\HeaderA{DataTreeSet-class}{Class DataTreeSet}{DataTreeSet.Rdash.class}
\aliasA{addData,DataTreeSet-method}{DataTreeSet-class}{addData,DataTreeSet.Rdash.method}
\aliasA{attachBgrd,DataTreeSet-method}{DataTreeSet-class}{attachBgrd,DataTreeSet.Rdash.method}
\aliasA{attachInten,DataTreeSet-method}{DataTreeSet-class}{attachInten,DataTreeSet.Rdash.method}
\aliasA{attachMask,DataTreeSet-method}{DataTreeSet-class}{attachMask,DataTreeSet.Rdash.method}
\aliasA{background}{DataTreeSet-class}{background}
\aliasA{background,DataTreeSet-method}{DataTreeSet-class}{background,DataTreeSet.Rdash.method}
\aliasA{background<\Rdash}{DataTreeSet-class}{background<.Rdash.}
\aliasA{background<-,DataTreeSet,data.frame-method}{DataTreeSet-class}{background<.Rdash.,DataTreeSet,data.frame.Rdash.method}
\aliasA{bgtreeNames}{DataTreeSet-class}{bgtreeNames}
\aliasA{bgtreeNames,DataTreeSet-method}{DataTreeSet-class}{bgtreeNames,DataTreeSet.Rdash.method}
\aliasA{DataTreeSet}{DataTreeSet-class}{DataTreeSet}
\aliasA{image,DataTreeSet-method}{DataTreeSet-class}{image,DataTreeSet.Rdash.method}
\aliasA{intensity}{DataTreeSet-class}{intensity}
\aliasA{intensity,DataTreeSet-method}{DataTreeSet-class}{intensity,DataTreeSet.Rdash.method}
\aliasA{intensity<\Rdash}{DataTreeSet-class}{intensity<.Rdash.}
\aliasA{intensity<-,DataTreeSet,data.frame-method}{DataTreeSet-class}{intensity<.Rdash.,DataTreeSet,data.frame.Rdash.method}
\aliasA{mm,DataTreeSet-method}{DataTreeSet-class}{mm,DataTreeSet.Rdash.method}
\aliasA{ncols,DataTreeSet-method}{DataTreeSet-class}{ncols,DataTreeSet.Rdash.method}
\aliasA{nrows,DataTreeSet-method}{DataTreeSet-class}{nrows,DataTreeSet.Rdash.method}
\aliasA{pm,DataTreeSet-method}{DataTreeSet-class}{pm,DataTreeSet.Rdash.method}
\aliasA{pmplot,DataTreeSet-method}{DataTreeSet-class}{pmplot,DataTreeSet.Rdash.method}
\aliasA{projectInfo,DataTreeSet-method}{DataTreeSet-class}{projectInfo,DataTreeSet.Rdash.method}
\aliasA{projectInfo<-,DataTreeSet,ProjectInfo-method}{DataTreeSet-class}{projectInfo<.Rdash.,DataTreeSet,ProjectInfo.Rdash.method}
\aliasA{rawCELName,DataTreeSet-method}{DataTreeSet-class}{rawCELName,DataTreeSet.Rdash.method}
\aliasA{removeBgrd,DataTreeSet-method}{DataTreeSet-class}{removeBgrd,DataTreeSet.Rdash.method}
\aliasA{removeInten,DataTreeSet-method}{DataTreeSet-class}{removeInten,DataTreeSet.Rdash.method}
\aliasA{removeMask,DataTreeSet-method}{DataTreeSet-class}{removeMask,DataTreeSet.Rdash.method}
\aliasA{validBgrd}{DataTreeSet-class}{validBgrd}
\aliasA{validBgrd,DataTreeSet-method}{DataTreeSet-class}{validBgrd,DataTreeSet.Rdash.method}
\aliasA{validData,DataTreeSet-method}{DataTreeSet-class}{validData,DataTreeSet.Rdash.method}
\aliasA{xpsBgCorrect,DataTreeSet-method}{DataTreeSet-class}{xpsBgCorrect,DataTreeSet.Rdash.method}
\aliasA{xpsDABGCall,DataTreeSet-method}{DataTreeSet-class}{xpsDABGCall,DataTreeSet.Rdash.method}
\aliasA{xpsINICall,DataTreeSet-method}{DataTreeSet-class}{xpsINICall,DataTreeSet.Rdash.method}
\aliasA{xpsMAS4,DataTreeSet-method}{DataTreeSet-class}{xpsMAS4,DataTreeSet.Rdash.method}
\aliasA{xpsMAS5,DataTreeSet-method}{DataTreeSet-class}{xpsMAS5,DataTreeSet.Rdash.method}
\aliasA{xpsMAS5Call,DataTreeSet-method}{DataTreeSet-class}{xpsMAS5Call,DataTreeSet.Rdash.method}
\aliasA{xpsNormalize,DataTreeSet-method}{DataTreeSet-class}{xpsNormalize,DataTreeSet.Rdash.method}
\aliasA{xpsPreprocess,DataTreeSet-method}{DataTreeSet-class}{xpsPreprocess,DataTreeSet.Rdash.method}
\aliasA{xpsRMA,DataTreeSet-method}{DataTreeSet-class}{xpsRMA,DataTreeSet.Rdash.method}
\aliasA{xpsSummarize,DataTreeSet-method}{DataTreeSet-class}{xpsSummarize,DataTreeSet.Rdash.method}
\keyword{classes}{DataTreeSet-class}
\begin{Description}\relax
This class provides the link to the \code{\LinkA{ROOT}{ROOT}} data 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 can be created using the functions \code{\LinkA{import.data}{import.data}} or \code{\LinkA{root.data}{root.data}}.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{bgtreenames}:] Object of class \code{"list"} representing the names of  
optional \code{\LinkA{ROOT}{ROOT}} background trees.
