ALLCools.clustering.doublets.coverage_doublets
Contents
ALLCools.clustering.doublets.coverage_doublets¶
Module Contents¶
- _calculate_cell_record(allc_path, output_path, cov_cutoff=2, resolution=100)[source]¶
Count the high coverage bins for each cell, save results to json
- calculate_blacklist_region(region_records, alpha=0.01)[source]¶
Collect highly covered regions by region-wise poisson FDR p value < alpha
- _calculate_cell_final_values(output_path, region_blacklist)[source]¶
Calculate final cell values while remove blacklist
- coverage_doublets(allc_dict: dict, resolution: int = 100, cov_cutoff=2, region_alpha=0.01, tmp_dir='doublets_temp_dir', cpu=1, keep_tmp=False)[source]¶
Quantify cell high coverage bins for doublets evaluation
- Parameters
allc_dict – dict with cell_id as key, allc_path as value
resolution – genome bin resolution to quantify, bps
cov_cutoff – cutoff the cov, sites within cov_cutoff < cov <= 2 * cov_cutoff will be count
region_alpha – FDR adjusted P-value cutoff
tmp_dir – temporary dir to save the results
cpu – number of cpu to use
keep_tmp – Whether save the tem_dir for debugging