DESeq2: counts – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

counts

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, 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

Examples

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

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

DESeq2

Differential gene expression analysis based on the negative binomial distribution

v1.30.1

LGPL (>= 3)

Authors

Michael Love [aut, cre], Constantin Ahlmann-Eltze [ctb], Kwame Forbes [ctb], Simon Anders [aut, ctb], Wolfgang Huber [aut, ctb]

Initial release