DESeq2 (version 1.12.3)

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

"counts"(object, normalized = FALSE, replaced = FALSE)
"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

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))