHMM-class}{A}
\aliasA{noStates}{SMAPHMM-class}{noStates}
\aliasA{Phi}{SMAPHMM-class}{Phi}
\aliasA{Pi}{SMAPHMM-class}{Pi}
\keyword{classes}{SMAPHMM-class}
\begin{Description}\relax
Holds parameters for a Hidden Markov Model (HMM) used in
the \pkg{SMAP} package.
\end{Description}
\begin{Section}{Objects from the Class}
Objects are not intended to be created directly but via the
constructor function \code{\LinkA{SMAPHMM}{SMAPHMM}}.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{A}:] Object of class \code{"matrix"} The transition
probability matrix between states.
\item[\code{Pi}:] Object of class \code{"numeric"} The initial
probabilities of starting in a certain state.
\item[\code{Phi}:] Object of class \code{"matrix"} A matrix that
specifies the paramaters of Gaussian distributions associated with
each hidden state. The first column specifies standard deviations,
the second specifies means.
\item[\code{noStates}:] Object of class \code{"numeric"} The number
of hidden states in the HMM.
}
\end{Section}
\begin{Section}{Methods}
\describe{
\item[A] \code{signature(object = "SMAPHMM")}: Returns the
transition matrix.
\item[Pi] \code{signature(object = "SMAPHMM")}: Returns the initial
probabilities.
\item[Phi] \code{signature(object = "SMAPHMM")}: Returns the
distribution parameter matrix.
\item[noStates] \code{signature(object = "SMAPHMM")}: Returns the
number of hidden states in the HMM.
}
\end{Section}
\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}{SMAPHMM}}
\end{SeeAlso}

