fst.STRUCTURE.popgen: Estimate Fst values between population clusters

In nicholasjclark/STRUCTURE.popgen: Population genetics calculations using STRUCTURE assignment probabilities

Description

This function assigns individuals to clusters using STRUCTURE assignment probabilities provided in the qmatrix. It then calculates pairwise Fst values between clusters.

Usage

fst.STRUCTURE.popgen(qmatrix, allele.dat, nclusters, nreps, NA.symbol,
  samp.snps, nsamp, ncores)

Arguments

qmatrix	Dataframe. The STRUCTURE qmatrix, with individuals in column 'ind'
allele.dat	Dataframe/matrix containing '/' separated allele data, with rownames representing individuals
nclusters	(optional) Integer. The number of clusters identified by STRUCTURE
nreps	Integer. The number of times to repeat estimations. Default is 100
NA.symbol	The code used to represent missing allele data
samp.snps	Logical. If TRUE, a specified number of SNPs will be randomly sampled in each iteration to account for uncertainty and speed computations. Default is FALSE
nsamp	(optional) Integer. The number of SNPs to sample during each iteration
ncores	Integer. The number of cores to split job across. Default is 1 (no parallelisation)

Value

Matrix of pairwise comparison confidence intervals

nicholasjclark/STRUCTURE.popgen documentation built on May 25, 2019, 10:38 p.m.