counts {DESeq2}R Documentation

Accessors for the 'counts' slot of a DESeqDataSet 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 'DESeqDataSet'
counts(object,normalized=FALSE)

## S4 replacement method for signature 'DESeqDataSet,matrix'
counts(object)<-value

## S4 method for signature 'DESeqDataSet'
counts(object, normalized = FALSE)

Arguments

object

a DESeqDataSet 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

Author(s)

Simon Anders

See Also

sizeFactors, normalizationFactors

Examples

dds <- makeExampleDESeqDataSet()
head(counts(dds))

[Package DESeq2 version 1.4.5 Index]