# Analysis of histone modification data using a HMM

## Documentation for package ‘histoneHMM’ version 1.7

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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