\name{RatioSnpSet-class}
\docType{class}
\alias{RatioSnpSet-class}
\title{Class for high throughput SNP-level data.  The assay data
  contains ratios of copy number.}
\description{Container for high throughput SNP data for platforms that
  provide ratios as SNP-level summaries of copy number}
\section{Objects from the Class}{
  Objects can be created by calls of the form \code{new("RatioSnpSet", calls, callsConfidence, ratio, ratioConfidence, ...)}.
}
\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"}}
  }
}
\section{Extends}{
  Class \code{\link[oligoClasses:SnpLevelSet-class]{SnpLevelSet}}, directly.
  Class \code{\link[Biobase:class.eSet]{eSet}},  by class "SnpLevelSet", distance 2.
  Class \code{\link[Biobase:class.VersionedBiobase]{VersionedBiobase}}, by class "SnpLevelSet", distance 3.
  Class \code{\link[Biobase:class.Versioned]{Versioned}}, by class "SnpLevelSet", distance 4.
}
\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}.}
	 }
}
\author{RS}
\seealso{\code{\link{RatioSnpSet-methods}}}
\examples{
showClass("RatioSnpSet")
}
\keyword{classes}