\HeaderA{findAmplif.func}{Function to determine high level amplifications}{findAmplif.func}
\keyword{models}{findAmplif.func}
\begin{Description}\relax
This function identifies high level amplifications by considering the
height, the width of an amplicon relative to the urrounding
clones. Only narrow peaks much higher than its neigbors are considered
as high level amplifications.
\end{Description}
\begin{Usage}
\begin{verbatim}
findAmplif.func(absValSingle = 1, absValRegion = 1.5, diffVal1 = 1,
diffVal2 = 0.5, maxSize = 10000, translen.matr = res3$translen.matrix,
trans.matr = res3$trans.matr, aber = res2$aber, outliers = res1$outlier,
pred = res1$pred.out, pred.obs = res1$pred.obs.out, statesres =
states.bic)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{absValSingle}] A clone is declared to be an amplification if it
is a focal aberration or an outlier and its value exceeds
absValSingle
\item[\code{absValRegion}] A clone is an amplification if if a clone belong
to a region with width less than maxSize and  observed value for a
clones is greater than absValRegion
\item[\code{diffVal1}] Clone is an amplification if it is an aberration and
greater by diffVal1 than max of the two surrounding stretches
\item[\code{diffVal2}] Clone is an amplification if it is an outlier, its
observed values is greater by diffVal2 than max of the two
surrounding stretches
\item[\code{maxSize}] The clones  may not be declared as amplifications if
they belong to the states with spanning more than maxSize
\item[\code{translen.matr}] State length matrix. The output of the
\code{\LinkA{findTrans.func}{findTrans.func}}
\item[\code{trans.matr}] Transition matrix. The output of the
\code{\LinkA{findTrans.func}{findTrans.func}}
\item[\code{aber}] Aberration matrix. The output of the
\code{\LinkA{findAber.func}{findAber.func}}
\item[\code{outliers}] Outliers matrix. The output of the
\code{\LinkA{findOutliers.func}{findOutliers.func}}
\item[\code{pred}] Predicted values matrix. The output of the
\code{\LinkA{findOutliers.func}{findOutliers.func}}
\item[\code{pred.obs}] Predicted values matrix with observed values assigned
to the outliers. The output of the \code{\LinkA{findOutliers.func}{findOutliers.func}}
\item[\code{statesres}] The states output of the \code{\LinkA{hmm.run.func}{hmm.run.func}}
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Note that all the distances are in Megabases and all the heights are
on log2ratio scale.
\end{Details}
\begin{Value}
\begin{ldescription}
\item[\code{amplif.matrix}] Binary matrix with a row for each clone and
column for each sample. "1" indicates amplification
\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}

