Analysis of histone modification data using a HMM

Documentation for package ‘histoneHMM’ version 1.8

histoneHMM-package	Analysis of histone modification data using a HMM
callRegions	call regions from a posterior matrix
Distribution-class	Class 'Distribution'
dzinba	Zero inflated negative binomial distribution
dzinba.copula	Density, CDF and random number generation from a bivariate zinba copula
em	Expectation maximization algorithm
EMResult-class	Expectation maximization algorithm
fit-method	Class 'Distribution'
fit.zinba.copula	Maximum likelihood fit of the zinba copula distribution
fitzinba	Fit parameters of a zero inflated negative binomial distribution
histoneHMM	Analysis of histone modification data using a HMM
hmm.posterior	HMM posterior
hmm.viterbi	Viterbi algorithm
logLikelihood-method	Class 'Distribution'
LogNormal-class	Class 'Distribution'
pzinba	Zero inflated negative binomial distribution
pzinba.copula	Density, CDF and random number generation from a bivariate zinba copula
run.bivariate.hmm	Bivariate HMM analysis
run.univariate.hmm	Univariate HMM analysis
rzinba	Zero inflated negative binomial distribution
rzinba.copula	Density, CDF and random number generation from a bivariate zinba copula
Zinba-class	Class 'Distribution'
zinba.hmm.posterior	Compute state posterior probabilities for a HMM with zinba emission distributions.
zinbacopula.hmm.posterior	State posterior probabilities for a HMM with zinba copula emission probabilities