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

In aghozlane/DESeq2shaman: 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)

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

## S4 method for signature 'DESeqDataSet'
counts(object, normalized = 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)
value	an integer matrix

Author(s)

Simon Anders

See Also

sizeFactors, normalizationFactors

Examples

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

aghozlane/DESeq2shaman documentation built on Nov. 1, 2019, 9:01 p.m.