snapatac2.pp.call_cells#

snapatac2.pp.call_cells(data, use_rep, inplace=True, n_jobs=8)[source]#

Calling cells based on the number of feature counts.

This implements Cell Ranger’s [cell calling algorithm](https://www.10xgenomics.com/support/software/cell-ranger/latest/algorithms-overview/cr-gex-algorithm), which is based on two primary algorithms: Order of magnitude (OrdMag) and EmptyDrops.

Currently only OrdMag is implemented.

Parameters:

  • data (AnnData | list[AnnData]) – The (annotated) data matrix of shape n_obs x n_vars. Rows correspond to cells and columns to regions. data can also be a list of AnnData objects. In this case, the function will be applied to each AnnData object in parallel.

  • use_rep (str | ndarray[float]) – The representation to use for filtering. This can be a string or a numpy array.

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

  • n_jobs (int) – Number of parallel jobs to use when data is a list.

Returns:

If inplace = True, directly subsets the data matrix. Otherwise return indices of cells that pass the filtering.

Return type:

np.ndarray | None

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