snapatac2.pp.call_doublets#

snapatac2.pp.call_doublets(adata, threshold='gmm', random_state=0, inplace=True)[source]#

Find doublet score threshold for calling doublets. pp.scrublet must be run first.

Parameters

  • adata (AnnData) – AnnData object

  • threshold (str | float) –

    Mannually specify a threshold or use one of the default methods to automatically identify a threshold:

    • ’gmm’: fit a 2-component gaussian mixture model.

    • ’scrublet’: the method used in the scrublet paper (not implemented).

  • random_state (int) – Random state

  • inplace (bool) – Whether update the AnnData object inplace

Returns

if inplace = True, it updates adata with the following fields:

  • adata.obs["is_doublet"]: boolean mask

  • adata.uns["scrublet"]["threshold"]: saved threshold

Return type

tuple[np.ndarray, float] | None