INNER CODE UNIT · Python
DeseqDataSet
scverse/PyDESeq2 · src/pydeseq2/dds.py:36
class DeseqDataSet(ad.AnnData):
r"""A class to implement dispersion and log fold-change (LFC) estimation.
The DeseqDataSet extends the `AnnData class <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.html#anndata.AnnData>`_.
As such, it implements the same methods and attributes, in addition to those that are specific to pydeseq2.
Dispersions and LFCs are estimated following the DESeq2 pipeline :cite:p:`DeseqDataSet-love2014moderated`.
Parameters
----------
adata
AnnData from which to initialize the DeseqDataSet.
Must have counts ('X') and sample metadata ('obs') fields.
If ``None``, both ``counts`` and ``metadata`` arguments must be provided.
counts
Raw counts.
One column per gene, rows are indexed by sample barcodes.
metadata
DataFrame containing sample metadata.