Coupled Hidden Markov Models
This package implements an exact and a variational inference for coupled Hidden Markov Models applied to the joint detection of copy number variations.
You can install the released version of CHMM from CRAN with:
install.packages("CHMM")This is a toy example (1 000 positions of 5 correlated samples) which shows you how to use the package.
data(toyexample)
# Variational inference of a coupled hidden Markov Chains
resCHMM <- coupledHMM(X = toydata, nb.states = 3, S = cor(toystatus),
omega.list = c(0.3, 0.5, 0.7, 0.9))
# Breakpoints positions and status of segments
info <- clusterseg(resCHMM$status)
Wang, Xiaoqiang, Lebarbier, Emilie, Aubert, Julie and Robin, Stéphane. "Variational Inference for Coupled Hidden Markov Models Applied to the Joint Detection of Copy Number Variations" The International Journal of Biostatistics, vol. 15, no. 1, 2019, pp. 20180023. https://doi.org/10.1515/ijb-2018-0023
Aubert, Julie, Wang, Xiaoqiang, Lebarbier, Emilie, Robin, Stéphane. "CHMM : an R package for coupled Hidden Markov Models". R User Conference 2017, Jul 2017, Bruxelles, Belgium. ⟨hal-01661257⟩