alleleFreqDiff

Generate a new vcfR object with only sites with an allele frequency difference above the given threshold

Usage

alleleFreqDiff(vcfR = NULL, pm = NULL, p1 = NULL, p2 = NULL, difference = NULL)

Arguments

vcfR

vcfR object

pm

data.frame containing two columns, "id" and "pop". The ids must match those in the vcfR object, but don't need to be in the same order. Each sample must be assigned to a population

p1

(character) name of parental population 1

p2

(character) name of parental population 2

difference

(numeric) allele frequency difference threshold, must be between 0 and 1

Value

vcfR object

Examples

#alleleFreqDiff(vcfR = example.vcfR, pm = example.popmap, p1 = 0, p2 = 20, difference = 0.5)