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\name{MultiSet}
\docType{class}
\alias{class:MultiSet}
\alias{MultiSet}
\alias{MultiSet-class}
\alias{initialize,MultiSet-method}
\alias{coerce,eSet,MultiSet-method}
\title{
Class to Contain and Describe High-Throughput Expression Level Assays.
}
\description{
Container for high-throughput assays and experimental
metadata. \code{MutliSet} is derived from
\code{\link{eSet-class}}. \code{MultiSet} differs from
\code{\link{ExpressionSet-class}} because \code{MultiSet} can contain
any element(s) in \code{assayData} (\code{ExpressionSet} must have an
element named \code{exprs}).
}
\section{Extends}{
Directly extends class \code{\link{eSet}}.
}
\section{Creating Objects}{
\code{new('MultiSet',
phenoData = [AnnotatedDataFrame],
experimentData = [MIAME],
annotation = [character],
protocolData = [AnnotatedDataFrame],
...)
}
\code{updateOldESet(oldESet,"MultiSet")}
\code{MultiSet} instances are usually created through
\code{new("MultiSet", ...)}. The \code{...} arguments to \code{new}
are matrices of expression data (with features
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.
\code{\link{updateOldESet}} will take a serialized instance (e.g., saved to a disk
file with \code{save} object created with earlier definitions of
the \code{eSet-class}, and update the object to
\code{MultiSet}. Warnings are issued when direct translation is not
possible; incorrectly created \code{oldESet} instances may not be updated.
}
\section{Slots}{
Inherited from \code{eSet}:
\describe{
\item{\code{assayData}:}{Contains zero or more matrices with equal
dimensions, and with column number equal to
\code{nrow(phenoData)}. Each matrix in \code{assayData} has rows
representing features (e.g., reporters) and columns representing
samples. Class:\code{\link{AssayData-class}}}
\item{\code{phenoData}:}{See \code{\link{eSet-class}}}
\item{\code{experimentData}:}{See \code{\link{eSet-class}}}
\item{\code{annotation}:}{See \code{\link{eSet-class}}}
\item{\code{protocolData}:}{See \code{\link{eSet-class}}}
}
}
\section{Methods}{
Class-specific methods: none
Derived from \code{\link{eSet-class}}:
\describe{
\item{\code{updateObject(object, ..., verbose=FALSE)}}{Update instance to current version, if necessary. See \code{\link{updateObject}} and \code{\link{eSet}}}
\item{\code{isCurrent(object)}}{Determine whether version of object is current. See \code{\link{isCurrent}}}
\item{\code{isVersioned(object)}}{Determine whether object contains a 'version' string describing its structure . See \code{\link{isVersioned}}}
\item{\code{sampleNames(MultiSet)} and \code{sampleNames(MultiSet)<-}:}{See \code{\link{eSet-class}}}
\item{\code{featureNames(MultiSet)}, \code{featureNames(MultiSet, value)<-}:}{See \code{\link{eSet-class}}}
\item{\code{dims(MultiSet)}:}{See \code{\link{eSet-class}}}
\item{\code{phenoData(MultiSet)}, \code{phenoData(MultiSet,value)<-}:}{See \code{\link{eSet-class}}}
\item{\code{varLabels(MultiSet)}, \code{varLabels(MultiSet, value)<-}:}{See \code{\link{eSet-class}}}
\item{\code{varMetadata(MultiSet)}, \code{varMetadata(MultiSet,value)<-}:}{See \code{\link{eSet-class}}}
\item{\code{pData(MultiSet)}, \code{pData(MultiSet,value)<-}:}{See \code{\link{eSet-class}}}
\item{\code{varMetadata(MultiSet)}, \code{varMetadata(MultiSet,value)}}{See \code{\link{eSet-class}}}
\item{\code{experimentData(MultiSet)},\code{experimentData(MultiSet,value)<-}:}{See \code{\link{eSet-class}}}
\item{\code{pubMedIds(MultiSet)}, \code{pubMedIds(MultiSet,value)}}{See \code{\link{eSet-class}}}
\item{\code{abstract(MultiSet)}:}{See \code{\link{eSet-class}}}
\item{\code{annotation(MultiSet)}, \code{annotation(MultiSet,value)<-}}{See \code{\link{eSet-class}}}
\item{\code{protocolData(MultiSet)}, \code{protocolData(MultiSet,value)<-}}{See \code{\link{eSet-class}}}
\item{\code{combine(MultiSet,MultiSet)}:}{See \code{\link{eSet-class}}}
\item{\code{storageMode(eSet)}, \code{storageMode(eSet,character)<-}:}{See \code{\link{eSet-class}}}
}
Standard generic methods:
\describe{
\item{\code{initialize(MultiSet)}:}{Object instantiation, used by \code{new}; not to be called directly by the user.}
\item{\code{validObject(MultiSet)}:}{Validity-checking method, ensuring that all elements of \code{assayData} are matricies with equal dimensions.}
\item{\code{as(eSet,MultiSet)}:}{Coerce the \code{eSet} portion of an object to \code{MultiSet}.}
\item{\code{show(MultiSet)}}{See \code{\link{eSet-class}}}
\item{\code{dim(MultiSet)}, \code{ncol}}{See \code{\link{eSet-class}}}
\item{\code{MultiSet[(index)}:}{See \code{\link{eSet-class}}}
\item{\code{MultiSet$}, \code{MultiSet$<-}}{See \code{\link{eSet-class}}}
}
}
\author{Biocore team}
\seealso{
\code{\link{eSet-class}}, \code{\link{ExpressionSet-class}}
}
\examples{
# create an instance of ExpressionSet
new("MultiSet")
}
\keyword{classes}
|
