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\name{makeSummarizedExperimentFromExpressionSet}
\alias{makeSummarizedExperimentFromExpressionSet}
\alias{naiveRangeMapper}
\alias{probeRangeMapper}
\alias{geneRangeMapper}
\alias{coerce,ExpressionSet,RangedSummarizedExperiment-method}
\alias{coerce,ExpressionSet,SummarizedExperiment-method}
\alias{coerce,RangedSummarizedExperiment,ExpressionSet-method}
\alias{coerce,SummarizedExperiment,ExpressionSet-method}
\title{Make a RangedSummarizedExperiment object from an ExpressionSet and
vice-versa}
\description{
Coercion between \link{RangedSummarizedExperiment} and
\link[Biobase]{ExpressionSet} is supported in both directions.
For going from \link[Biobase]{ExpressionSet} to
\link{RangedSummarizedExperiment}, the
\code{makeSummarizedExperimentFromExpressionSet} function is also
provided to let the user control how to map features to ranges.
}
\usage{
makeSummarizedExperimentFromExpressionSet(from,
mapFun=naiveRangeMapper,
...)
## range mapping functions
naiveRangeMapper(from)
probeRangeMapper(from)
geneRangeMapper(txDbPackage, key = "ENTREZID")
}
\arguments{
\item{from}{
An \link[Biobase]{ExpressionSet} object.
}
\item{mapFun}{
A function which takes an \link[Biobase]{ExpressionSet} object and
returns a \link{GRanges}, or \link{GRangesList} object which
corresponds to the genomic ranges used in the ExpressionSet. The
\link[base]{rownames} of the returned \link[GenomicRanges]{GRanges}
are used to match the \link[Biobase]{featureNames} of the
\link[Biobase]{ExpressionSet}.
The \code{naiveRangeMapper} function is used by default.
}
\item{...}{
Additional arguments passed to \code{mapFun}.
}
\item{txDbPackage}{
A character string with the Transcript Database to use for the mapping.
}
\item{key}{
A character string with the Gene key to use for the mapping.
}
}
\value{
\code{makeSummarizedExperimentFromExpressionSet} takes an
\link[Biobase]{ExpressionSet} object as input and a \emph{range mapping
function} that maps the features to ranges. It then returns a
\link{RangedSummarizedExperiment} object that corresponds to the input.
The range mapping functions return a \link{GRanges} object, with the
\code{rownames} corresponding to the \link[Biobase]{featureNames} of
the \link[Biobase]{ExpressionSet} object.
}
\author{Jim Hester, \url{james.f.hester@gmail.com}}
\seealso{
\itemize{
\item \link{RangedSummarizedExperiment} objects.
\item \link[Biobase]{ExpressionSet} objects in the \pkg{Biobase} package.
\item \link[GenomicFeatures]{TxDb} objects in the \pkg{GenomicFeatures}
package.
}
}
\examples{
## ---------------------------------------------------------------------
## GOING FROM ExpressionSet TO SummarizedExperiment
## ---------------------------------------------------------------------
data(sample.ExpressionSet, package="Biobase")
# naive coercion
makeSummarizedExperimentFromExpressionSet(sample.ExpressionSet)
as(sample.ExpressionSet, "RangedSummarizedExperiment")
as(sample.ExpressionSet, "SummarizedExperiment")
# using probe range mapper
makeSummarizedExperimentFromExpressionSet(sample.ExpressionSet, probeRangeMapper)
# using the gene range mapper
se <- makeSummarizedExperimentFromExpressionSet(
sample.ExpressionSet,
geneRangeMapper("TxDb.Hsapiens.UCSC.hg19.knownGene")
)
se
rowData(se) # duplicate row names
## ---------------------------------------------------------------------
## GOING FROM SummarizedExperiment TO ExpressionSet
## ---------------------------------------------------------------------
example(RangedSummarizedExperiment) # to create 'rse'
rse
as(rse, "ExpressionSet")
}
\keyword{manip}
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