inmoose.deseq2.DESeqDataSet.DESeqDataSet.counts

DESeqDataSet.counts(normalized=False, replaced=False)

Accessor for the counts of a DESeqDataSet, which are stored as a matrix of non-negative integer, with one row per observation and one column per feature.

Parameters:

• normalized (bool, optional) – Flag indicating whether to divide the counts by the size factors or normalization factors before returning. Normalization factors (if present) always preempt size factors.

• replaced (bool, optional) – Flag indicating whether to return the counts with outliers replaced instead of the original counts. This flag is meaningful only after a call to DESeq().

Returns:

the count data, possibly normalized, possibly with outliers replaced

Return type:

ndarray