dynamo.pp.filter_genes_by_pattern¶

dynamo.pp.filter_genes_by_pattern(adata, patterns=('MT-', 'RPS', 'RPL', 'MRPS', 'MRPL', 'ERCC-'), drop_genes=False)[source]¶

Utility function to filter mitochondria, ribsome protein and ERCC spike-in genes, etc.

Parameters:

adata (AnnData) – an AnnData object.
patterns (Tuple[str] (default: ('MT-', 'RPS', 'RPL', 'MRPS', 'MRPL', 'ERCC-'))) – the patterns used to filter genes. Defaults to (“MT-”, “RPS”, “RPL”, “MRPS”, “MRPL”, “ERCC-“).
drop_genes (bool (default: False)) – whether inplace drop the genes from the AnnData object. Defaults to False.

Return type:

Optional[List[bool]]

Returns:

A list of indices of matched genes if drop_genes is False. Otherwise, returns none.