grassp.pp.remove_contaminants

remove_contaminants(data, filter_columns=None, filter_value=None, inplace=True)

Remove contaminant proteins from the data matrix.

Parameters:

data AnnData

The annotated data matrix with proteins as observations (rows).

filter_columns Optional[List[str]] (default: None)

Column names in data.obs to use for filtering contaminants. If None, uses columns specified in data.uns[‘RawInfo’][‘filter_columns’].

filter_value Optional[str] (default: None)

If provided, first convert filter columns to boolean by comparing to this value. If None, assumes filter columns are already boolean.

inplace bool (default: True)

Whether to modify data in place or return a copy.

Return type:

AnnData | None

Returns:

AnnData or None If inplace=False, returns filtered data. If inplace=True, returns None.