polyRAD (version 1.6)

AddGenotypePosteriorProb: Estimate Posterior Probabilities of Genotypes

Description

Given a "RADdata" object containing genotype prior probabilities and genotype likelihoods, this function estimates genotype posterior probabilities and adds them to the $posteriorProb slot of the object.

Usage

AddGenotypePosteriorProb(object, ...)

Value

A "RADdata" object identical to that passed to the function, but with a list added to the $posteriorProb slot. Each item of the list is a three dimensional array, with allele copy number in the first dimension, taxa in the second dimension, and alleles in the third dimension. For each allele and taxa, posterior probabilities will sum to one across all potential allele copy numbers. There will be one such array for each possible ploidy, corresponding to object$priorProb.

Arguments

object

A "RADdata" object. Prior genotype probabilities and genotype likelihood should have already been added.

...

Potential future arguments (none currently in use).

Author

Lindsay V. Clark

Details

If AddPriorTimesLikelihood has not already been run on the object, it will be run by AddGenotypePosteriorProb in order to perform the necessary calculations.

See Also

AddGenotypeLikelihood, AddGenotypePriorProb_Mapping2Parents

Examples

# load dataset and set some parameters
data(exampleRAD_mapping)
exampleRAD_mapping <- SetDonorParent(exampleRAD_mapping, "parent1")
exampleRAD_mapping <- SetRecurrentParent(exampleRAD_mapping, "parent2")
exampleRAD_mapping <- AddAlleleFreqMapping(exampleRAD_mapping,
                                           expectedFreqs = c(0.25, 0.75),
                                           allowedDeviation = 0.08)
exampleRAD_mapping <- AddGenotypeLikelihood(exampleRAD_mapping)
exampleRAD_mapping <- AddGenotypePriorProb_Mapping2Parents(exampleRAD_mapping,
                                                      n.gen.backcrossing = 1)
                                                      
# estimate posterior probabilities
exampleRAD_mapping <- AddGenotypePosteriorProb(exampleRAD_mapping)
# examine the results
exampleRAD_mapping$posteriorProb[[1]][,3,]