AddAlleleFreqHWE {polyRAD} | R Documentation |
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 |
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