# A Hidden Markov Model for high throughput genotyping arrays

## Documentation for package ‘VanillaICE’ version 1.6.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

breaks | Identify breakpoints from the hidden Markov model predictions
copynumberEmission | Emission probabilities for copy number
genotypeEmission | Emission probabilities for di-allelic genotype calls
genotypeEmissionCrlmm | Estimate the emission probabilities using confidence scores from CRLMM
hmm | Wrapper for fitting the HMM
locusLevelData | Basic data elements required for the HMM
transitionProbability | Compute the transition probability
viterbi | viterbi algorithm