INNER CODE UNIT · Python

cooks_outlier

scverse/PyDESeq2 · src/pydeseq2/dds.py:1026

    def cooks_outlier(self):
        """Filter p-values based on Cooks outliers."""
        if "_pvalue_cooks_outlier" in self.var.keys():
            return self.var["_pvalue_cooks_outlier"]

        num_samples = self.n_obs
        num_vars = self.obsm["design_matrix"].shape[-1]
        cooks_cutoff = f.ppf(0.99, num_vars, num_samples - num_vars)

        # As in DESeq2, only take samples with 3 or more replicates when looking for
        # max cooks.
        use_for_max = n_or_more_replicates(self.obsm["design_matrix"], 3)

        # If for a gene there are 3 samples or more that have more counts than the
        # maximum cooks sample, don't count this gene as an outlier.

        # Take into account whether we already replaced outliers
        if (

View source record →