\HeaderA{findCluster}{Clustering of genomic regions}{findCluster}
\methaliasA{findCluster.profileChr}{findCluster}{findCluster.profileChr}
\begin{Description}\relax
The function \code{findCluster} allows the clustering of regions.
\end{Description}
\begin{Usage}
\begin{verbatim}
findCluster.profileChr(profileChr, region="Region", genome=TRUE,
                       lambda=10, nmin=1, nmax=10, type="tricubic",
                       param=c(d=6), verbose=FALSE, ...)

\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{profileChr}] Object of class \code{profileChr}.
\item[\code{region}] Label which indicated where outliers are detected.
\item[\code{genome}] If \code{TRUE}, the "MSHR
clustering by chromosome" clustering step is run otherwise it is the "HCSR
clustering throughout the genome" clustering step.
\item[\code{lambda}] Penalty \eqn{\lambda*}{}.
\item[\code{nmin}] Minimal number of cluster to find.
\item[\code{nmax}] Maximal number of cluster to find.
\item[\code{type}] Type of kernel to use in the penalty term (this arguments is passed to the
\code{\LinkA{kernelpen}{kernelpen}} function).
\item[\code{param}] Parameters of the kernel (this arguments is passed to the
\code{\LinkA{kernelpen}{kernelpen}} function).
\item[\code{verbose}] If \code{TRUE} some information are printed
\item[\code{...}] Risk alpha used in \code{\LinkA{detectOutliers}{detectOutliers}}.
\end{ldescription}
\end{Arguments}
\begin{Value}
An object of class \code{profileChr} with the following element added
to the data.frame \code{profileValues}:

either:

\begin{ldescription}
\item[\code{ZoneChr}] indicates the regions which belongs to the same HCSR
(if \code{genome=FALSE}).
\item[\code{ZoneGen}] indicates HCSR which belongs to the same cluster (if \code{genome=TRUE}).
\end{ldescription}
\end{Value}
\begin{Author}\relax
Philippe Hupé, \email{Philippe.Hupe@curie.fr}.
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{glad}{glad}}, \code{\LinkA{detectOutliers}{detectOutliers}}
\end{SeeAlso}

