\HeaderA{findTrans.func}{Funtion identifying the transitions}{findTrans.func}
\keyword{models}{findTrans.func}
\begin{Description}\relax
This function identifies the start and end of the states (regions with
the constant estimated copy number).
\end{Description}
\begin{Usage}
\begin{verbatim}
findTrans.func(outliers = res1$outliers, aber = res2$aber, statesres =
states.bic)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{outliers}] Binary matrix of the outliers (generally output of the
\code{\LinkA{findOutliers.func}{findOutliers.func}})
\item[\code{aber}] Binary matrix of the focal aberrations (generally output
of the \code{\LinkA{findAber.func}{findAber.func}})
\item[\code{statesres}] The states output of the \code{\LinkA{hmm.run.func}{hmm.run.func}}
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The transitions end is placed at the last non-focal aberration clone
of the contiguous region containing clones belonging to the same state
and transitions start is placed at the first non-focal aberration
clone of the contiguous region containing clones belonging to the same
state.
\end{Details}
\begin{Value}
\begin{ldescription}
\item[\code{trans.matrix}] Matrix with a row for each clone and column for
each sample. The starts of the states are indicated by "1" , the end
are by "2" and the focal aberrations are coded as "3"
\item[\code{translen.matrix}] Matrix with a row for each clone and column for
each sample. The entries are the length of the region to which a
clone belongs. Zero length is assigned to the focal
aberrations. This output may be buggy at the moment.
\end{ldescription}
\end{Value}
\begin{Author}\relax
Jane Fridlyand
\end{Author}
\begin{References}\relax
Application of Hidden Markov Models to the analysis of the array CGH
data, Fridlyand et.al., \emph{JMVA}, 2004.
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{aCGH}{aCGH}}
\end{SeeAlso}

