counts {DESeq}R Documentation

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

Description

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 signature 'CountDataSet'
counts(object, normalized=FALSE)
## S4 replacement method for signature 'CountDataSet,matrix'
counts(object) <- value

Arguments

object

a CountDataSet object.

normalized

logical indicating whether or not to divide the counts by the size factors before returning.

value

integer matrix.

Author(s)

Simon Anders, sanders@fs.tum.de

Examples

   cds <- makeExampleCountDataSet()
   head( counts( cds ) )

[Package DESeq version 1.6.1 Index]