INNER CODE UNIT · Python
deseq2
scverse/PyDESeq2 · src/pydeseq2/dds.py:474
def deseq2(self, fit_type: Literal["parametric", "mean"] | None = None) -> None:
"""Perform dispersion and log fold-change (LFC) estimation.
Wrapper for the first part of the PyDESeq2 pipeline.
Parameters
----------
fit_type
Either None, ``"parametric"`` or ``"mean"`` for the type of fitting of dispersions to the mean intensity.``"parametric"``: fit a dispersion-mean relation via a robust gamma-family GLM. ``"mean"``: use the mean of gene-wise dispersion estimates.
If None, the fit_type provided at class initialization is used. (default: ``None``).
"""
if fit_type is not None:
self.fit_type = fit_type
if not self.quiet:
print(f"Using {self.fit_type} fit type.")