AddGenotypePriorProb_Even: Add Uniform Priors to a RADdata Object

Description

To estimate genotype posterior probabilities based on read depth alone, without taking any population parameters into account, this function can be used to set a uniform prior probability on all possible genotypes. This function is not part of any pipeline but can be used for very rough and quick genotype estimates, when followed by AddGenotypeLikelihood, AddGenotypePosteriorProb, AddPloidyChiSq, and GetWeightedMeanGenotypes or GetProbableGenotypes.

Usage

AddGenotypePriorProb_Even(object, ...)

Value

A “RADdata” object identical that passed to the function, but with data stored in one new slot:

priorProb: A two-dimensional list of matrices, with rows corresponding to object$possiblePloidies and columns corresponding to unique values in object$taxaPloidy. Each item in the list is a matrix. For each matrix, allele copy number (from zero to the total ploidy) is in rows, and alleles are in columns. Each value is $1 / (ploidy + 1).$

Arguments

object: A RADdata object.
...: Additional arguments (none implemented).

Author

Lindsay V. Clark

Examples

Run this code

data(exampleRAD)

exampleRAD <- AddGenotypePriorProb_Even(exampleRAD)
exampleRAD$priorProb

# finish protocol to get genotypes
exampleRAD <- AddGenotypeLikelihood(exampleRAD)
exampleRAD <- AddPloidyChiSq(exampleRAD)
exampleRAD <- AddGenotypePosteriorProb(exampleRAD)

genmat <- GetWeightedMeanGenotypes(exampleRAD)
genmat