ALLCools.count_matrix.mcad

Module Contents

_read_region_bed(bed_path)[source]
bin_sf(cov, mc, p)[source]
_count_single_allc(allc_path, bed_path, mc_pattern, output_dir, cutoff=0.9, reverse_value=False)[source]
generate_mcad(allc_table, bed_path, output_prefix, mc_context, cpu=1, cleanup=True, cutoff=0.9, reverse_value=False)[source]
Parameters
  • allc_table – {allc_table_doc}

  • bed_path – {bed_path_doc}

  • cpu – {cpu_doc}

  • output_prefix – Output prefix of the MCAD, a suffix “.mcad” will be added.

  • mc_context – {mc_context_doc}

  • cleanup – Whether remove temp files or not

  • cutoff – Values smaller than cutoff will be stored as 0, which reduces the file size

  • reverse_value – If true, use cdf instead of sf to make hyper-methylation events having higher values