Make a RangedSummarizedExperiment object from an ExpressionSet and vice-versa
Coercion between RangedSummarizedExperiment and ExpressionSet is supported in both directions.
For going from ExpressionSet to
RangedSummarizedExperiment, the
makeSummarizedExperimentFromExpressionSet function is also
provided to let the user control how to map features to ranges.
makeSummarizedExperimentFromExpressionSet(from,
mapFun=naiveRangeMapper,
...)
## range mapping functions
naiveRangeMapper(from)
probeRangeMapper(from)
geneRangeMapper(txDbPackage, key = "ENTREZID")from |
An ExpressionSet object. |
mapFun |
A function which takes an ExpressionSet object and returns a GRanges, or GRangesList object which corresponds to the genomic ranges used in the ExpressionSet. The rownames of the returned GRanges are used to match the featureNames of the ExpressionSet. The |
... |
Additional arguments passed to |
txDbPackage |
A character string with the Transcript Database to use for the mapping. |
key |
A character string with the Gene key to use for the mapping. |
makeSummarizedExperimentFromExpressionSet takes an
ExpressionSet object as input and a range mapping
function that maps the features to ranges. It then returns a
RangedSummarizedExperiment object that corresponds to the input.
The range mapping functions return a GRanges object, with the
rownames corresponding to the featureNames of
the ExpressionSet object.
Jim Hester, james.f.hester@gmail.com
RangedSummarizedExperiment objects.
ExpressionSet objects in the Biobase package.
TxDb objects in the GenomicFeatures package.
## ---------------------------------------------------------------------
## 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")Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.