StAMPP (version 1.5.1)

stamppFst: Fst Computation

Description

This function calculates pairwise Fst values along with confidence intervals and p-values between populations according to the method proposed by Wright(1949) and updated by Weir and Cockerham (1984).

Usage

stamppFst(geno, nboots = 100, percent = 95, nclusters = 1)

Arguments

geno

a data frame containing allele frequency data generated from stamppConvert, or a genlight object containing genotype data, individual IDs, population IDs and ploidy levels.

nboots

number of bootstraps to perform across loci to generate confidence intervals and p-values

percent

the percentile to calculate the confidence interval around

nclusters

the number of proccesor treads or cores to use during calculations.

Value

An object list with the components:

Fsts

a matrix of pairwise Fst values between populations

Pvalues

a matrix of p-values for each of the pairwise Fst values containined in the 'Fsts' matrix

Bootstraps

a dataframe of each Fst value generated during Bootstrapping and the associated confidence intervals

If nboots<2, no bootstrapping is performed and therefore only a matrix of Fst values is returned.

Details

If possible, using multiple processing threads or cores is recommended to assist in calculating Fst values over a large number of bootstraps.

References

Wright S (1949) The Genetical Structure of Populations. Annals of Human Genetics 15, 323-354. <doi:10.1111/j.1469-1809.1949.tb02451.x>

Weir BS, Cockerham CC (1984) Estimating F Statistics for the ANalysis of Population Structure. Evolution 38, 1358-1370. <doi:10.2307/2408641>

Examples

# NOT RUN {
# import genotype data and convert to allele frequecies 
data(potato.mini, package="StAMPP")
potato.freq <- stamppConvert(potato.mini, "r")

# Calculate pairwise Fst values between each population
potato.fst <- stamppFst(potato.freq, 100, 95, 1)
# }