\HeaderA{as.data.frame.profileCGH}{profileCGH consercion}{as.data.frame.profileCGH}
\begin{Description}\relax
Convert a profileCGH object into a data.frame.
\end{Description}
\begin{Usage}
\begin{verbatim}
as.data.frame.profileCGH(x, row.names = NULL, optional = FALSE)

\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] The object to converted into data.frame.
\item[\code{row.names}] NULL or a character vector giving the row names for the
data frame.  Missing values are not allowed.
\item[\code{optional}] logical. If 'TRUE', setting row names and converting column
names (to syntactic names) is optional.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The attributes \code{profileValues} and \code{profileValuesNA}
are binded into a data.frame.
\end{Details}
\begin{Value}
\end{Value}
\begin{Note}\relax
People interested in tools dealing with array CGH analysis can
visit our web-page \url{http://bioinfo.curie.fr}.
\end{Note}
\begin{Author}\relax
Philippe Hupé, \email{glad@curie.fr}
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{as.profileCGH}{as.profileCGH}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}

data(snijders)

### Creation of "profileCGH" object
profileCGH <- as.profileCGH(gm13330)


###########################################################
###
###  glad function as described in Hupé et al. (2004)
###
###########################################################

res <- glad(profileCGH, mediancenter=FALSE,
                smoothfunc="lawsglad", bandwidth=10, round=2,
                model="Gaussian", lkern="Exponential", qlambda=0.999,
                base=FALSE,
                lambdabreak=8, lambdacluster=8, lambdaclusterGen=40,
                type="tricubic", param=c(d=6),
                alpha=0.001, msize=5,
                method="centroid", nmax=8,
                verbose=FALSE)

res <- as.data.frame(res)

\end{ExampleCode}
\end{Examples}

