\HeaderA{HmmPredict-class}{Class for the hidden Markov model results}{HmmPredict.Rdash.class}
\aliasA{breakpoints}{HmmPredict-class}{breakpoints}
\aliasA{breakpoints,HmmPredict-method}{HmmPredict-class}{breakpoints,HmmPredict.Rdash.method}
\aliasA{breakpoints<\Rdash}{HmmPredict-class}{breakpoints<.Rdash.}
\aliasA{breakpoints<-,HmmPredict,ANY-method}{HmmPredict-class}{breakpoints<.Rdash.,HmmPredict,ANY.Rdash.method}
\aliasA{breakpoints<-,HmmPredict-method}{HmmPredict-class}{breakpoints<.Rdash.,HmmPredict.Rdash.method}
\aliasA{calculateBreakpoints,HmmPredict-method}{HmmPredict-class}{calculateBreakpoints,HmmPredict.Rdash.method}
\aliasA{chromosome,chromosome-method}{HmmPredict-class}{chromosome,chromosome.Rdash.method}
\aliasA{chromosome,HmmPredict-method}{HmmPredict-class}{chromosome,HmmPredict.Rdash.method}
\aliasA{fData,HmmPredict-method}{HmmPredict-class}{fData,HmmPredict.Rdash.method}
\aliasA{featureData,HmmPredict-method}{HmmPredict-class}{featureData,HmmPredict.Rdash.method}
\aliasA{featureNames,HmmPredict-method}{HmmPredict-class}{featureNames,HmmPredict.Rdash.method}
\aliasA{getPar,HmmPredict-method}{HmmPredict-class}{getPar,HmmPredict.Rdash.method}
\aliasA{initialize,HmmPredict-method}{HmmPredict-class}{initialize,HmmPredict.Rdash.method}
\aliasA{position,HmmPredict-method}{HmmPredict-class}{position,HmmPredict.Rdash.method}
\aliasA{predictions}{HmmPredict-class}{predictions}
\aliasA{predictions,HmmPredict-method}{HmmPredict-class}{predictions,HmmPredict.Rdash.method}
\aliasA{predictions<\Rdash}{HmmPredict-class}{predictions<.Rdash.}
\aliasA{predictions<-,HmmPredict,matrix-method}{HmmPredict-class}{predictions<.Rdash.,HmmPredict,matrix.Rdash.method}
\aliasA{sampleNames,HmmPredict-method}{HmmPredict-class}{sampleNames,HmmPredict.Rdash.method}
\aliasA{show,HmmPredict-method}{HmmPredict-class}{show,HmmPredict.Rdash.method}
\aliasA{SnpClass,HmmPredict-method}{HmmPredict-class}{SnpClass,HmmPredict.Rdash.method}
\aliasA{states,HmmPredict-method}{HmmPredict-class}{states,HmmPredict.Rdash.method}
\aliasA{summary,HmmPredict-method}{HmmPredict-class}{summary,HmmPredict.Rdash.method}
\aliasA{[,HmmPredict-method}{HmmPredict-class}{[,HmmPredict.Rdash.method}
\keyword{classes}{HmmPredict-class}
\begin{Description}\relax
Contains the predictions for the hidden states and a list
of breakpoint matrices.  Each element in the list corresponds to the
breakpoints identified in one sample.
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form \code{new("HmmPredict", states, predictions, breakpoints, SnpClass)}.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{states}:] Object of class \code{character}. Character
string of the hidden states.
\item[\code{predictions}:] Object of class \code{matrix}. Matrix
of predictions.
\item[\code{breakpoints}:] Object of class \code{list}.  List of
matrices.  Each element is the matrix of breakpoints for one sample.
\item[\code{SnpClass}:] Object of class \code{character}. The
class of SNP data (e.g., \code{oligoSnpSet}) 
\item[\code{featureData}:] Object of class \code{AnnotatedDataFrame}
}
\end{Section}
\begin{Section}{Methods}
\describe{
\item[SnpClass] \code{signature(object = "HmmPredict")}: Accessor
for class of SNP data
\item[[] \code{signature(x = "HmmPredict")}: Subsetting the predictions
\item[breakpoints] \code{signature(object = "HmmPredict")}: Accessor
for the list of breakpoints
\item[breakpoints<-] \code{signature(object = "HmmPredict", value = "data.frame")}:
Replacement method for breakpoints    
\item[fData] \code{signature(object="HmmPredict")}: Accessor for the
data frame of all feature-level (SNP-level) annotation (e.g., physical
position)
\item[featureData] \code{signature(object = "HmmPredict")}: Accessor
for the featureData
\item[featureNames] \code{signature(object = "HmmPredict")}:
Character string of SNP identifiers
\item[getPar] \code{signature(object = "HmmPredict")}: Graphical parameters.
\item[initialize] \code{signature(.Object = "HmmPredict")}  
\item[position] \code{signature(object = "HmmPredict")}: Accessor
for the physical position of SNPs in the object \code{HmmPredict}
\item[predictions] \code{signature(object = "HmmPredict")}: Accessor
for the predictions
\item[predictions<-] \code{signature(object = "HmmPredict",
        value="matrix")}: Replacement method for predictions    
\item[sampleNames] \code{signature(object = "HmmPredict")}: Sample names
\item[show] \code{signature(object = "HmmPredict")}
\item[states] \code{signature(object = "HmmPredict")}: Accessor for
hidden states
}
\end{Section}
\begin{Author}\relax
R. Scharpf
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{hmm}{hmm}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
showClass("HmmPredict")
\end{ExampleCode}
\end{Examples}

