polyRAD (version 2.0.0)

AddAlleleFreqHWE: 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 RADdata
AddAlleleFreqHWE(object, excludeTaxa = GetBlankTaxa(object), ...)

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.

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.

Author

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