AddAlleleFreqHWE: Estimate Allele Frequencies in a RADdata Object Assuming...

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

Estimate Allele Frequencies in a RADdata Object Assuming Hardy-Weinberg Equilibrium

Description

Allele frequencies are estimated based on the best parameters available. object$alleleFreqByTaxa is used if available. If object$alleleFreqByTaxa is null, GetWeightedMeanGenotypes is used, and if that isn't possible object$depthRatio is used. From whichever of the three options is used, column means are taken, the output of which is stored as object$alleleFreq.

Usage

AddAlleleFreqHWE(object, ...)
## S3 method for class 'RADdata'
AddAlleleFreqHWE(object, excludeTaxa = GetBlankTaxa(object), ...)

Arguments

object	A "RADdata" object.
excludeTaxa	A character vector indicating taxa that should be excluded from the calculation.
...	Included to allow more arguments in the future, although none are currently used.

Value

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

Author(s)

Lindsay V. Clark

See Also

AddAlleleFreqMapping, AddGenotypePriorProb_HWE

Examples

# load in an example dataset
data(exampleRAD)
exampleRAD

# add allele frequencies
exampleRAD <- AddAlleleFreqHWE(exampleRAD)
exampleRAD$alleleFreq

lvclark/polyRAD documentation built on June 14, 2025, 10:08 p.m.