INNER CODE UNIT · Python
vst
scverse/PyDESeq2 · src/pydeseq2/dds.py:308
def vst(
self,
use_design: bool = False,
fit_type: Literal["parametric", "mean"] | None = None,
) -> None:
"""Fit a variance stabilizing transformation, and apply it to normalized counts.
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. (default: ``False``).
fit_type
* ``None``: fit_type provided at initialization to fit
the dispersions trend curve.
* ``"parametric"``: fit a dispersion-mean relation via a robust