\HeaderA{affectationGNL}{Label Assignment}{affectationGNL}
\methaliasA{affectationGNL.profileCGH}{affectationGNL}{affectationGNL.profileCGH}
\begin{Description}\relax
The function \code{affectation.profileCGH} gives a status (gained,
normal or lost) to each BAC.
\end{Description}
\begin{Usage}
\begin{verbatim}
affectationGNL.profileCGH(profileCGH, alpha=0.001, region="Region", verbose=FALSE, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{profileCGH}] Object of class \code{\LinkA{profileCGH}{profileCGH}}.
\item[\code{alpha}] Outlier detected in lost or gained region that lie
between the \eqn{\alpha/2}{} lower tail and the \eqn{\alpha/2}{} upper tail of the estimated distribution of the
normal DNA population are considered as normal.
\item[\code{region}] Specifies the name of the variable which has been used
during the MSHR clustering by chromosome step.
\item[\code{verbose}] If \code{TRUE} some information are printed
\item[\code{...}] 
\end{ldescription}
\end{Arguments}
\begin{Value}
An object of class \code{\LinkA{profileCGH}{profileCGH}} with the following added information in
the data.frame attribute \code{profileValues} :
\begin{ldescription}
\item[\code{ZoneGNL}] Gain is coded by 1, Loss  by -1 and Normal by 0.
\end{ldescription}
\end{Value}
\begin{Author}\relax
Philippe Hupé, \email{Philippe.Hupe@curie.fr}.
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{glad}{glad}}.
\end{SeeAlso}

