schicluster.loop

loop_bkg.py corresponding to draft/loop_bkg_cell, which calculates E and T from cell imputed matrix merge_cell_to_group.py corresponding to loop_sumcell_chr, which aggregates the cell E, T to cluster level E, E2, T, T2, O,

Submodules

• schicluster.loop.compare_loop
• schicluster.loop.loop_bkg
• schicluster.loop.loop_calling
• schicluster.loop.merge_cell_to_group
• schicluster.loop.merge_group
• schicluster.loop.merge_raw_matrix
• schicluster.loop.shuffle_fdr
• schicluster.loop.snakemake

Package Contents

call_loop(cell_table_path, output_dir, chrom_size_path, shuffle=True, chunk_size=200, dist=5050000, cap=5, pad=5, gap=2, resolution=10000, min_cutoff=1e-06, keep_cell_matrix=False, cpu_per_job=10, log_e=True, raw_resolution_str=None, downsample_shuffle=None, black_list_path=None, fdr_pad=7, fdr_min_dist=5, fdr_max_dist=500, fdr_thres=0.1, dist_thres=20000, size_thres=1, cleanup=True)