ALLCools.dmr
Contents
ALLCools.dmr
¶
Submodules¶
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 –
- 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 –