INNER CODE UNIT · Python

_fit_MoM_dispersions

scverse/PyDESeq2 · src/pydeseq2/dds.py:1099

    def _fit_MoM_dispersions(self) -> None:
        """Rough method of moments initial dispersions fit.

        Estimates are the max of "robust" and "method of moments" estimates.
        """
        # Check that size_factors are available. If not, compute them.
        if "normed_counts" not in self.layers:
            self.fit_size_factors(fit_type=self.size_factors_fit_type)

        normed_counts = self.layers["normed_counts"][:, self.non_zero_idx]
        rde = self.inference.fit_rough_dispersions(
            normed_counts,
            self.obsm["design_matrix"].values,
        )
        mde = self.inference.fit_moments_dispersions(
            normed_counts, self.obs["size_factors"].to_numpy()
        )
        alpha_hat = np.minimum(rde, mde)

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