ExamineGenotype: Plots to Examine Genotype Calling at a Single Taxon and Allele

Description

For a given taxon and allele, this function generates barplots showing read depth ratio, posterior mean genotype, genotype prior probabilities, genotype likelihoods, and genotype posterior probabilities. It is intended as a sanity check on genotype calling, as well as a means to visually demonstrate the concept of Bayesian genotype calling.

Usage

ExamineGenotype(object, ...)
# S3 method for RADdata
ExamineGenotype(object, taxon, allele, pldindex = 1, ...)

Value

A barplot is generated. Invisibly, a list is returned:

alleleDepth: Sequence read depth for the selected allele.
antiAlleleDepth: Sequence read depth for all other alleles at the locus.
depthRatio: Proportion of reads at this taxon and locus belonging to this allele.
priorProb: A vector of genotype prior probabilities.
genotypeLikelhood: A vector of genotype likelihoods.
posteriorProb: A vector of genotype posterior probabilities.
postMean: The posterior mean genotype on a scale of 0 to 1.

Arguments

object: A RADdata object for which genotype calling has already been performed.
taxon: A single character string indicating the taxon to show.
allele: A single character string indicating the allele to show.
pldindex: An index of which inheritance mode to use within object$possiblePloidies.
...: Other arguments (none implemented).

Author

Lindsay V. Clark

Examples

Run this code

data(exampleRAD)

exampleRAD <- IterateHWE(exampleRAD)

eg <- ExamineGenotype(exampleRAD, "sample088", "loc1_T")

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