\HeaderA{AnalysisTreeSet-class}{Class AnalysisTreeSet}{AnalysisTreeSet.Rdash.class}
\aliasA{AnalysisTreeSet}{AnalysisTreeSet-class}{AnalysisTreeSet}
\aliasA{filterTreeset}{AnalysisTreeSet-class}{filterTreeset}
\aliasA{filterTreeset,AnalysisTreeSet-method}{AnalysisTreeSet-class}{filterTreeset,AnalysisTreeSet.Rdash.method}
\aliasA{getTreeData,AnalysisTreeSet-method}{AnalysisTreeSet-class}{getTreeData,AnalysisTreeSet.Rdash.method}
\aliasA{validData,AnalysisTreeSet-method}{AnalysisTreeSet-class}{validData,AnalysisTreeSet.Rdash.method}
\aliasA{validFilter}{AnalysisTreeSet-class}{validFilter}
\aliasA{validFilter,AnalysisTreeSet-method}{AnalysisTreeSet-class}{validFilter,AnalysisTreeSet.Rdash.method}
\aliasA{volcanoplot,AnalysisTreeSet-method}{AnalysisTreeSet-class}{volcanoplot,AnalysisTreeSet.Rdash.method}
\keyword{classes}{AnalysisTreeSet-class}
\begin{Description}\relax
This class provides the link to the \code{\LinkA{ROOT}{ROOT}} analysis file and 
the \code{\LinkA{ROOT}{ROOT}} trees contained therein. It extends class \code{\LinkA{ProcesSet}{ProcesSet}}.
\end{Description}
\begin{Section}{Objects from the Class}
Objects are currently created using function \code{\LinkA{unifilter}{unifilter}}.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{fltrset}:] Object of class \code{"FilterTreeSet"} providing indirect access to 
the \code{\LinkA{ExprTreeSet}{ExprTreeSet.Rdash.class}} used and the \code{\LinkA{UniFilter}{UniFilter.Rdash.class}} settings.
\item[\code{scheme}:] Object of class \code{"SchemeTreeSet"} providing access to 
\code{\LinkA{ROOT}{ROOT}} scheme file.
\item[\code{data}:] Object of class \code{"data.frame"}. The data.frame contains
the data of the unitest stored in \code{\LinkA{ROOT}{ROOT}} data trees.
\item[\code{params}:] Object of class \code{"list"} representing relevant parameters.
\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}} trees are stored,
currently \sQuote{UniFilterSet}.
\item[\code{settype}:] Object of class \code{"character"} describing the type of treeset
stored in \code{setname}, currently \sQuote{unifilter}.
\item[\code{rootfile}:] Object of class \code{"character"} representing the name 
of the \code{\LinkA{ROOT}{ROOT}} 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{ProcesSet}{ProcesSet.Rdash.class}"}, directly.
Class \code{"\LinkA{TreeSet}{TreeSet.Rdash.class}"}, by class "ProcesSet", distance 2.
\end{Section}
\begin{Section}{Methods}
\describe{
\item[filterTreeset] \code{signature(object = "AnalysisTreeSet")}: extracts slot \code{fltrset}.
\item[getTreeData] \code{signature(object = "AnalysisTreeSet")}: exports tree data and returns
a data.frame.
\item[validData] \code{signature(object = "AnalysisTreeSet")}: extracts data.frame \code{data}.
\item[validFilter] \code{signature(object = "AnalysisTreeSet")}: extracts data.frame \code{data}
from \code{fltrset}.
\item[volcanoplot] \code{signature(x = "AnalysisTreeSet")}: creates a volcano-plot.
}
\end{Section}
\begin{Author}\relax
Christian Stratowa
\end{Author}
\begin{SeeAlso}\relax
related classes \code{\LinkA{FilterTreeSet}{FilterTreeSet.Rdash.class}}.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
showClass("AnalysisTreeSet")
\end{ExampleCode}
\end{Examples}

