AddPloidyChiSq: Chi-Square Test on Genotype Likelihood Distributions

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

Chi-Square Test on Genotype Likelihood Distributions

Description

This function is intended to help identify the correct inheritance mode for each locus in a "RADdata" object. Expected genotype frequencies are taken from object$priorProb. Observed genotype frequencies are estimated from object$genotypeLikelihood, where each taxon has a partial assignment to each genotype, proportional to genotype likelihoods. A chi-squared statistic is then estimated.

Usage

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

Arguments

object	A "RADdata" object. Genotype prior probabilities and likelihoods should have been added.
excludeTaxa	A character vector indicating names of taxa to exclude from calculations.
...	Additional arguments to be passed to other methods (none currently in use).

Details

Parents (in mapping populations) and blank taxa are automatically excluded from calculations.

Genotypes with zero prior probability would result in an infinite A chi-squared statistic and therefore are excluded from the calculation. However, the total number of observations (total number of taxa) remains the same, so that if there are many taxa with high likelihood for a genotype with zero prior probability, chi-squared will be high.

Value

A "RADdata" object identical to the one passed to the function, but with a matrix added to the $ploidyChiSq slot. This matrix has inheritance rows (matching object$priorProb) in rows and alleles in columns. object$ploidyChiSq contains the chi-squared values.

Author(s)

Lindsay V. Clark

See Also

AddGenotypeLikelihood, AddPloidyLikelihood

Examples

# load dataset and set some parameters
data(exampleRAD_mapping)
exampleRAD_mapping <- SetDonorParent(exampleRAD_mapping, "parent1")
exampleRAD_mapping <- SetRecurrentParent(exampleRAD_mapping, "parent2")
exampleRAD_mapping <- AddAlleleFreqMapping(exampleRAD_mapping,
                                           expectedFreqs = c(0.25, 0.75),
                                           allowedDeviation = 0.08)
exampleRAD_mapping <- AddGenotypeLikelihood(exampleRAD_mapping)
exampleRAD_mapping <- AddGenotypePriorProb_Mapping2Parents(exampleRAD_mapping,
                                                      n.gen.backcrossing = 1)
                                                      
# get chi-squared values
exampleRAD_mapping <- AddPloidyChiSq(exampleRAD_mapping)
# view chi-squared and p-values (diploid only)
exampleRAD_mapping$ploidyChiSq

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