AddAlleleFreqByTaxa: Estimate Local Allele Frequencies for Each Taxon Based on...

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

Estimate Local Allele Frequencies for Each Taxon Based on Population Structure

Description

This function estimates allele frequencies per taxon, rather than for the whole population. The best estimated genotypes (either object$depthRatio or GetWeightedMeanGenotypes(object)) are regressed against principal coordinate axes. The regression coefficients are then in turn used to predict allele frequencies from PC axes. Allele frequencies outside of a user-defined range are then adjusted so that they fall within that range.

Usage

AddAlleleFreqByTaxa(object, ...)
## S3 method for class 'RADdata'
AddAlleleFreqByTaxa(object, minfreq = 0.0001, ...)

Arguments

object	A "RADdata" object. AddPCA should have already been run.
minfreq	The minimum allowable allele frequency to be output. The maximum allowable allele frequency will be calculated as 1 - minfreq.
...	Additional arguments (none implemented).

Details

For every allele, all PC axes stored in object$PCA are used for generating regression coefficients and making predictions, regardless of whether they are significantly associated with the allele.

object$depthRatio has missing data for loci with no reads; these missing data are omitted on a per-allele basis when calculating regression coefficients. However, allele frequencies are output for all taxa at all alleles, because there are no missing data in the PC axes. The output of GetWeightedMeanGenotypes has no missing data, so missing data are not an issue when calculating regression coefficients using that method.

After predicting allele frequencies from the regression coefficients, the function loops through all loci and taxa to adjust allele frequencies if necessary. This is needed because otherwise some allele frequencies will be below zero or above one (typically in subpopulations where alleles are near fixation), which interferes with prior genotype probability estimation. For a given taxon and locus, any allele frequencies below minfreq are adjusted to be equal to minfreq, and any allele frequencies above 1 - minfreq are adjusted to be 1 - minfreq. Remaining allele frequencies are adjusted so that all allele frequencies for the taxon and locus sum to one.

Value

A "RADdata" object identical to the one passed to the function, but with a matrix of allele frequencies added to the $alleleFreqByTaxa slot. Taxa are in rows and alleles in columns.

Author(s)

Lindsay V. Clark

See Also

AddGenotypePriorProb_ByTaxa

Examples

# load data
data(exampleRAD)
# do PCA
exampleRAD <- AddPCA(exampleRAD, nPcsInit = 3)

# get allele frequencies
exampleRAD <- AddAlleleFreqByTaxa(exampleRAD)

exampleRAD$alleleFreqByTaxa[1:10,]

polyRAD documentation built on Nov. 10, 2022, 5:14 p.m.