schicluster.loop.merge_cell_to_group

Module Contents

merge_cells_for_single_chromosome(output_dir, output_prefix, merge_type='E')

Merge cell’s E and T matrix to group matrices, sum only, not normalized by n_cells yet E: Matrix normalized by global diagonal backgrounds, calculated from loop_bkg E2: Sum of square of E, used to calculate global t statistics T: Matrix normalized by global diagonal and local backgrounds, then minus E (T is the delta matrix), calculated from loop_bkg T2: Sum of square of T, used to calculate local t statistics

read_single_cool_chrom(cool_path, chrom, chrom2=None)

chrom_sum_iterator(input_cool_list, chrom_sizes, chrom_offset, total_cells)

save_single_matrix_type(input_cool_list, output_cool, bins_df, chrom_sizes, chrom_offset, total_cells)

merge_cool(input_cool_tsv_file, output_cool)

merge_group_chunks_to_group_cools(chrom_size_path, resolution, group, output_dir, matrix_types=('E', 'E2', 'T', 'T2', 'Q', 'Q2'))

merge_group_to_bigger_group_cools(chrom_size_path, resolution, group, output_dir, group_list, shuffle, matrix_types=('E', 'E2', 'T', 'T2', 'Q', 'Q2'))

Sum all the group average cool files, and finally divide the total number of cells to get a group cell number normalized cool file in the end.