Dynamic Programming Algorithm for Peak Detection in ChIP-Seq Data

A quadratic time dynamic programming algorithm can be used to compute an approximate solution to the problem of finding the most likely changepoints with respect to the Poisson likelihood, subject to a constraint on the number of segments, and the changes which must alternate: up, down, up, down, etc. For more info read < http://proceedings.mlr.press/v37/hocking15.html> "PeakSeg: constrained optimal segmentation and supervised penalty learning for peak detection in count data" by TD Hocking et al, proceedings of ICML2015.


Reference manual

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2017.08.15 by Toby Dylan Hocking, 3 months ago

Browse source code at https://github.com/cran/PeakSegDP

Authors: Toby Dylan Hocking, Guillem Rigaill

Documentation:   PDF Manual  

GPL-3 license

Suggests ggplot2, testthat, penaltyLearning

Suggested by PeakSegOptimal.

See at CRAN