mappingFunctions {GenomicRanges}R Documentation

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


  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"))
[Package GenomicRanges version 1.20.3 Index]