counts,DESeqDataSet-method {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, 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))

[Package DESeq2 version 1.32.0 Index]