stamppFst {StAMPP}R Documentation

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

number of proccesor treads or cores to use during calculations.

Details

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

Value

An object list with the components: Fstsa matrix of pairwise Fst values between populations Pvaluesa matrix of p-values for each of the pairwise Fst values containined in the 'Fsts' matrix Bootstrapsa 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.

Author(s)

Luke Pembleton <luke.pembleton at agriculture.vic.gov.au>

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

# 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)

[Package StAMPP version 1.6.3 Index]