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.
"counts"(object, normalized = FALSE, replaced = FALSE)"counts"(object) <- value
- logical indicating whether or not to divide the counts by the size factors or normalization factors before returning (normalization factors always preempt size factors)
- after a
DESeqcall, this argument will return the counts with outliers replaced instead of the original counts, and optionally
normalized. The replaced counts are stored by
- an integer matrix
dds <- makeExampleDESeqDataSet(m=4) head(counts(dds)) dds <- estimateSizeFactors(dds) # run this or DESeq() first head(counts(dds, normalized=TRUE))
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