cellspec.pp.filter_variants

cellspec.pp.filter_variants(adata, min_cells=None, min_fraction=None, inplace=True)

Filter variants based on presence across cells/samples.

Parameters:

• adata (ad.AnnData) – AnnData object with variants

• min_cells (int, optional) – Minimum number of cells/samples a variant must be present in

• min_fraction (float, optional) – Minimum fraction of cells/samples a variant must be present in (0-1)

• inplace (bool, default True) – Modify adata in place or return copy

Return type:

AnnData | None

Returns:

ad.AnnData or None Filtered AnnData (if inplace=False), otherwise None

Examples

>>> import cellspec as spc
>>> # Keep variants present in at least 3 cells
>>> spc.pp.filter_variants(adata, min_cells=3)

>>> # Keep variants present in at least 1% of cells
>>> spc.pp.filter_variants(adata, min_fraction=0.01)

Notes

Presence is determined by .X (binary presence/absence matrix).