muon.atac.tl.count_fragments_features
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)