A Hidden Markov Model for high throughput genotyping arrays

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Documentation for package ‘VanillaICE’ version 1.6.0

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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