accessors: Accessor functions for DEXSeqDataSet details

In DEXSeq: Inference of differential exon usage in RNA-Seq

Description

Accessor functions of the DEXSeqDataSet object.

Usage

  featureCounts(object, normalized=FALSE)

  featureIDs( object )
  featureIDs( object ) <- value

  exonIDs( object )
  exonIDs( object ) <- value

  groupIDs( object )
  groupIDs( object ) <- value

  geneIDs( object )
  geneIDs( object ) <- value

  sampleAnnotation( object )
  

Arguments

object	An DEXSeqDataSet object.
value	A character vector to replace previous values.
normalized	Logical indicating whether or not to divide the counts by the size factors or normalization factors before returning (normalization factors always preempt size factors)

Value

'featureCounts' access the counts per exonic region or feature region names. 'featureIDs' and 'exonIDs' are accessor functions for the exon bin or features identifiers. 'groupIDs' and 'geneIDs' are accessor functions for the character vector grouping the features, for example exonIDs from the same gene are grouped together by having the same value in the geneIDs. 'sampleAnnotation' is an accessor for the information from the samples.

Examples

  data(pasillaDEXSeqDataSet, package="pasilla")
  head( featureCounts( dxd ) )
  head( featureIDs(dxd))
  head( exonIDs(dxd))

DEXSeq documentation built on Nov. 8, 2020, 5:11 p.m.