MACS3.Signal.HMMR_Signal_Processing module

Module description:

This code is free software; you can redistribute it and/or modify it under the terms of the BSD License (see the file LICENSE included with the distribution).

MACS3.Signal.HMMR_Signal_Processing.extract_signals_from_regions(signals, regions, binsize=10, hmm_type='gaussian')

Return type:

list

MACS3.Signal.HMMR_Signal_Processing.generate_digested_signals(petrack, weight_mapping)

Generate digested pileup signals (four tracks) using weight mapping

Return type:

list

return: list of four signals in dictionary, with key as chromosome name and value as a p-v array.

ret[0] – dictionary for short ret[1] – dictionary for mono ret[2] – dictionary for di ret[3] – dictionary for tri

MACS3.Signal.HMMR_Signal_Processing.generate_weight_mapping(fraglen_list, means, stddevs, min_frag_p=0.001)

Generate weights for each fragment length in short, mono, di, and tri-signals track

return: list of four dictionaries, with key as fraglen and value as the weight.

ret[0] – dictionary for short ret[1] – dictionary for mono ret[2] – dictionary for di ret[3] – dictionary for tri

Return type:

list

MACS3.Signal.HMMR_Signal_Processing.get_weighted_density(x, m, v, w)

Description:

Parameters:

• x (1.) – the observed value

• m (2.) – the mean of gaussian

• v (3.) – the variance of the gaussian

• w (4.) – the weight

Return type:

typedef

return value: