\HeaderA{runGLAD}{Results of segmenting an aCGHList data object using the GLAD library}{runGLAD}
\keyword{methods}{runGLAD}
\begin{Description}\relax
This function allows the detection of breakpoints in genomic profiles
obtained by array CGH technology and affects a status (gain, normal
or lost) to each clone.  It requires that the library \code{GLAD} is loaded.
\end{Description}
\begin{Usage}
\begin{verbatim}
runGLAD(input, smoothfunc="lawsglad", base=FALSE, sigma = NULL, bandwidth=10,
round=2, lambdabreak=8, lambdacluster=8, lambdaclusterGen=40,
type="tricubic", param=c(d=6), alpha=0.001, method="centroid",
nmax=8, verbose=FALSE, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{input}] An object of class \code{\LinkA{MAList}{MAList}} or \code{\LinkA{SegList}{SegList}}
\item[\code{smoothfunc}] Type of algorithm used to smooth \code{LogRatio} by a
piecewise constant function. Choose either \code{lawsglad}, \code{\LinkA{aws}{aws}} or
\code{\LinkA{laws}{laws}}.
\item[\code{base}] If \code{TRUE}, the position of clone is the physical position onto
the chromosome, otherwise the rank position is used.
\item[\code{sigma}] Value to be passed to either argument \code{sigma2}   
of\code{ \LinkA{aws}{aws}} function or \code{shape} of
\code{\LinkA{laws}{laws}}. If \code{NULL}, sigma is calculated from
the data.
\item[\code{bandwidth}] Set the maximal bandwidth \code{hmax} in the
\code{\LinkA{aws}{aws}} or  \code{\LinkA{laws}{laws}} function. For
example, if \code{bandwidth=10} then the \code{hmax} value is set
to 10*\eqn{X_N}{} where \eqn{X_N}{} is the position of the last clone.
\item[\code{round}] The smoothing results are rounded or not depending on
the \code{round} argument. The \code{round} value is passed to the
argument \code{digits} of the \code{\LinkA{round}{round}} function.
\item[\code{lambdabreak}] Penalty term (\eqn{\lambda'}{}) used during the 
\bold{Optimization of the number of breakpoints} step.
\item[\code{lambdacluster}] Penalty term (\eqn{\lambda*}{}) used during the \bold{MSHR
clustering by chromosome} step.
\item[\code{lambdaclusterGen}] Penalty term (\eqn{\lambda*}{}) used during the \bold{HCSR
clustering throughout the genome} step.
\item[\code{type}] Type of kernel function used in the penalty term during the \bold{Optimization of the
number of breakpoints} step, the \bold{MSHR
clustering by chromosome} step and the \bold{HCSR
clustering throughout the genome} step.
\item[\code{param}] Parameter of kernel used in the penalty term.
\item[\code{alpha}] Parameter for ?????.
\item[\code{method}] The agglomeration method to be used during the \bold{MSHR
clustering by chromosome} and the \bold{HCSR
clustering throughout the genome} clustering steps.
\item[\code{nmax}] Maximum number of clusters (N*max) allowed during
the the \bold{MSHR
clustering by chromosome} and the \bold{HCSR
clustering throughout the genome} clustering steps.
\item[\code{verbose}] If \code{TRUE} some information are printed
\item[\code{...}] 
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
For a detailed explanation of the GLAD algorithm please see the
relevant section of the GLAD manual: \code{\LinkA{glad}{glad}}
\end{Details}
\begin{Value}
The function returns an object of class \code{\LinkA{SegList}{SegList}}
\end{Value}
\begin{SeeAlso}\relax
\code{\LinkA{glad}{glad}}
\code{\LinkA{MAList}{MAList}}
\code{\LinkA{runHomHMM}{runHomHMM}}
\code{\LinkA{runDNAcopy}{runDNAcopy}}
\code{\LinkA{SegList}{SegList}}
\end{SeeAlso}

