ALLCools.dmr

Package Contents

call_dmr(output_dir, replicate_label=None, p_value_cutoff=0.001, frac_delta_cutoff=0.2, max_dist=250, residual_quantile=0.6, corr_cutoff=0.3, dms_ratio=0.8, cpu=1, chrom=None)[source]

Call DMR from DMS results.

Parameters
  • output_dir

  • replicate_label

  • p_value_cutoff

  • frac_delta_cutoff

  • max_dist

  • residual_quantile

  • corr_cutoff

  • dms_ratio

  • cpu

  • chrom

collapse_replicates(region_ds, replicate_label, state_da='dmr_state')[source]
call_dms(output_dir, allc_paths, samples, chrom_size_path, cpu=1, max_row_count=50, n_permute=3000, min_pvalue=0.01, region=None)

Call DMS from multiple ALLC files

Parameters
  • output_dir

  • allc_paths

  • samples

  • chrom_size_path

  • cpu

  • max_row_count

  • n_permute

  • min_pvalue

  • region

methylpy_to_region_ds(dmr_path, output_dir)[source]