\HeaderA{RatioSnpSet-class}{Class for high throughput SNP-level data.  The assay data
contains ratios of copy number.}{RatioSnpSet.Rdash.class}
\keyword{classes}{RatioSnpSet-class}
\begin{Description}\relax
Container for high throughput SNP data for platforms that
provide ratios as SNP-level summaries of copy number
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form \code{new("RatioSnpSet", calls, callsConfidence, ratio, ratioConfidence, ...)}.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{assayData}:] Object of class \code{"AssayData"} 
\item[\code{phenoData}:] Object of class \code{"AnnotatedDataFrame"} 
\item[\code{featureData}:] Object of class \code{"AnnotatedDataFrame"} 
\item[\code{experimentData}:] Object of class \code{"MIAME"} 
\item[\code{annotation}:] Object of class \code{"character"} 
\item[\code{.\_\_classVersion\_\_}:] Object of class \code{"Versions"}
}
\end{Section}
\begin{Section}{Extends}
Class \code{\LinkA{SnpLevelSet}{SnpLevelSet}}, directly.
Class \code{\LinkA{eSet}{eSet}},  by class "SnpLevelSet", distance 2.
Class \code{\LinkA{VersionedBiobase}{VersionedBiobase}}, by class "SnpLevelSet", distance 3.
Class \code{\LinkA{Versioned}{Versioned}}, by class "SnpLevelSet", distance 4.
\end{Section}
\begin{Section}{Methods}
\describe{
\item[cnConfidence] \code{signature(object = "RatioSnpSet")}:
Accessor for confidence scores for the ratios 
\item[cnConfidence<-] \code{signature(object = "RatioSnpSet", value
        = "matrix")}: Replacement method for ratio confidence scores
\item[copyNumber] \code{signature(object = "RatioSnpSet")}: Accessor
for ratios.  See also \code{ratio}.
\item[copyNumber<-] \code{signature(object = "RatioSnpSet", value =
        "matrix")}: Replacement method for ratios. 
\item[initialize] \code{signature(.Object = "RatioSnpSet")}
\item[ratioConfidence] \code{signature(object = "RatioSnpSet")}:
Accessor for confidence scores of the ratios.  See also \code{cnConfidence}.
}
\end{Section}
\begin{Author}\relax
RS
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{RatioSnpSet-methods}{RatioSnpSet.Rdash.methods}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
showClass("RatioSnpSet")
\end{ExampleCode}
\end{Examples}

