INNER CODE UNIT · Python

__init__

scverse/PyDESeq2 · src/pydeseq2/dds.py:164

    def __init__(
        self,
        *,
        adata: ad.AnnData | None = None,
        counts: pd.DataFrame | None = None,
        metadata: pd.DataFrame | None = None,
        design: str | pd.DataFrame = "~condition",
        design_factors: str | list[str] | None = None,
        continuous_factors: list[str] | None = None,
        ref_level: list[str] | None = None,
        fit_type: Literal["parametric", "mean"] = "parametric",
        size_factors_fit_type: Literal["ratio", "poscounts", "iterative"] = "ratio",
        control_genes: np.ndarray | list[str] | list[int] | pd.Index | None = None,
        min_mu: float = 0.5,
        min_disp: float = 1e-8,
        max_disp: float = 10.0,
        refit_cooks: bool = True,
        min_replicates: int = 7,

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