GenomicRanges (version 1.20.8)

makeSummarizedExperimentFromExpressionSet: Make an SummarizedExperiment object from an ExpressionSet

Description

makeSummarizedExperimentFromExpressionSet takes a ExpressionSet object as input and a Range mapping function that maps the features to ranges. It then returns a SummarizedExperiment object.

Usage

makeSummarizedExperimentFromExpressionSet(from, mapFun=naiveRangeMapper)

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. naiveRangeMapper.

Value

A SummarizedExperiment object that corresponds to the input.

See Also

naiveRangeMapper, probeRangeMapper, geneRangeMapper

Examples

  library(Biobase)
  data(sample.ExpressionSet, package = "Biobase")

  # using the naive coercion
  makeSummarizedExperimentFromExpressionSet(sample.ExpressionSet)

  # using probe range mapper
  makeSummarizedExperimentFromExpressionSet(sample.ExpressionSet, probeRangeMapper)

  # using the gene range mapper
  makeSummarizedExperimentFromExpressionSet(sample.ExpressionSet,
                                            geneRangeMapper("TxDb.Hsapiens.UCSC.hg19.knownGene"))