\HeaderA{root.scheme}{Create class SchemeTreeSet accessing ROOT scheme file}{root.scheme}
\keyword{manip}{root.scheme}
\begin{Description}\relax
Create class SchemeTreeSet accessing ROOT scheme file.
\end{Description}
\begin{Usage}
\begin{verbatim}
root.scheme(rootfile = character(0), add.mask = FALSE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{rootfile}] name of ROOT scheme file, including full path.
\item[\code{add.mask}] if \code{TRUE} mask information will be included as slot \code{mask}.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
An S4 class \code{\LinkA{SchemeTreeSet}{SchemeTreeSet}} will be created, serving as R wrapper to the 
\code{\LinkA{ROOT}{ROOT}} scheme file \code{rootfile}.
\end{Details}
\begin{Value}
A \code{SchemeTreeSet} object.
\end{Value}
\begin{Note}\relax
Use this function to access the \code{\LinkA{ROOT}{ROOT}} scheme file from 
new R sessions to avoid creating a new \code{\LinkA{ROOT}{ROOT}} scheme file for every R session.

Do not set \code{add.mask=TRUE} for exon arrays unless you know that your computer has 
sufficient RAM.
\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}}, \code{\LinkA{SchemeTreeSet}{SchemeTreeSet}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
## create class SchemeSet to access the ROOT scheme file for the Test3 GeneChip
scheme.test3 <- root.scheme(paste(.path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
str(scheme.test3)

## Not run: 
## scheme set for existing human root exon scheme file
scheme.huex10stv2r2.na22 <- root.scheme("/my/path/schemes/Scheme_HuEx10stv2r2_na22.root")
## End(Not run)
\end{ExampleCode}
\end{Examples}

