\HeaderA{SegList-class}{Segmentation States - class}{SegList.Rdash.class}
\aliasA{print.SegList}{SegList-class}{print.SegList}
\keyword{classes}{SegList-class}
\keyword{data}{SegList-class}
\begin{Description}\relax
A list based class for storing the results of a segmentation algorithm.
They are generally created by running one of the following functions
\code{\LinkA{runHomHMM}{runHomHMM}}, \code{\LinkA{runGLAD}{runGLAD}} or \code{\LinkA{runDNAcopy}{runDNAcopy}} on an \code{\LinkA{MAList}{MAList} object}.
\end{Description}
\begin{Section}{Slots/List Components}
Objects should contain the following list components:
\Tabular{ll}{
\code{pred}:& Predicted value of the state.\\
\code{disp}:& Dispersion.\\
\code{obs}:& Observed value.\\
\code{state}:& Numeric value.\\
\code{nstates.hmm}: & The number of states per chromosome.  Each row represents a chromosome and each column is an array.\\
\code{genes}:& data.frame that contains the chromosome and position on the chromosome for each clone.  Used for plotting functions.\\
}
Optional:\\
\Tabular{ll}{
\code{rpred}:& Smoothed value for the clone.\\
\code{prob}:& Probability of the clone being in the assigned state.\\
}
\end{Section}
\begin{Section}{Methods}
\code{SegLists} can be subsetted and combined.  They also return dimensions
so functions such as \code{\LinkA{dim}{dim}}, \code{\LinkA{nrow}{nrow}} and \code{\LinkA{ncol}{ncol}} are also defined.  \code{SegList}
inherits the \code{\LinkA{show}{show}} method from the Limma class \code{\LinkA{LargeDataObject}{LargeDataObject}}.  This
means that the \code{SegList} will print in a relatively compact way.
\end{Section}
\begin{Author}\relax
Mike Smith
\end{Author}

