muon.atac.tl.count_fragments_features#

muon.atac.tl.count_fragments_features(data: Union[anndata._core.anndata.AnnData, mudata._core.mudata.MuData], features: Optional[pandas.core.frame.DataFrame] = None, extend_upstream: int = 2000.0, extend_downstream: int = 0) anndata._core.anndata.AnnData#

Count fragments overlapping given Features. Returns cells x features matrix.

data

AnnData object with peak counts or multimodal MuData object with ‘atac’ modality.

features

A DataFrame with feature annotation, e.g. genes. Annotation has to contain columns: Chromosome, Start, End.

extend_upsteam

Number of nucleotides to extend every gene upstream (2000 by default to extend gene coordinates to promoter regions)

extend_downstream

Number of nucleotides to extend every gene downstream (0 by default)