counts

0th

Percentile

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

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

Aliases
  • counts
  • counts,DESeqDataSet-method
  • counts<-,DESeqDataSet,matrix-method
Examples

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

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

Documentation reproduced from package DESeq2, version 1.12.3, License: LGPL (>= 3)

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