stamppFst: Fst Computation
In StAMPP: Statistical Analysis of Mixed Ploidy Populations

Description Usage Arguments Details Value Author(s) References Examples

View source: R/stamppFst.R

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)

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

`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.

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

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.

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

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>

# 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)