\HeaderA{SnpSet}{Class to Contain Objects Describing High-Throughput SNP Assays.}{SnpSet}
\aliasA{class:SnpSet}{SnpSet}{class:SnpSet}
\aliasA{exprs,SnpSet-method}{SnpSet}{exprs,SnpSet.Rdash.method}
\aliasA{exprs<-,SnpSet,matrix-method}{SnpSet}{exprs<.Rdash.,SnpSet,matrix.Rdash.method}
\aliasA{initialize,SnpSet-method}{SnpSet}{initialize,SnpSet.Rdash.method}
\aliasA{snpCall,SnpSet-method}{SnpSet}{snpCall,SnpSet.Rdash.method}
\aliasA{snpCall<-,SnpSet,matrix-method}{SnpSet}{snpCall<.Rdash.,SnpSet,matrix.Rdash.method}
\aliasA{snpCallProbability,SnpSet-method}{SnpSet}{snpCallProbability,SnpSet.Rdash.method}
\aliasA{snpCallProbability<-,SnpSet,matrix-method}{SnpSet}{snpCallProbability<.Rdash.,SnpSet,matrix.Rdash.method}
\aliasA{SnpSet-class}{SnpSet}{SnpSet.Rdash.class}
\keyword{classes}{SnpSet}
\begin{Description}\relax
Container for high-throughput assays and experimental
metadata. \code{SnpSet} class is derived from
\code{\LinkA{eSet}{eSet}}, and requires matrices \code{call},
\code{callProbability} as assay data members.
\end{Description}
\begin{Section}{Extends}
Directly extends class \code{\LinkA{eSet}{eSet}}.
\end{Section}
\begin{Section}{Creating Objects}
\code{new('SnpSet',
    phenoData = [AnnotatedDataFrame],
    experimentData = [MIAME],
    annotation = [character],
    protocolData = [AnnotatedDataFrame],
    call = [matrix],
    callProbability = [matrix],
    ...)
  }

\code{SnpSet} instances are usually created through
\code{new("SnpSet", ...)}. Usually the arguments to \code{new}
include \code{call} (a matrix of genotypic calls, with features (SNPs)
corresponding to rows and samples to columns), \code{phenoData},
\code{experimentData}, \code{annotation}, and \code{protocolData}. 
\code{phenoData}, \code{experimentData}, \code{annotation} and
\code{protocolData} can be missing, in which case they are assigned
default values.
\end{Section}
\begin{Section}{Slots}
Inherited from \code{eSet}:
\describe{
\item[\code{assayData}:] Contains matrices with equal
dimensions, and with column number equal to
\code{nrow(phenoData)}. \code{assayData} must contain a matrix
\code{call} with rows representing features (e.g., SNPs)
and columns representing samples, and a matrix
\code{callProbability} describing the certainty of the
call. The content of \code{call} and \code{callProbability} are
not enforced by the class. Additional matrices of
identical size may also be included in
\code{assayData}. Class:\code{\LinkA{AssayData-class}{AssayData.Rdash.class}} 
\item[\code{phenoData}:] See \code{\LinkA{eSet}{eSet}}
\item[\code{experimentData}:] See \code{\LinkA{eSet}{eSet}}
\item[\code{annotation}:] See \code{\LinkA{eSet}{eSet}}
\item[\code{protocolData}:] See \code{\LinkA{eSet}{eSet}}
}
\end{Section}
\begin{Section}{Methods}
Class-specific methods:
\describe{
\item[\code{snpCall(SnpSet)}, \code{snpCall(SnpSet,matrix)<-}] Access and
set elements named \code{call} in the \code{AssayData}
slot.

\item[\code{exprs(SnpSet)}, \code{exprs(SnpSet,matrix)<-}] Synonym
for \code{snpCall}.

