\HeaderA{CallTreeSet-class}{Class CallTreeSet}{CallTreeSet.Rdash.class}
\aliasA{attachCall,CallTreeSet-method}{CallTreeSet-class}{attachCall,CallTreeSet.Rdash.method}
\aliasA{attachPVal,CallTreeSet-method}{CallTreeSet-class}{attachPVal,CallTreeSet.Rdash.method}
\aliasA{callplot,CallTreeSet-method}{CallTreeSet-class}{callplot,CallTreeSet.Rdash.method}
\aliasA{CallTreeSet}{CallTreeSet-class}{CallTreeSet}
\aliasA{presCall,CallTreeSet-method}{CallTreeSet-class}{presCall,CallTreeSet.Rdash.method}
\aliasA{presCall<-,CallTreeSet,data.frame-method}{CallTreeSet-class}{presCall<.Rdash.,CallTreeSet,data.frame.Rdash.method}
\aliasA{pvalData,CallTreeSet-method}{CallTreeSet-class}{pvalData,CallTreeSet.Rdash.method}
\aliasA{pvalData<-,CallTreeSet,data.frame-method}{CallTreeSet-class}{pvalData<.Rdash.,CallTreeSet,data.frame.Rdash.method}
\aliasA{removeCall,CallTreeSet-method}{CallTreeSet-class}{removeCall,CallTreeSet.Rdash.method}
\aliasA{removePVal,CallTreeSet-method}{CallTreeSet-class}{removePVal,CallTreeSet.Rdash.method}
\aliasA{validCall}{CallTreeSet-class}{validCall}
\aliasA{validCall,CallTreeSet-method}{CallTreeSet-class}{validCall,CallTreeSet.Rdash.method}
\keyword{classes}{CallTreeSet-class}
\begin{Description}\relax
This class provides the link to the \code{\LinkA{ROOT}{ROOT}} call 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 created using functions \code{\LinkA{mas5.call}{mas5.call}} or \code{\LinkA{dabg.call}{dabg.call}}, respectively.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{calltype}:] Object of class \code{"character"} representing the call type, 
i.e. \sQuote{mas5} or \sQuote{dabg}.
\item[\code{detcall}:] Object of class \code{"data.frame"}. The data.frame can contain 
the detection calls stored in \code{\LinkA{ROOT}{ROOT}} call trees.
\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 can contain 
the data (i.e. p-values) stored in \code{\LinkA{ROOT}{ROOT}} call 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}} call trees are stored,
usually \sQuote{CallTreeSet}.
\item[\code{settype}:] Object of class \code{"character"} describing the type of treeset
stored in \code{setname}, usually \sQuote{preprocess}.
\item[\code{rootfile}:] Object of class \code{"character"} representing the name 
of the \code{\LinkA{ROOT}{ROOT}} call 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[attachCall] \code{signature(object = "CallTreeSet")}: exports detection call data from 
\code{\LinkA{ROOT}{ROOT}} call file and and saves as data.frame \code{detcall}.
\item[attachPVal] \code{signature(object = "CallTreeSet")}: exports call p-values from 
\code{\LinkA{ROOT}{ROOT}} call file and and saves as data.frame \code{data}.
\item[callplot] \code{signature(x = "CallTreeSet")}: creates a barplot of percent present
and absent calls.
\item[presCall] \code{signature(object = "CallTreeSet")}: extracts the detection call data.frame.
\item[presCall<-] \code{signature(object = "CallTreeSet", value = "data.frame")}: replaces the detection call data.frame.
\item[pvalData] \code{signature(object = "CallTreeSet")}: extracts the detection p-value data.frame.
\item[pvalData<-] \code{signature(object = "CallTreeSet", value = "data.frame")}: replaces the detection p-value data.frame.
\item[removeCall] \code{signature(object = "CallTreeSet")}: replaces data.frame \code{detcall} 
with an empty data.frame of dim(0,0).
\item[removePVal] \code{signature(object = "CallTreeSet")}: replaces data.frame \code{data} 
with an empty data.frame of dim(0,0).
\item[validCall] \code{signature(object = "CallTreeSet")}: extracts a subset of columns 
from data.frame \code{detcall}.
}
\end{Section}
\begin{Author}\relax
Christian Stratowa
\end{Author}
\begin{SeeAlso}\relax
related classes \code{\LinkA{DataTreeSet}{DataTreeSet.Rdash.class}}, \code{\LinkA{ExprTreeSet}{ExprTreeSet.Rdash.class}}.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
showClass("CallTreeSet")
\end{ExampleCode}
\end{Examples}

