INNER CODE UNIT · Python
vst_fit
scverse/PyDESeq2 · src/pydeseq2/dds.py:342
def vst_fit(
self,
use_design: bool = False,
) -> None:
"""Fit a variance stabilizing transformation.
This method should be called before `vst_transform`.
Results are stored in ``dds.layers["vst_counts"]``.
Parameters
----------
use_design
Whether to use the full design matrix to fit dispersions and the trend curve.
If False, only an intercept is used.
Only useful if ``fit_type = "parametric"`. (default: ``False``).
"""
# Start by fitting median-of-ratio size factors if not already present,