INNER CODE UNIT · Python

refit

scverse/PyDESeq2 · src/pydeseq2/dds.py:1003

    def refit(self) -> None:
        """Refit Cook outliers.

        Replace values that are filtered out based on the Cooks distance with imputed values, and then re-run the whole DESeq2 pipeline on replaced values.
        """
        # Replace outlier counts
        self._replace_outliers()
        if not self.quiet:
            print(
                f"Replacing {sum(self.var['replaced'])} outlier genes.\n",
                file=sys.stderr,
            )

        if sum(self.var["replaced"]) > 0:
            # Refit dispersions and LFCs for genes that had outliers replaced
            self._refit_without_outliers()
        else:
            # Store the fact that no sample was refitted

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