AddGenotypePriorProb_ByTaxa: Estimate Prior Genotype Probabilities on a Per-Taxon Basis

Description

Using local allele frequencies estimated by AddAlleleFreqByTaxa and assuming Hardy-Weinberg Equilibruim or inbreeding on a local scale, AddGenotypePriorProb_ByTaxa estimates prior genotype probabilities at each taxon, allele, and possible ploidy. These are then stored in the $priorProb slot of the "RADdata" object.

Usage

AddGenotypePriorProb_ByTaxa(object, ...)
# S3 method for RADdata
AddGenotypePriorProb_ByTaxa(object, selfing.rate = 0, ...)

Value

A "RADdata" object identical to that passed to the function, but with a two-dimensional list added to the $priorProb slot. Each row in the list corresponds to one ploidy in object$possiblePloidies, and each column to a unique ploidy in object$taxaPloidy. Each item is a three-dimensional array with allele copy number in the first dimension, taxa in the second dimension, and alleles in the third dimension. The values in the array are prior genotype probabilities. Additionally, "taxon" is recorded in the "priorType" attribute.

Arguments

object: A "RADdata" object. AddAlleleFreqByTaxa should have already been run.
selfing.rate: A number ranging from zero to one indicating the frequency of self-fertilization in the species.
...: Additional arguments (none implemented).

Author

Lindsay V. Clark

Examples

Run this code

# load data
data(exampleRAD)
# do PCA
exampleRAD <- AddPCA(exampleRAD, nPcsInit = 3)
# get allele frequencies
exampleRAD <- AddAlleleFreqByTaxa(exampleRAD)

# add prior probabilities
exampleRAD <- AddGenotypePriorProb_ByTaxa(exampleRAD)

exampleRAD$priorProb[[1,1]][,1,]
exampleRAD$priorProb[[2,1]][,1,]
exampleRAD$priorProb[[1,1]][,2,]
exampleRAD$priorProb[[2,1]][,2,]
exampleRAD$priorProb[[1,2]][,1,]

# try it with inbreeding, for diploid samples only
exampleRAD2 <- SubsetByTaxon(exampleRAD, GetTaxa(exampleRAD)[exampleRAD$taxaPloidy == 2])
exampleRAD2 <- AddGenotypePriorProb_ByTaxa(exampleRAD2, selfing.rate = 0.5)

exampleRAD2$priorProb[[1,1]][,1,]