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]