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zinb-peakcaller's Introduction

ZINB Peak Caller

Peak caller based on the Zero Inflated Negative Binomial (ZINB) distribution Cusco &al 2016 Bioinformatics.

The algorithm works in two phases:

  1. Fit the distribution parameters on the entire vector by using multiple random initialization.
  2. Fit the distribution parameters on widows of size WS using the optimization on the entire vector as initialization.

How to use

To get a binary vector with a threshold at a p-value of

vectB = Peaks_Caller(vect)

To get the p-value vector

vectB = Peaks_Caller(vect,getPval=True)

Note: By default, the distribution parameters inside windows are computed in parallel, using all the cores of the machine (Ncore=-1).

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