genotypeEmission {VanillaICE}R Documentation

Emission probabilities for di-allelic genotype calls

Description

Emission probabilities for di-allelic genotype calls

Usage

genotypeEmission(genotypes, states, probHomCall, probMissing, verbose=TRUE)

Arguments

genotypes matrix of integers (1=AA, 2=AB, 3=BB, 4=other)
states character string of hidden states
probHomCall numeric: probability of a homozygous genotype call specified in the same order as the hidden states
probMissing numeric: probability of a missing genotype call specified in the same order as the hidden states
verbose logical

Details

By default, missing genotype calls will be assumed to be independent of the hidden state. This is not always appropriate, but is easiest to implement in terms of a default.

Value

array Array of emission probabilities. Dimension 1: SNPs, Dimension 2: samples, Dimension3: states

[Package VanillaICE version 1.4.0 Index]