CHMM (version 0.1.1)

Coupled Hidden Markov Models

Description

An exact and a variational inference for coupled Hidden Markov Models applied to the joint detection of copy number variations.

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Install

install.packages('CHMM')

Monthly Downloads

190

Version

0.1.1

License

GPL-2

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Repository

http://github.com/julieaubert/CHMM

Maintainer

J Aubert

Last Published

September 29th, 2017

Functions in CHMM (0.1.1)

CHMM_VEM

Perform variational inference of coupled Hidden Markov Models.

Emis.Gauss

coupledHMM

Perform inference of coupled hidden markov models.

init.EM

Initialization step of the CHMM_EM function.

Wl Internal function calculating Wl.

clusterseg

Summarize the results of the coupled HMM.

init.VEM

Initialization step of the CHMM_VEM function.

toydata

Toy example - observations for 5 correlated samples.

BackwardR

Backward step

CHMM_EM

Perform exact inference of coupled hidden markov models.

toystatus

Toy example - status for 5 correlated samples.

viterbi_algo

Implementation of the Viterbi algorithm

ForwardR

Forward step

ExpGrid

Wl Internal function calculating Wl.

Emis.LRR

EmisGb.Gauss