rapids_singlecell.pp.filter_cells

rapids_singlecell.pp.filter_cells(adata, *, qc_var, min_count=None, max_count=None, verbose=True)

Filter cell outliers based on counts and numbers of genes expressed.

Filter cells based on numerical columns in the obs by selecting those with a feature count greater than a specified maximum or less than a specified minimum. It is recommended to run calculate_qc_metrics() before using this function. You can run this function on n_genes or n_counts before running calculate_qc_metrics().

Parameters:

adata AnnData

AnnData object

qc_var str

column in .obs with numerical entries to filter against

min_count float (default: None)

Lower bound on number of a given feature to keep cell

max_count float (default: None)

Upper bound on number of a given feature to keep cell

verbose bool (default: True)

Print number of discarded cells

Return type:

None

Returns:

a filtered AnnData object inplace