Accessors for the 'counts' slot of a DEXSeqResults object.

The counts slot holds the count data as a matrix of non-negative integer count values, one row for each observational unit (gene or the like), and one column for each sample.

Usage

# S4 method for class 'DEXSeqResults'
counts(object,normalized=FALSE)

Arguments

object: a DEXSeqResults object.
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

an integer matrix

Examples

  data(pasillaDEXSeqDataSet, package="pasilla")
  head( counts( dxd ))
#>                  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
#> FBgn0000256:E001   92   28   43   54  131   51   49 1390  829   923  1115  2495
#> FBgn0000256:E002  124   80   91   76  224   82   95 1358  777   875  1093  2402
#> FBgn0000256:E003  340  241  262  347  670  260  297 1142  616   704   822  1956
#> FBgn0000256:E004  250  189  201  219  507  242  250 1232  668   765   950  2119
#> FBgn0000256:E005   96   38   39   71   76   57   62 1386  819   927  1098  2550
#> FBgn0000256:E006    1    0    1    0    2    0    2 1481  857   965  1169  2624
#>                  [,13] [,14]
#> FBgn0000256:E001  1054  1052
#> FBgn0000256:E002  1023  1006
#> FBgn0000256:E003   845   804
#> FBgn0000256:E004   863   851
#> FBgn0000256:E005  1048  1039
#> FBgn0000256:E006  1105  1099