ALLCools.count_matrix.dataset

Module Contents

ALLOW_QUANT_TYPES = ['count', 'hypo-score', 'hyper-score'][source]
bin_sf(cov, mc, p)[source]
cell_sf(cell_count_df)[source]
class Quant(mc_types, quant_type, kwargs)[source]
class CountQuantifier(mc_types)[source]

Sum count by mC type for single region in single ALLC

read_line(self, line)[source]
summary(self)[source]
determine_datasets(regions, quantifiers, chrom_size_path, tmp_dir)[source]
count_single_region_set(allc_table, region_config, obs_dim, region_dim)[source]

Get cell-by-region-by-mc_types count matrix, save to zarr

calculate_pv(data, reverse_value, obs_dim, var_dim, cutoff=0.9)[source]
count_single_zarr(allc_table, region_config, obs_dim, region_dim, output_path, obs_dim_dtype, count_dtype='uint32')[source]

process single region set and its quantifiers

generate_dataset(allc_table, output_path, regions, quantifiers, chrom_size_path, obs_dim='cell', cpu=1, chunk_size=None)[source]

{generate_dataset_doc}

Parameters
  • allc_table – {allc_table_doc}

  • output_path – Output path of the MCDS dataset

  • regions – {regions_doc}

  • quantifiers – {quantifiers_doc}

  • chrom_size_path – {chrom_size_path_doc}

  • obs_dim – {obs_dim_doc}

  • cpu – {cpu_basic_doc}

  • chunk_size – {chunk_size_doc}

Returns

Return type

output_path