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muon.atac.tl.nucleosome_signal

muon.atac.tl.nucleosome_signal#

muon.atac.tl.nucleosome_signal(data: AnnData | MuData, n: int | float = None, nucleosome_free_upper_bound: int = 147, mononuleosomal_upper_bound: int = 294, barcodes: str | None = None)#

Computes the ratio of nucleosomal cut fragments to nucleosome-free fragments per cell. Nucleosome-free fragments are shorter than 147 bp while mono-mucleosomal fragments are between 147 bp and 294 bp long.

Parameters:

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

  • n – Number of fragments to count. If None, 1e4 fragments * number of cells.

  • nucleosome_free_upper_bound – Number of bases up to which a fragment counts as nucleosome free. Default: 147

  • mononuleosomal_upper_bound – Number of bases up to which a fragment counts as mononuleosomal. Default: 294

  • barcodes – Column name in the .obs of the AnnData with barcodes corresponding to the ones in the fragments file.

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