\HeaderA{removeBreakpoints}{Remove breakpoints}{removeBreakpoints}
\methaliasA{removeBreakpoints.profileChr}{removeBreakpoints}{removeBreakpoints.profileChr}
\aliasA{removeLevel}{removeBreakpoints}{removeLevel}
\methaliasA{removeLevel.profileChr}{removeBreakpoints}{removeLevel.profileChr}
\begin{Description}\relax
This function optimizes the number of breakpoints.
\end{Description}
\begin{Usage}
\begin{verbatim}
removeBreakpoints.profileChr(profileChr, lambda=10, type="tricubic", param=c(d=6), verbose=FALSE, ...)
removeLevel.profileChr <- function(profileChr, lambda=10, ...)

\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{profileChr}] Object of class \code{profileChr}.
\item[\code{lambda}] Penalty term (\eqn{\lambda'}{}) used during the 
"Optimization of the number of breakpoints" step.
\item[\code{type}] Type of kernel used in the penalty term.
\item[\code{param}] Parameter for the kernel used in the penalty term.
\item[\code{verbose}] If \code{TRUE} some information are printed
\item[\code{...}] Argument to be passed to \code{\LinkA{detectOutliers}{detectOutliers}}, typically \code{alpha}.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The function \code{removeBreakpoints} uses the results of
\code{\LinkA{chrBreakpoints}{chrBreakpoints}} and optimizes the number of breakpoints
previously detected: when a breakpoint is removed, then it is flagged
out by -1 in the vector \code{Breakpoints} of the data.frame
attribute of the object of class \code{\LinkA{profileChr}{profileChr}}. \code{removeBreakpoints} is
used within the global function \code{\LinkA{glad}{glad}}.
\end{Details}
\begin{Value}
Data frame.
\end{Value}
\begin{Author}\relax
Philippe Hupé, \url{Philippe.Hupe@curie.fr}.
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{chrBreakpoints}{chrBreakpoints}},\code{\LinkA{glad}{glad}}, \code{\LinkA{kernelpen}{kernelpen}}.
\end{SeeAlso}

