INNER CODE UNIT · Python

contrast

scverse/PyDESeq2 · src/pydeseq2/dds.py:540

    def contrast(self, *args, **kwargs):
        """Get a contrast for a simple pairwise comparison."""
        try:
            return self.formulaic_contrasts.contrast(*args, **kwargs)
        except AttributeError:
            raise AttributeError(
                "The contrast() method requires a formula-based design. "
                "When using a precomputed design matrix (DataFrame), "
                "pass the contrast vector directly instead."
            ) from None

    def fit_size_factors(
        self,
        fit_type: Literal["ratio", "poscounts", "iterative"] | None = None,
        control_genes: np.ndarray | list[str] | list[int] | pd.Index | None = None,
    ) -> None:
        """Fit sample-wise deseq2 normalization (size) factors.

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