schicluster.compartment.call_compartment

Module Contents

get_cpg_profile(fasta_path, hdf_output_path, cell_url=None, chrom_size_path=None, resolution=100000)

compartment_strength(matrix, comp, cpg_ratio)

single_chrom_compartment(matrix, cpg_ratio, calc_strength=False)

single_cell_compartment(cell_url, cpg_profile, calc_strength, output_prefix, mode, resolution, chrom_sizes, chrom1, pos1, chrom2, pos2)

aggregate_compartment(cell_table, temp_dir, bins, output_path, calc_strength)

multiple_cell_compartment(cell_table_path, output_prefix, cpg_profile_path, cpu=10, calc_strength=False, mode='cool', chrom_size_path=None, resolution=100000, chrom1=1, pos1=2, chrom2=5, pos2=6)