makeSummarizedExperimentFromExpressionSet: Make a RangedSummarizedExperiment object from an...

View source: R/makeSummarizedExperimentFromExpressionSet.R

makeSummarizedExperimentFromExpressionSetR Documentation

Make a RangedSummarizedExperiment object from an ExpressionSet and vice-versa

Description

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.

Usage

makeSummarizedExperimentFromExpressionSet(from,
                                          mapFun=naiveRangeMapper,
                                          ...)

## range mapping functions
naiveRangeMapper(from)
probeRangeMapper(from)
geneRangeMapper(txDbPackage, key = "ENTREZID")

Arguments

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 naiveRangeMapper function is used by default.

...

Additional arguments passed to mapFun.

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.

Value

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.

Author(s)

Jim Hester, james.f.hester@gmail.com

See Also

  • RangedSummarizedExperiment objects.

  • ExpressionSet objects in the Biobase package.

  • TxDb objects in the 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")

Bioconductor/SummarizedExperiment documentation built on Nov. 4, 2022, 11:59 a.m.