\HeaderA{attachBgrd-methods}{Attach/Remove Background Intensities}{attachBgrd.Rdash.methods}
\aliasA{attachBgrd}{attachBgrd-methods}{attachBgrd}
\aliasA{removeBgrd}{attachBgrd-methods}{removeBgrd}
\aliasA{removeBgrd-methods}{attachBgrd-methods}{removeBgrd.Rdash.methods}
\keyword{methods}{attachBgrd-methods}
\begin{Description}\relax
Attach/remove background intensities to/from \code{\LinkA{DataTreeSet}{DataTreeSet}}.

\emph{Usage}

\code{attachBgrd(object, treenames = "*")}

\code{removeBgrd(object)}
\end{Description}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] Object of class \code{"DataTreeSet"}.
\item[\code{treenames}] Object of class \code{"list"} representing the names of the 
\code{\LinkA{ROOT}{ROOT}} background trees.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Whenever one of the \code{\LinkA{bgcorrect}{bgcorrect}} methods will be applied to raw CEL intensities,
the background intensities will be stored in \code{\LinkA{ROOT}{ROOT}} background trees.
However, the background intensities will not be saved as data.frame \code{bgrd},
thus avoiding memory problems. Function \code{attachBgrd} allows to fill slot \code{bgrd}
on demand.

\code{attachBgrd} exports intensities from background trees from \code{\LinkA{ROOT}{ROOT}}
data file and saves as data.frame \code{bgrd}. \code{treenames} is a vector of
tree names to attach; for \code{treenames="*"} all trees from slot \code{treenames}
will be exported and background intensities attached as data.frame \code{bgrd}.

\code{removeBgrd} removes background intensities from \code{\LinkA{DataTreeSet}{DataTreeSet}} and
replaces data.frame \code{bgrd} with an empty data.frame of dim(0,0).
\end{Details}
\begin{Value}
A \code{\LinkA{DataTreeSet}{DataTreeSet}} object.
\end{Value}
\begin{Note}\relax
Do not use \code{attachBgrd} unless you know that your computer has sufficient RAM,
especially when using exon arrays. It may be advisible to use a subset of \code{treenames}
only.
\end{Note}
\begin{Author}\relax
Christian Stratowa
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{attachInten}{attachInten}}, \code{\LinkA{removeInten}{removeInten}}
\end{SeeAlso}

