gl.fst.pop: Calculates a pairwise Fst values for populations in a...

In dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Calculates a pairwise Fst values for populations in a genlight object

Description

This script calculates pairwise Fst values based on the implementation in the StAMPP package (?stamppFst). It allows to run bootstrap to estimate probability of Fst values to be different from zero. For detailed information please check the help pages (?stamppFst).

Usage

gl.fst.pop(x, nboots = 1, percent = 95, nclusters = 1, verbose = NULL)

Arguments

x	Name of the genlight containing the SNP genotypes [required].
nboots	Number of bootstraps to perform across loci to generate confidence intervals and p-values [default 1].
percent	Percentile to calculate the confidence interval around [default 95].
nclusters	Number of processor threads or cores to use during calculations [default 1].
verbose	Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log ; 3, progress and results summary; 5, full report [default 2, unless specified using gl.set.verbosity].

Value

A matrix of distances between populations (class dist), if nboots =1, otherwise a list with Fsts (in a matrix), Pvalues (a matrix of pvalues), Bootstraps results (data frame of all runs). Hint: Use as.matrix(as.dist(fsts)) if you want to have a squared matrix with symmetric entries returned, instead of a dist object.

Author(s)

Bernd Gruber (bugs? Post to https://groups.google.com/d/forum/dartr)

Examples

test <- gl.filter.callrate(platypus.gl,threshold = 1)
test <- gl.filter.monomorphs(test)
out <- gl.fst.pop(test, nboots=1)

dartR documentation built on June 8, 2023, 6:48 a.m.