\HeaderA{findAber.func}{Function to  determines focal aberrations}{findAber.func}
\keyword{models}{findAber.func}
\begin{Description}\relax
The function identifies clones that are focal aberrations.
\end{Description}
\begin{Usage}
\begin{verbatim}
findAber.func(maxClones = 1, maxLen = 1000, statesres = states.bic)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{maxClones}] Maximum number of clones assigned to the same state
which can be considered to be focal aberrations
\item[\code{maxLen}] Maximum lengeth of the region containing clones assigned
to the state so that those clones can be considered to be focal
aberrations
\item[\code{statesres}] The states output of the \code{\LinkA{hmm.run.func}{hmm.run.func}}
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The focal aberrations are the one or more clones assigned to the
state different from the states of the surrounding clones.  They may
indicate copy number polymorphisms or interesting high or low focal
changes.
\end{Details}
\begin{Value}
\begin{ldescription}
\item[\code{aber}] Binary matrix with a row for each clone and column for
each sample. 1 indicates presence of a focal aberrations, 0 lack
of such.
\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., JMVA, 2004
\end{References}