\item[\code{bgrd}:] Object of class \code{"data.frame"}. The data.frame can contain 
background intensities stored in \code{\LinkA{ROOT}{ROOT}} background trees.
\item[\code{projectinfo}:] Object of class \code{"ProjectInfo"} containing information 
about the project.
\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 (e.g. intensities) 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}} data trees are stored,
usually \sQuote{DataTreeSet}.
\item[\code{settype}:] Object of class \code{"character"} describing the type of treeset
stored in \code{setname}, usually \sQuote{rawdata}.
\item[\code{rootfile}:] Object of class \code{"character"} representing the name 
of the \code{\LinkA{ROOT}{ROOT}} data 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[addData] \code{signature(object = "DataTreeSet")}: import additional CEL-files and 
update \code{\LinkA{ROOT}{ROOT}} data file \code{rootfile}.
\item[attachBgrd] \code{signature(object = "DataTreeSet")}: exports background trees from 
\code{\LinkA{ROOT}{ROOT}} data file and and saves as data.frame \code{bgrd}.
\item[attachInten] \code{signature(object = "DataTreeSet")}: exports intensity trees from 
\code{\LinkA{ROOT}{ROOT}} data file and and saves as data.frame \code{data}.
\item[attachMask] \code{signature(object = "DataTreeSet")}: exports scheme tree from 
\code{\LinkA{ROOT}{ROOT}} scheme file and and saves as data.frame \code{mask} of slot \code{scheme}.
\item[background] \code{signature(object = "DataTreeSet")}: extracts slot \code{bgrd}.
\item[background<-] \code{signature(object = "DataTreeSet", value = "data.frame")}: replaces slot \code{bgrd}.
\item[bgtreeNames] \code{signature(object = "DataTreeSet")}: extracts slot \code{bgtreenames}.
\item[image] \code{signature(x = "DataTreeSet")}: creates an image for each column from
data.frame \code{data} or  \code{bgrd}, respectively.
\item[intensity] \code{signature(object = "DataTreeSet")}: extracts slot \code{data}.
\item[intensity<-] \code{signature(object = "DataTreeSet", value = "data.frame")}: replaces slot \code{data}.
\item[mm] \code{signature(object = "DataTreeSet")}: extracts the mismatch intensities.
\item[ncols] \code{signature(object = "DataTreeSet")}: extracts the physical number of 
array columns from slot \code{scheme}.
\item[nrows] \code{signature(object = "DataTreeSet")}: extracts the physical number of 
array rows from slot \code{scheme}.
\item[pm] \code{signature(object = "DataTreeSet")}: extracts the perfect match intensities.
\item[pmplot] \code{signature(x = "DataTreeSet")}: creates a barplot of mean perfect match and
mismatch intensities.
\item[projectInfo] \code{signature(object = "DataTreeSet")}: extracts slot \code{projectinfo}.
\item[projectInfo<-] \code{signature(object = "DataTreeSet", value = "ProjectInfo")}: replaces slot \code{projectinfo}.
\item[rawCELName] \code{signature(object = "DataTreeSet")}: returns the name(s) of the 
imported raw CEL-files.
\item[removeBgrd] \code{signature(object = "DataTreeSet")}: replaces data.frame \code{bgrd} 
with an empty data.frame of dim(0,0).
\item[removeInten] \code{signature(object = "DataTreeSet")}: replaces data.frame \code{data} 
with an empty data.frame of dim(0,0).
\item[removeMask] \code{signature(object = "DataTreeSet")}: replaces data.frame \code{mask} 
from slot \code{scheme} with an empty data.frame of dim(0,0).
\item[validBgrd] \code{signature(object = "DataTreeSet")}: extracts the valid data 
from data.frame \code{bgrd}.
\item[validData] \code{signature(object = "DataTreeSet")}: extracts a subset of valid data 
from data.frame \code{data}.
\item[xpsBgCorrect] \code{signature(object = "DataTreeSet")}: applies background correction methods.
See \code{\LinkA{bgcorrect}{bgcorrect}}.
\item[xpsDABGCall] \code{signature(object = "DataTreeSet")}: computes DABG call.
\item[xpsINICall] \code{signature(object = "DataTreeSet")}: computes I/NI call.
\item[xpsMAS4] \code{signature(object = "DataTreeSet")}: computes MAS4 expression levels.
\item[xpsMAS5] \code{signature(object = "DataTreeSet")}: computes MAS5 expression levels.
\item[xpsMAS5Call] \code{signature(object = "DataTreeSet")}: computes MAS5 detection call.
\item[xpsNormalize] \code{signature(object = "DataTreeSet")}: applies normalization methods.
\item[xpsPreprocess] \code{signature(object = "DataTreeSet")}: applies normalization methods.
\item[xpsRMA] \code{signature(object = "DataTreeSet")}: computes RMA expression levels.
\item[xpsSummarize] \code{signature(object = "DataTreeSet")}: applies summarization methods.
}
\end{Section}
\begin{Author}\relax
Christian Stratowa
\end{Author}
\begin{SeeAlso}\relax
related classes \code{\LinkA{ExprTreeSet}{ExprTreeSet.Rdash.class}}, \code{\LinkA{CallTreeSet}{CallTreeSet.Rdash.class}}.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
showClass("DataTreeSet")
\end{ExampleCode}
\end{Examples}

