\HeaderA{copynumber}{Retrieve copynumber data from cgh objects.}{copynumber}
\aliasA{calls}{copynumber}{calls}
\aliasA{calls<\Rdash}{copynumber}{calls<.Rdash.}
\aliasA{copynumber<\Rdash}{copynumber}{copynumber<.Rdash.}
\aliasA{segmented}{copynumber}{segmented}
\aliasA{segmented<\Rdash}{copynumber}{segmented<.Rdash.}
\keyword{manip}{copynumber}
\begin{Description}\relax
These generic functions access the copynumber values
of assay data stored in an object derived from the \code{\LinkA{cghRaw-class}{cghRaw.Rdash.class}}, 
\code{\LinkA{cghSeg-class}{cghSeg.Rdash.class}} or \code{\LinkA{cghCall-class}{cghCall.Rdash.class}}.
\end{Description}
\begin{Usage}
\begin{verbatim}
copynumber(object)
copynumber(object) <- value
segmented(object)
segmented(object) <- value
calls(object)
calls(object) <- value
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] Object derived from class \code{cghRaw}, \code{cghSeg}, or \code{cghCall}
\item[\code{value}] Matrix with rows representing features and columns samples.
\end{ldescription}
\end{Arguments}
\begin{Value}
\code{copynumber} returns a matrix of copynumber values;
\end{Value}
\begin{Author}\relax
Sjoerd Vosse
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{cghRaw-class}{cghRaw.Rdash.class}}, \code{\LinkA{cghSeg-class}{cghSeg.Rdash.class}}, \code{\LinkA{cghCall-class}{cghCall.Rdash.class}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
        data(WiltingCalled)
        log2ratios <- copynumber(WiltingCalled)
        segments <- segmented(WiltingCalled)
        calls <- calls(WiltingCalled)   
\end{ExampleCode}
\end{Examples}

