Accessor functions for DEXSeqDataSet details

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 ) )
#>                  treated1fb treated2fb treated3fb untreated1fb untreated2fb
#> FBgn0000256:E001         92         28         43           54          131
#> FBgn0000256:E002        124         80         91           76          224
#> FBgn0000256:E003        340        241        262          347          670
#> FBgn0000256:E004        250        189        201          219          507
#> FBgn0000256:E005         96         38         39           71           76
#> FBgn0000256:E006          1          0          1            0            2
#>                  untreated3fb untreated4fb
#> FBgn0000256:E001           51           49
#> FBgn0000256:E002           82           95
#> FBgn0000256:E003          260          297
#> FBgn0000256:E004          242          250
#> FBgn0000256:E005           57           62
#> FBgn0000256:E006            0            2
  head( featureIDs(dxd))
#> [1] "E001" "E002" "E003" "E004" "E005" "E006"
  head( exonIDs(dxd))
#> [1] "E001" "E002" "E003" "E004" "E005" "E006"