\HeaderA{AnnotatedSnpCopyNumberSet-class}{Class "AnnotatedSnpCopyNumberSet"}{AnnotatedSnpCopyNumberSet.Rdash.class}
\aliasA{alleleA,AnnotatedSnpCopyNumberSet-method}{AnnotatedSnpCopyNumberSet-class}{alleleA,AnnotatedSnpCopyNumberSet.Rdash.method}
\aliasA{alleleA,SnpCopyNumberSet-method}{AnnotatedSnpCopyNumberSet-class}{alleleA,SnpCopyNumberSet.Rdash.method}
\aliasA{alleleB,AnnotatedSnpCopyNumberSet-method}{AnnotatedSnpCopyNumberSet-class}{alleleB,AnnotatedSnpCopyNumberSet.Rdash.method}
\aliasA{alleleB,SnpCopyNumberSet-method}{AnnotatedSnpCopyNumberSet-class}{alleleB,SnpCopyNumberSet.Rdash.method}
\aliasA{chromosome,AnnotatedSnpCopyNumberSet-method}{AnnotatedSnpCopyNumberSet-class}{chromosome,AnnotatedSnpCopyNumberSet.Rdash.method}
\aliasA{chromosomeAnnotation,AnnotatedSnpCopyNumberSet-method}{AnnotatedSnpCopyNumberSet-class}{chromosomeAnnotation,AnnotatedSnpCopyNumberSet.Rdash.method}
\aliasA{chromosomeAnnotation<-,AnnotatedSnpCopyNumberSet,data.frame-method}{AnnotatedSnpCopyNumberSet-class}{chromosomeAnnotation<.Rdash.,AnnotatedSnpCopyNumberSet,data.frame.Rdash.method}
\aliasA{coerce,AnnotatedSnpCopyNumberSet,AnnotatedSnpSet-method}{AnnotatedSnpCopyNumberSet-class}{coerce,AnnotatedSnpCopyNumberSet,AnnotatedSnpSet.Rdash.method}
\aliasA{dbSnpId,AnnotatedSnpCopyNumberSet-method}{AnnotatedSnpCopyNumberSet-class}{dbSnpId,AnnotatedSnpCopyNumberSet.Rdash.method}
\aliasA{enzyme,AnnotatedSnpCopyNumberSet-method}{AnnotatedSnpCopyNumberSet-class}{enzyme,AnnotatedSnpCopyNumberSet.Rdash.method}
\aliasA{fragmentLength,AnnotatedSnpCopyNumberSet-method}{AnnotatedSnpCopyNumberSet-class}{fragmentLength,AnnotatedSnpCopyNumberSet.Rdash.method}
\aliasA{plotSnp,AnnotatedSnpCopyNumberSet-method}{AnnotatedSnpCopyNumberSet-class}{plotSnp,AnnotatedSnpCopyNumberSet.Rdash.method}
\aliasA{position,AnnotatedSnpCopyNumberSet-method}{AnnotatedSnpCopyNumberSet-class}{position,AnnotatedSnpCopyNumberSet.Rdash.method}
\keyword{classes}{AnnotatedSnpCopyNumberSet-class}
\begin{Description}\relax
Container for copy number data
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form \code{new("AnnotatedSnpCopyNumberSet", phenoData, experimentData, annotation, copyNumber, cnConfidence, snpLocation, chromosomeAnnotation, chromosome)}.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{chromosomeAnnotation}:] Object of class \code{data.frame}  
\item[\code{assayData}:] Object of class \code{AssayData}  
\item[\code{phenoData}:] Object of class \code{AnnotatedDataFrame} 
\item[\code{experimentData}:] Object of class \code{MIAME}  
\item[\code{featureData}:] Object of class  \code{AnnotatedDataFrame}.  Contains annotation for the SNP's,
such as chromosome, physical position, and alleles.     
\item[\code{annotation}:] For 100k chips, "mapping50kHind240",
"mapping50kXba240" , or "mapping100k".  For 500k chips, mmust be
"mapping250kNsp" or "mapping250kSty"
\item[\code{.\_\_classVersion\_\_}:] Object of class \code{Versions} 
}
\end{Section}
\begin{Section}{Extends}
Class \code{SnpCopyNumberSet}, directly.
Class \code{eSet}, by class \code{SnpCopyNumberSet}.
Class \code{VersionedBiobase}, by class \code{SnpCopyNumberSet}.
Class \code{Versioned}, by class \code{SnpCopyNumberSet}.
\end{Section}
\begin{Section}{Methods}
\describe{
Methods for AnnotatedSnpCopyNumberSet
}
\end{Section}
\begin{Note}\relax
\end{Note}
\begin{Author}\relax
\end{Author}
\begin{References}\relax
\end{References}
\begin{SeeAlso}\relax
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
\end{ExampleCode}
\end{Examples}