\item[\code{snpCallProbability(SnpSet)},
\code{snpCallProbability<-(SnpSet,matrix)<-}] Access and set
elements named \code{callProbability} in the \code{AssayData}
slot.  }

Derived from \code{\LinkA{eSet}{eSet}}:
\describe{
\item[\code{updateObject(object, ..., verbose=FALSE)}] Update instance to current version, if necessary. See \code{\LinkA{updateObject}{updateObject}} and \code{\LinkA{eSet}{eSet}}
\item[\code{isCurrent(object)}] Determine whether version of object is current. See \code{\LinkA{isCurrent}{isCurrent}}
\item[\code{isVersioned(object)}] Determine whether object contains a 'version' string describing its structure . See \code{\LinkA{isVersioned}{isVersioned}}
\item[\code{sampleNames(SnpSet)} and \code{sampleNames(SnpSet)<-}:] See \code{\LinkA{eSet}{eSet}}
\item[\code{featureNames(SnpSet)}, \code{featureNames(SnpSet, value)<-}:] See \code{\LinkA{eSet}{eSet}}
\item[\code{dims(SnpSet)}:] See \code{\LinkA{eSet}{eSet}}
\item[\code{phenoData(SnpSet)}, \code{phenoData(SnpSet,value)<-}:] See \code{\LinkA{eSet}{eSet}}
\item[\code{varLabels(SnpSet)}, \code{varLabels(SnpSet, value)<-}:] See \code{\LinkA{eSet}{eSet}}
\item[\code{varMetadata(SnpSet)}, \code{varMetadata(SnpSet,value)<-}:] See \code{\LinkA{eSet}{eSet}}
\item[\code{pData(SnpSet)}, \code{pData(SnpSet,value)<-}:] See \code{\LinkA{eSet}{eSet}}
\item[\code{varMetadata(SnpSet)}, \code{varMetadata(SnpSet,value)}] See \code{\LinkA{eSet}{eSet}}
\item[\code{experimentData(SnpSet)},\code{experimentData(SnpSet,value)<-}:] See \code{\LinkA{eSet}{eSet}}
\item[\code{pubMedIds(SnpSet)}, \code{pubMedIds(SnpSet,value)}] See \code{\LinkA{eSet}{eSet}}
\item[\code{abstract(SnpSet)}:] See \code{\LinkA{eSet}{eSet}}
\item[\code{annotation(SnpSet)}, \code{annotation(SnpSet,value)<-}] See \code{\LinkA{eSet}{eSet}}
\item[\code{protocolData(SnpSet)}, \code{protocolData(SnpSet,value)<-}] See \code{\LinkA{eSet}{eSet}}
\item[\code{combine(SnpSet,SnpSet)}:] See \code{\LinkA{eSet}{eSet}}
\item[\code{storageMode(eSet)}, \code{storageMode(eSet,character)<-}:] See \code{\LinkA{eSet}{eSet}}
}

Standard generic methods:
\describe{
\item[\code{initialize(SnpSet)}:] Object instantiation, used by \code{new}; not to be called directly by the user.
\item[\code{validObject(SnpSet)}:] Validity-checking method, ensuring that \code{call} and \code{callProbability} is a member of \code{assayData}. \code{checkValidity(SnpSet)} imposes this validity check, and the validity checks of \code{eSet}.
\item[\code{show(SnpSet)}] See \code{\LinkA{eSet}{eSet}}
\item[\code{dim(SnpSet)}, \code{ncol}] See \code{\LinkA{eSet}{eSet}}
\item[\code{SnpSet[(index)}:] See \code{\LinkA{eSet}{eSet}}
\item[\code{SnpSet\$}, \code{SnpSet\$<-}] See \code{\LinkA{eSet}{eSet}}
}
\end{Section}
\begin{Author}\relax
Martin Morgan, V.J. Carey, after initial design by R. Gentleman
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{eSet}{eSet}}, \code{\LinkA{ExpressionSet}{ExpressionSet}}
\end{SeeAlso}

