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]