INNER CODE UNIT · Python

fit_LFC

scverse/PyDESeq2 · src/pydeseq2/dds.py:899

    def fit_LFC(self) -> None:
        """Fit log fold change (LFC) coefficients.

        In the 2-level setting, the intercept corresponds to the base mean, while the second is the actual LFC coefficient, in natural log scale.
        """
        # Check that MAP dispersions are available. If not, compute them.
        if "dispersions" not in self.var:
            self.fit_MAP_dispersions()

        # Convert design matrix to numpy for speed
        design_matrix = self.obsm["design_matrix"].values

        if not self.quiet:
            print("Fitting LFCs...", file=sys.stderr)
        start = time.time()
        mle_lfcs_, mu_, hat_diagonals_, converged_ = self.inference.irls(
            counts=self.X[:, self.non_zero_idx],
            size_factors=self.obs["size_factors"].to_numpy(),

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