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.

  • 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.