AddAlleleFreqMapping: Estimate Allele Frequencies in a Mapping Population

Description

Estimate allele frequencies using data from a mapping population, assuming a fixed set of allele frequencies are possible.

Usage

AddAlleleFreqMapping(object, ...)
# S3 method for RADdata
AddAlleleFreqMapping(object, expectedFreqs = seq(0, 1, 0.25),
                     allowedDeviation = 0.05,
                     excludeTaxa = c(GetDonorParent(object),
                                     GetRecurrentParent(object),
                                     GetBlankTaxa(object)), …)

Arguments

object

A "RADdata" object. The donor and recurrent parent should have been assigned with SetDonorParent and SetRecurrentParent, respectively. If this is not a backcross population, it does not matter which is the donor or recurrent parent.

expectedFreqs

A numeric vector listing all expected allele frequencies in the mapping population.

allowedDeviation

A value indicating how far an observed allele frequency can deviate from an expected allele frequency and still be categorized as that allele frequency. Must be no more than half the smallest interval seen in expectedFreqs.

excludeTaxa

A character vector indicating taxa that should be excluded from the allele frequency estimate.

…

Arguments to be passed to the method for "RADdata".

Value

A "RADdata" object identical to the one passed to the function, but with allele frequencies added to object$alleleFreq, and "mapping" as the "alleleFreqType" attribute.

Details

Allele frequencies are first estimated as the column means of object$depthRatio (unless posterior genotype probabilities and ploidy chi-squared values have already been calculated, in which case GetWeightedMeanGenotypes is run and the column means of its output are taken), excluding any taxa listed in excludeTaxa. These are then categorized based on which, if any, expected allele frequency they match with, based on the intervals described by expectedFreqs and allowedDeviation. If an allele frequency does not fall within any of these intervals it is classified as NA; otherwise it is converted to the matching value in expectedFreqs.

Examples

Run this code

# NOT RUN {
# load example dataset
data(exampleRAD_mapping)
exampleRAD_mapping

# specify parents
exampleRAD_mapping <- SetDonorParent(exampleRAD_mapping, "parent1")
exampleRAD_mapping <- SetRecurrentParent(exampleRAD_mapping, "parent2")

# estimate allele frequencies in diploid BC1 population
exampleRAD_mapping <- AddAlleleFreqMapping(exampleRAD_mapping,
                        expectedFreqs = c(0.25, 0.75),
                        allowedDeviation = 0.08)
                        
exampleRAD_mapping$alleleFreq
# }