\HeaderA{attachMask-methods}{Attach/Remove Scheme Mask}{attachMask.Rdash.methods}
\aliasA{attachMask}{attachMask-methods}{attachMask}
\aliasA{removeMask}{attachMask-methods}{removeMask}
\aliasA{removeMask-methods}{attachMask-methods}{removeMask.Rdash.methods}
\keyword{methods}{attachMask-methods}
\begin{Description}\relax
Attach/remove scheme mask to/from \code{\LinkA{SchemeTreeSet}{SchemeTreeSet}} or to slot \code{scheme}
of \code{\LinkA{DataTreeSet}{DataTreeSet}}.
\end{Description}
\begin{Usage}
\begin{verbatim}
attachMask(object)

removeMask(object)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] Object of class \code{"SchemeTreeSet"} or \code{"DataTreeSet"}.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
\code{attachMask} exports mask from scheme tree from \code{\LinkA{ROOT}{ROOT}} scheme file
and and saves mask as data.frame \code{mask} of slot \code{scheme}.

\code{removeMask} removes mask from \code{\LinkA{SchemeTreeSet}{SchemeTreeSet}} or from slot \code{scheme}
of \code{\LinkA{DataTreeSet}{DataTreeSet}} and replaces data.frame \code{mask} with an empty data.frame
of dim(0,0).
\end{Details}
\begin{Value}
A \code{\LinkA{DataTreeSet}{DataTreeSet}} object or \code{\LinkA{SchemeTreeSet}{SchemeTreeSet}}.
\end{Value}
\begin{Note}\relax
Do not use \code{attachMask} unless you know that your computer has sufficient RAM,
especially for exon array schemes.
\end{Note}
\begin{Author}\relax
Christian Stratowa
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{import.expr.scheme}{import.expr.scheme}}, \code{\LinkA{import.exon.scheme}{import.exon.scheme}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
## load existing ROOT scheme file
scheme.test3 <- root.scheme(paste(.path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
dim(chipMask(scheme.test3))

scheme.test3 <- attachMask(scheme.test3)
dim(chipMask(scheme.test3))
head(chipMask(scheme.test3))

scheme.test3 <- removeMask(scheme.test3)
dim(chipMask(scheme.test3))
\end{ExampleCode}
\end{Examples}

