counts: Accessors for the 'counts' slot of a DESeqDataSet object.

In DESeq2: Differential gene expression analysis based on the negative binomial distribution

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, replaced = FALSE)

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

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)
replaced	after a DESeq call, this argument will return the counts with outliers replaced instead of the original counts, and optionally normalized. The replaced counts are stored by DESeq in assays(object)[['replaceCounts']].
value	an integer matrix

Author(s)

Simon Anders

See Also

sizeFactors, normalizationFactors

Examples

dds <- makeExampleDESeqDataSet(m=4)
head(counts(dds))

dds <- estimateSizeFactors(dds) # run this or DESeq() first
head(counts(dds, normalized=TRUE))

DESeq2 documentation built on Feb. 22, 2021, 10 a.m.