HiConfidence

This package helps to construct confidence matrices for Hi-C replicates

Usage

1. Generate Confidence matrix for the pair of replicates:

calculate_confidence(Hi-C_matrix_rep1,Hi-C_matrix_rep2,k_parameter)

2. Choose the best parameter k based on correlation of IS with window_size:

choose_k(Hi-C_reps_file_names)

3. Construct chromatin profile in the area around averaged TADs boundary using correction for replicates' confidence:

average_tad(Hi-C_reps_file_names, k_parameter, tads_positions, area_size)

4. Generate Hi-C maps in lower resolution using correction for replicates' confidence:

downsampling(Hi-C_reps_file_names, k_parameter, factor, output_file_name)

See test_example.py for more examples.