pairwise_genetic_diff: Pairwise genetic differentiation across populations

In vcfR: Manipulate and Visualize VCF Data

Pairwise genetic differentiation across populations

Description

pairwise_genetic_diff Calculate measures of genetic differentiation across all population pairs.

Usage

pairwise_genetic_diff(vcf, pops, method = "nei")

Arguments

vcf	a vcfR object
pops	factor indicating populations
method	the method to measure differentiation

Value

a data frame containing the pairwise population differentiation indices of interest across all pairs of populations in the population factor.

Author(s)

Javier F. Tabima

See Also

genetic_diff in vcfR

Examples

data(vcfR_example)
pops <- as.factor(rep(c('a','b'), each = 9))
myDiff <- pairwise_genetic_diff(vcf, pops, method = "nei")
colMeans(myDiff[,c(4:ncol(myDiff))], na.rm = TRUE)
pops <- as.factor(rep(c('a','b','c'), each = 6))
myDiff <- pairwise_genetic_diff(vcf, pops, method = "nei")
colMeans(myDiff[,c(4:ncol(myDiff))], na.rm = TRUE)

vcfR documentation built on Feb. 16, 2023, 8:12 p.m.