ALLCools.dmr.call_dmr

Module Contents

_call_dmr_single_chrom(dms_dir, output_dir, chrom, 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)[source]

Call DMR for single chromosome, see call_dmr for doc

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]