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.


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install.packages("PeakSegDP")

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