\HeaderA{cghExSet-class}{Class "cghExSet" for combining CGH and expression data}{cghExSet.Rdash.class}
\aliasA{cloneMeta}{cghExSet-class}{cloneMeta}
\aliasA{cloneMeta,cghExSet-method}{cghExSet-class}{cloneMeta,cghExSet.Rdash.method}
\aliasA{cloneNames}{cghExSet-class}{cloneNames}
\aliasA{cloneNames,cghExSet-method}{cghExSet-class}{cloneNames,cghExSet.Rdash.method}
\aliasA{exprs,cghExSet-method}{cghExSet-class}{exprs,cghExSet.Rdash.method}
\aliasA{initialize,cghExSet-method}{cghExSet-class}{initialize,cghExSet.Rdash.method}
\aliasA{logRatios,cghExSet-method}{cghExSet-class}{logRatios,cghExSet.Rdash.method}
\aliasA{make\_cghExSet}{cghExSet-class}{make.Rul.cghExSet}
\aliasA{show,cghExSet-method}{cghExSet-class}{show,cghExSet.Rdash.method}
\keyword{classes}{cghExSet-class}
\begin{Description}\relax
combination of an ExpressionSet and CGH assay results
\end{Description}
\begin{Usage}
\begin{verbatim}
make_cghExSet(exprs, logRatios, cloneMeta, pd, mi, anno) # pd is AnnotatedDataFrame, mi is MIAME
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{exprs}] matrix of expression assay results 
\item[\code{logRatios}] matrix of aCGH assay results 
\item[\code{cloneMeta}] AnnotatedDataFrame for aCGH clone descriptions
\item[\code{pd}] AnnotatedDataFrame for sample level data 
\item[\code{mi}] \code{\LinkA{MIAME}{MIAME}} instance for experiment documentation 
\item[\code{anno}] character string with annotation platform descriptor for expression data
\end{ldescription}
\end{Arguments}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form \code{new("cghExSet", phenoData, experimentData, annotation, exprs, logRatios, cloneMeta)}.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{cghAssays}:] Object of class \code{"AssayData"} rectangular
representation of logRatio data from CGH 
\item[\code{cloneMeta}:] Object of class \code{"AnnotatedDataFrame"} information
on chromosome and offset of clones
\item[\code{assayData}:] Object of class \code{"AssayData"} expression assay results 
\item[\code{phenoData}:] Object of class \code{"AnnotatedDataFrame"} sample level data 
\item[\code{featureData}:] Object of class \code{"AnnotatedDataFrame"} reporter
level metadata for expression assay results 
\item[\code{experimentData}:] Object of class \code{"MIAME"} container for
experiment documentation 
\item[\code{annotation}:] Object of class \code{"character"} identifiers for
expression and CGH platforms, as a named vector with elements named 'exprs'
and 'logRatios' 
\item[\code{.\_\_classVersion\_\_}:] Object of class \code{"Versions"}  
}
\end{Section}
\begin{Section}{Extends}
Class \code{\LinkA{eSet-class}{eSet.Rdash.class}}, directly.
Class \code{\LinkA{VersionedBiobase-class}{VersionedBiobase.Rdash.class}}, by class "eSet", distance 2.
Class \code{\LinkA{Versioned-class}{Versioned.Rdash.class}}, by class "eSet", distance 3.
\end{Section}
\begin{Section}{Methods}
\describe{
\item[cloneMeta] \code{signature(cghSet = "cghExSet")}: extract annotated data
frame on clone locations for CGH component 
\item[cloneNames] \code{signature(cghSet = "cghExSet")}: extract character vector
of clone IDs for CGH component 
\item[exprs] \code{signature(object = "cghExSet")}: extract expression assay results 
\item[initialize] \code{signature(.Object = "cghExSet")}: infrastructure 
\item[logRatios] \code{signature(cghSet = "cghExSet")}: extract CGH assay results 
\item[show] \code{signature(object = "cghExSet")}: display object in concise form 
}
\end{Section}
\begin{Author}\relax
V Carey <stvjc@channing.harvard.edu>
\end{Author}
\begin{References}\relax
R. M. Neve Cancer Cell Dec 2006
\end{References}
\begin{Examples}
\begin{ExampleCode}
showClass("cghExSet")
data(neveExCGH)
logRatios(neveExCGH)[1:4,]
exprs(neveExCGH)[1:4,]
\end{ExampleCode}
\end{Examples}

