featureCounts {DEXSeq} | R Documentation

## Accessor functions for DEXSeqDataSet details

### 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))

[Package DEXSeq version 1.24.4 Index]