\HeaderA{AnnotatedSnpCallSet-class}{Class "AnnotatedSnpCallSet"}{AnnotatedSnpCallSet.Rdash.class}
\aliasA{alleleA,SnpCallSet-class}{AnnotatedSnpCallSet-class}{alleleA,SnpCallSet.Rdash.class}
\aliasA{alleleB,SnpCallSet-class}{AnnotatedSnpCallSet-class}{alleleB,SnpCallSet.Rdash.class}
\aliasA{chromosomeAnnotation,AnnotatedSnpCallSet-method}{AnnotatedSnpCallSet-class}{chromosomeAnnotation,AnnotatedSnpCallSet.Rdash.method}
\aliasA{chromosomeAnnotation<-,AnnotatedSnpCallSet,data.frame-method}{AnnotatedSnpCallSet-class}{chromosomeAnnotation<.Rdash.,AnnotatedSnpCallSet,data.frame.Rdash.method}
\keyword{classes}{AnnotatedSnpCallSet-class}
\begin{Description}\relax
Container for genotype call data accompanied by SNP annotation
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form \code{new("AnnotatedSnpCallSet", phenoData, experimentData, annotation, calls, callsConfidence, 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{featureData}:] Object of class
\code{AnnotatedDataFrame} contains annotation for the SNP's, such as chromosome, physical position, and alleles.     
\item[\code{experimentData}:] Object of class \code{MIAME}
\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{SnpCallSet}, directly.
Class \code{eSet}, by class \code{SnpCallSet}.
Class \code{VersionedBiobase}, by class \code{SnpCallSet}.
Class \code{Versioned}, by class \code{SnpCallSet}.
\end{Section}
\begin{Section}{Methods}
\describe{
}
\end{Section}
\begin{Note}\relax
\end{Note}
\begin{Author}\relax
Robert Scharpf
\end{Author}
\begin{SeeAlso}\relax
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
\end{ExampleCode}
\end{Examples}

