hmm_peaks

make_peaks.hmm_peaks(z_scores, i_to_p=1 / 1000, p_to_p=1 / 1.5, peak_center=10, spread=2)

Fit peaks to the provided z_scores data set using the vertibi algorithm.

Parameters

Name	Type	Description	Default
z_scores		(2xn array) required: first column is position (ie bp location) second column is a modified z_score for that position.	required
i_to_p		(float) value should be between zero and 1, represents probability of transitioning from inernal state to peak state. The default value is 1/2000, based on asseumption of geometrically distributed transcript lengths with mean length 1000. Should be a robust parameter.	1 / 1000
p_to_p		(float) The probability of a peak to peak transition. Default 1/1.5.	1 / 1.5
peak_center		(float) the mean of the emission probability distribution for the peak state.	10
spread		(float) the standard deviation of the peak emmission distribution.	2

Returns

Type	Description
peaks:	(2xn array) with the first column being position and the second column being a peak assignment.