\HeaderA{SMAPProfile-class}{Class "SMAPProfile"}{SMAPProfile.Rdash.class}
\aliasA{HMM}{SMAPProfile-class}{HMM}
\aliasA{observations}{SMAPProfile-class}{observations}
\aliasA{P}{SMAPProfile-class}{P}
\aliasA{Q}{SMAPProfile-class}{Q}
\keyword{classes}{SMAPProfile-class}
\begin{Description}\relax
Holds results from running \code{\LinkA{smap}{smap}}.
\end{Description}
\begin{Section}{Objects from the Class}
Objects are not intended to be created directly but as a result from
running \code{\LinkA{smap}{smap}.}
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{HMM}:] Object of class \code{"SMAPHMM"}
\item[\code{observations}:] Object of class \code{"SMAPObservations"}
\item[\code{P}:] Object of class \code{"numeric"} The log joint
posterior probability of the state sequence \code{Q} and
parameters of \code{HMM} given the \code{observations}.
\item[\code{Q}:] Object of class \code{"numeric"} The optimal state
sequance (path) in the HMM.
\item[\code{name}:] Object of class \code{"character"} The name of
the object.
}
\end{Section}
\begin{Section}{Methods}
\describe{
\item[P] \code{signature(object = "SMAPProfile")}: Returns the log
joint posterior probability. 
\item[Q] \code{signature(object = "SMAPProfile")}: Returns the
optimal state sequence.
\item[HMM] \code{signature(object = "SMAPProfile")}: Returns the
optimized HMM.
\item[name] \code{signature(object = "SMAPProfile")}: Returns the
name of the profile.
\item[observations] \code{signature(object = "SMAPProfile")}:
Returns the observations.
\item[plot] \code{signature(x = "SMAPProfile", y = "missing")}: A
plot method for the result profile.
\item[[] \code{signature(x = "SMAPProfile")}: Creates a new object
of class SMAPProfile with extracted elements as specified by the
indices provided.
}
\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{SMAPProfiles-class}{SMAPProfiles.Rdash.class}}
\end{SeeAlso}

