genotypeEmission {VanillaICE}R Documentation

Emission probabilities for di-allelic genotype calls

Description

Emission probabilities for di-allelic genotype calls

Usage

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

Arguments

genotypes matrix of integers (1=AA, 2=AB, 3=BB, 4=other)
conf Confidence estimates of the genotype calls obtained from crlmm (optional).
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

CRLMM provides confidences estimates of the genotype calls that can be integrated to improve the HMM. Because CRLMM will genotype all SNPs, the probMissing argument is unecessary.

Value

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

[Package VanillaICE version 1.6.0 Index]