INNER CODE UNIT · Python

calculate_cooks

scverse/PyDESeq2 · src/pydeseq2/dds.py:947

    def calculate_cooks(self) -> None:
        """Compute Cook's distance for outlier detection.

        Measures the contribution of a single entry to the output of LFC estimation.
        """
        # Check that MAP dispersions are available. If not, compute them.
        if "dispersions" not in self.var:
            self.fit_MAP_dispersions()

        if not self.quiet:
            print("Calculating cook's distance...", file=sys.stderr)

        start = time.time()
        num_vars = self.obsm["design_matrix"].shape[-1]

        # Calculate dispersion
        dispersions = robust_method_of_moments_disp(
            self.layers["normed_counts"][:, self.var["non_zero"]],

View source record →