\HeaderA{SchemeTreeSet-class}{Class SchemeTreeSet}{SchemeTreeSet.Rdash.class}
\aliasA{attachMask,SchemeTreeSet-method}{SchemeTreeSet-class}{attachMask,SchemeTreeSet.Rdash.method}
\aliasA{chipMask}{SchemeTreeSet-class}{chipMask}
\aliasA{chipMask,SchemeTreeSet-method}{SchemeTreeSet-class}{chipMask,SchemeTreeSet.Rdash.method}
\aliasA{chipMask<\Rdash}{SchemeTreeSet-class}{chipMask<.Rdash.}
\aliasA{chipMask<-,SchemeTreeSet,data.frame-method}{SchemeTreeSet-class}{chipMask<.Rdash.,SchemeTreeSet,data.frame.Rdash.method}
\aliasA{chipName}{SchemeTreeSet-class}{chipName}
\aliasA{chipName,SchemeTreeSet-method}{SchemeTreeSet-class}{chipName,SchemeTreeSet.Rdash.method}
\aliasA{chipType}{SchemeTreeSet-class}{chipType}
\aliasA{chipType,SchemeTreeSet-method}{SchemeTreeSet-class}{chipType,SchemeTreeSet.Rdash.method}
\aliasA{chipType<\Rdash}{SchemeTreeSet-class}{chipType<.Rdash.}
\aliasA{chipType<-,SchemeTreeSet,character-method}{SchemeTreeSet-class}{chipType<.Rdash.,SchemeTreeSet,character.Rdash.method}
\aliasA{export,SchemeTreeSet-method}{SchemeTreeSet-class}{export,SchemeTreeSet.Rdash.method}
\aliasA{ncols}{SchemeTreeSet-class}{ncols}
\aliasA{ncols,SchemeTreeSet-method}{SchemeTreeSet-class}{ncols,SchemeTreeSet.Rdash.method}
\aliasA{nrows}{SchemeTreeSet-class}{nrows}
\aliasA{nrows,SchemeTreeSet-method}{SchemeTreeSet-class}{nrows,SchemeTreeSet.Rdash.method}
\aliasA{probeInfo}{SchemeTreeSet-class}{probeInfo}
\aliasA{probeInfo,SchemeTreeSet-method}{SchemeTreeSet-class}{probeInfo,SchemeTreeSet.Rdash.method}
\aliasA{removeMask,SchemeTreeSet-method}{SchemeTreeSet-class}{removeMask,SchemeTreeSet.Rdash.method}
\aliasA{SchemeTreeSet}{SchemeTreeSet-class}{SchemeTreeSet}
\keyword{classes}{SchemeTreeSet-class}
\begin{Description}\relax
This class provides the link to the \code{\LinkA{ROOT}{ROOT}} scheme file and 
the \code{\LinkA{ROOT}{ROOT}} trees contained therein. It extends class \code{\LinkA{TreeSet}{TreeSet}}.
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created using the functions \code{\LinkA{import.expr.scheme}{import.expr.scheme}},
\code{\LinkA{import.exon.scheme}{import.exon.scheme}}, \code{\LinkA{import.genome.scheme}{import.genome.scheme}} or \code{\LinkA{root.scheme}{root.scheme}}.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{chipname}:] Object of class \code{"character"} representing the Affymetrix
chip name.
\item[\code{chiptype}:] Object of class \code{"character"} representing the chip tpye, 
either \sQuote{GeneChip}, \sQuote{GenomeChip} or \sQuote{ExonChip}.
\item[\code{probeinfo}:] Object of class \code{"list"} representing chip information, 
including nrows, ncols, number of probes, etc.
\item[\code{mask}:] Object of class \code{"data.frame"}. The data.frame can contain the mask 
used to identify the probes as e.g. PM, MM or control probes.
\item[\code{setname}:] Object of class \code{"character"} representing the name to the
\code{\LinkA{ROOT}{ROOT}} file subdirectoy where the \code{\LinkA{ROOT}{ROOT}} scheme trees are stored;
it is identical to \code{chipname}.
\item[\code{settype}:] Object of class \code{"character"} describing the type of treeset
stored in \code{setname}, i.e. \sQuote{scheme}.
\item[\code{rootfile}:] Object of class \code{"character"} representing the name 
of the \code{\LinkA{ROOT}{ROOT}} scheme file, including full path.
\item[\code{filedir}:] Object of class \code{"character"} describing the full path to
the system directory where \code{rootfile} is stored.
\item[\code{numtrees}:] Object of class \code{"numeric"} representing the number of 
\code{\LinkA{ROOT}{ROOT}} trees stored in subdirectoy \code{setname}.
\item[\code{treenames}:] Object of class \code{"list"} representing the names of the 
\code{\LinkA{ROOT}{ROOT}} trees stored in subdirectoy \code{setname}.
}
\end{Section}
\begin{Section}{Extends}
Class \code{"\LinkA{TreeSet}{TreeSet.Rdash.class}"}, directly.
\end{Section}
\begin{Section}{Methods}
\describe{
\item[attachMask] \code{signature(object = "SchemeTreeSet")}: exports scheme tree from 
\code{\LinkA{ROOT}{ROOT}} scheme file and and saves as data.frame \code{mask}.
\item[chipMask] \code{signature(object = "SchemeTreeSet")}: extracts data.frame \code{mask}.
\item[chipMask<-] \code{signature(object = "SchemeTreeSet", value = "data.frame")}: replaces 
data.frame \code{mask}.
\item[chipName] \code{signature(object = "SchemeTreeSet")}: extracts slot \code{chipname}.
\item[chipType] \code{signature(object = "SchemeTreeSet")}: extracts slot \code{chiptype}.
\item[chipType<-] \code{signature(object = "SchemeTreeSet", value = "character")}: replaces 
slot \code{chiptype}.
\item[export] \code{signature(object = "SchemeTreeSet")}: exports \code{\LinkA{ROOT}{ROOT}} trees 
as text file, see \code{\LinkA{export-methods}{export.Rdash.methods}}.
\item[ncols] \code{signature(object = "SchemeTreeSet")}: extracts the physical number of 
array columns from slot \code{probeinfo}.
\item[nrows] \code{signature(object = "SchemeTreeSet")}: extracts the physical number of 
array rows from slot \code{probeinfo}.
\item[probeInfo] \code{signature(object = "SchemeTreeSet")}: extracts slot \code{probeinfo}.
\item[removeMask] \code{signature(object = "SchemeTreeSet")}: replaces data.frame \code{mask} 
with an empty data.frame of dim(0,0).
}
\end{Section}
\begin{Author}\relax
Christian Stratowa
\end{Author}
\begin{Examples}
\begin{ExampleCode}
showClass("SchemeTreeSet")
\end{ExampleCode}
\end{Examples}

