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

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

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 class 'RADdata'
ExamineGenotype(object, taxon, allele, pldindex = 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).

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.

Author(s)

Lindsay V. Clark

Examples

data(exampleRAD)

exampleRAD <- IterateHWE(exampleRAD)

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

lvclark/polyRAD documentation built on Jan. 15, 2024, 4:19 a.m.