INNER CODE UNIT · Python
fit_MAP_dispersions
scverse/PyDESeq2 · src/pydeseq2/dds.py:848
def fit_MAP_dispersions(self) -> None:
"""Fit Maximum a Posteriori dispersion estimates.
After MAP dispersions are fit, filter genes for which we don't apply shrinkage.
"""
# Check that the dispersion prior variance is available. If not, compute it.
if "prior_disp_var" not in self.uns:
self.fit_dispersion_prior()
# Convert design matrix to numpy for speed
design_matrix = self.obsm["design_matrix"].values
if not self.quiet:
print("Fitting MAP dispersions...", file=sys.stderr)
start = time.time()
dispersions_, l_bfgs_b_converged_ = self.inference.alpha_mle(
counts=self.X[:, self.non_zero_idx],
design_matrix=design_matrix,