\HeaderA{find.genomic.events}{Finds the genomic events associated with each of the array CGH samples}{find.genomic.events}
\keyword{models}{find.genomic.events}
\begin{Description}\relax
Finds the genomic events associated with each of the array CGH
samples. Events include whole chromosomal gains and losses,
aberrations, transitions, amplifications and their respective counts
and sizes. The hmm states has to be computed before using this
function.
\end{Description}
\begin{Usage}
\begin{verbatim}
find.genomic.events(aCGH.obj, maxChrom = 23, factor = 5, maxClones = 1,
                    maxLen = 1000, absValSingle = 1, absValRegion = 1,
                    diffVal1 = 1, diffVal2 = .5, maxSize = 10000,
                    pChrom.min = .9, medChrom.min = .1)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{aCGH.obj}] Object of class \code{\LinkA{aCGH}{aCGH}}.

\item[\code{maxChrom}] Highest chromosomal number to find events.
\item[\code{factor}] Determines outliers. See \code{\LinkA{findOutliers.func}{findOutliers.func}}.
\item[\code{maxClones}] Determines aberrations. See \code{\LinkA{findAber.func}{findAber.func}}.
\item[\code{maxLen}] Determines aberrations. See \code{\LinkA{findAber.func}{findAber.func}}.
\item[\code{absValSingle}] Determines amplifications. See \code{\LinkA{findAmplif.func}{findAmplif.func}}.
\item[\code{absValRegion}] Determines amplifications. See \code{\LinkA{findAmplif.func}{findAmplif.func}}.
\item[\code{diffVal1}] Determines amplifications. See \code{\LinkA{findAmplif.func}{findAmplif.func}}.
\item[\code{diffVal2}] Determines amplifications. See \code{\LinkA{findAmplif.func}{findAmplif.func}}.
\item[\code{maxSize}] Determines amplifications. See \code{\LinkA{findAmplif.func}{findAmplif.func}}.
\item[\code{pChrom.min}] Determines whole chromosomal gains and losses. Chromosome should
contain no transitions, have its absolute median equal or greater
than \code{medChrom.min} and at least \code{medChrom.min} has to be
greater or less than 0.

\item[\code{medChrom.min}] Determines whole chromosomal gains and losses. Chromosome should
contain no transitions, have its absolute median equal or greater
than \code{medChrom.min} and at least \code{medChrom.min} has to be
greater or less than 0.

\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The default parameters generally work. Threshold for merging may be
changed depending on the expected normal cell contamination and/or
expected magnitude of the changes. AIC model generally works,
however, may need to be readjusted depending on how liberal or
conservative one wants to be in finding genomic events. We recommend
BIC criterion with delta = 1 for noisier data.
\end{Details}
\begin{Value}
\begin{ldescription}
\item[\code{num.transitions}] matrix of dimensions maxChrom by number of samples. It contains
number of transitions that were recorded on a given chromosome for a
given sample.

\item[\code{num.amplifications}] matrix of dimensions maxChrom by number of samples It contains
number of amplifications that were recorded on a given chromosome
for a given sample.

\item[\code{num.aberrations}] matrix of dimensions maxChrom by number of samples. It contains
number of focal aberrations that were recorded on a given chromosome
for a given sample.

\item[\code{num.outliers}] matrix of dimensions maxChrom by number of samples.  It contains
number of outliers that were recorded on a given chromosome for a
given sample.

\item[\code{num.transitions.binary}] binary matrix of dimensions maxChrom by number of samples. Non-zero
entry indicates whether 1 or more transitions were recorded on a
given chromosome for a given sample.

\item[\code{num.amplifications.binary}] binary matrix of dimensions maxChrom by number of samples. Non-zero
entry indicates whether 1 or more amplifications were recorded on a
given chromosome for a given sample.

\item[\code{num.aberrations.binary}] binary matrix of dimensions maxChrom by number of samples. Non-zero
entry indicates whether 1 or more focal aberrations were recorded on
a given chromosome for a given sample.

\item[\code{num.outliers.binary}] binary matrix of dimensions maxChrom by number of samples. Non-zero
entry indicates whether 1 or more outliers were recorded on a given
chromosome for a given sample.

\item[\code{whole.chrom.gain.loss}] matrix of dimensions maxChrom by number of samples. Positive entry
indicates that a given chromosome was gained in a given sample,
negative entry indicates that a given chromosome was lost in a given
sample, 0 entry is normal chromosome and NA marks chromosomes with
one or more transition.

\item[\code{size.amplicons}] matrix of dimensions maxChrom by number of samples. Reports size of
a given chromosome that is amplified (kb units) in a given sample.

\item[\code{num.amplicons}] matrix of dimensions maxChrom by number of samples. Reports number
of disjoint amplicons on a given chromosome for a given sample.

\item[\code{outliers}] list containing 3 matrices of dimensions number of clones by number
of samples. See \code{\LinkA{findOutliers.func}{findOutliers.func}}.

\item[\code{aberrations}] list containing a matrix of dimensions number of clones by number
of samples. See \code{\LinkA{findAber.func}{findAber.func}}.

\item[\code{transitions}] list containing 2 matrices of dimensions number of clones by number
of samples. See \code{\LinkA{findTrans.func}{findTrans.func}}.

\item[\code{amplifications}] list containing a matrix of dimensions number of clones by number
of samples. See \code{\LinkA{findAmplif.func}{findAmplif.func}}.

\end{ldescription}
\end{Value}
\begin{SeeAlso}\relax
\code{\LinkA{aCGH}{aCGH}}
\code{\LinkA{find.hmm.states}{find.hmm.states}}
\code{\LinkA{mergeFunc}{mergeFunc}}
\code{\LinkA{findAber.func}{findAber.func}}
\code{\LinkA{findTrans.func}{findTrans.func}}
\code{\LinkA{findAmplif.func}{findAmplif.func}}
\code{\LinkA{findOutliers.func}{findOutliers.func}}
\end{SeeAlso}

