AddGenotypePriorProb_Even: Add Uniform Priors to a RADdata Object

In lvclark/polyRAD: Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids

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, ...)

Arguments

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

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).

Note

Values in object$ploidyChiSq may not be particularly meaningful under uniform priors.

Author(s)

Lindsay V. Clark

See Also

AddGenotypePriorProb_HWE

Examples

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

lvclark/polyRAD documentation built on Jan. 15, 2024, 4:19 a.m.