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GenomicRanges (version 1.20.8)

mappingFunctions: Mapping Functions used in makeSummarizedExperimentFromExpressionSet

Description

These mapping functions are used in the mapFun argument to makeSummarizedExperimentFromExpressionSet.

Usage

naiveRangeMapper(from)


  probeRangeMapper(from)


  geneRangeMapper(txDbPackage, key = "ENTREZID")

Arguments

from
An ExpressionSet object.
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

A GRanges object, with the rownames corresponding to the featureNames of the ExpressionSet object.

Examples

Run this code

  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"))

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