GetLikelyGen: Output the Most Likely Genotype

Description

For a single taxon in a "RADdata" object, GetLikelyGen returns the most likely genotype (expressed in allele copy number) for each allele and each possible ploidy. The likelihoods used for determining genotypes are those stored in object$genotypeLikelihood.

Usage

GetLikelyGen(object, taxon, minLikelihoodRatio = 10)

Value

A matrix with ploidies in rows (named with ploidies converted to character format) and alleles in columns. Each value indicates the most likely number of copies of that allele that the taxon has, assuming that ploidy.

Arguments

object: A "RADdata" object.
taxon: A character string indicating the taxon for which genotypes should be returned.
minLikelihoodRatio: A number indicating the minimum ratio of the likelihood of the most likely genotype to the likelihood of the second-most likely genotype for any genotype to be output for a given allele. If this number is one or less, all of the most likely genotypes will be output regardless of likelihood ratio. Where filtering is required so that only high confidence genotypes are retained, this number should be increased.

Author

Lindsay V. Clark

Examples

Run this code

# load dataset for this example
data(exampleRAD)
# add allele frequencies and genotype likelihoods
exampleRAD <- AddAlleleFreqHWE(exampleRAD)
exampleRAD <- AddGenotypeLikelihood(exampleRAD)

# get most likely genotypes
GetLikelyGen(exampleRAD, "sample001")
GetLikelyGen(exampleRAD, "sample082")

# try different filtering
GetLikelyGen(exampleRAD, "sample001", minLikelihoodRatio = 1)
GetLikelyGen(exampleRAD, "sample001", minLikelihoodRatio = 100)