snapatac2.pp.filter_doublets#

snapatac2.pp.filter_doublets(adata, probability_threshold=0.5, score_threshold=None, inplace=True, n_jobs=8, verbose=True)[source]#

Remove doublets. scrublet() must be ran first in order to use this function.

Parameters:

  • adata (AnnData | list[AnnData]) – The (annotated) data matrix of shape n_obs x n_vars. Rows correspond to cells and columns to regions.

  • probability_threshold (Optional[float]) – Threshold for doublet probability.

  • score_threshold (Optional[float]) – Threshold for doublet score.

  • inplace (bool) – Perform computation inplace or return result.

  • n_jobs (int) – Number of jobs to run in parallel.

  • verbose (bool) – Whether to print progress messages.

Returns:

If inplace = True, directly subsets the data matrix. Otherwise return a boolean index mask that does filtering, where True means that the cell is kept, False means the cell is removed.

Return type:

np.ndarray | None