muon.atac.tl.fetch_regions_to_df

muon.atac.tl.fetch_regions_to_df(fragment_path: str, features: DataFrame | str, extend_upstream: int = 0, extend_downstream: int = 0, relative_coordinates=False) → DataFrame

Parse peak annotation file and return it as DataFrame.

Parameters:

• fragment_path – Location of the fragments file (must be tabix indexed).

• features – A DataFrame with feature annotation, e.g. genes or a string of format chr1:1-2000000 or`chr1-1-2000000`. 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)

• relative_coordinates – Return the coordinates with their relative position to the middle of the features.