popsFST: Pairwise FST among populations and across multiple loci

In poolABC: Approximate Bayesian Computation with Pooled Sequencing Data

Pairwise FST among populations and across multiple loci

Description

This functions calculates pairwise FST values according to Hudson's estimator following Bathia. FST values are calculated for each pairwise combination of the populations present in the data (defined by the nPops parameter).

Usage

popsFST(nPops, Pop_pi, coverage)

Arguments

nPops	is an integer indicating how many populations are present in the data.
Pop_pi	is a list of allele frequencies. Each entry of that list is a matrix representing a different locus. Each row of that matrix should correspond to a different population and each column to a different site
coverage	is a list containing depths of coverage. Each entry of that list is a matrix representing a different locus. Each row of that matrix should correspond to a different population and each column to a different site

Details

This functions performs pairwise comparisons of multiple populations and thus returns multiple FST values, one for each comparison. Additionally, this function computes FST for multiple loci, returning a value for each pairwise comparison per locus.

Value

a list where each entry corresponds to a different locus. Each of those entries is a upper triangular matrix with the pairwise FST values between each population.

poolABC documentation built on Aug. 8, 2023, 5:14 p.m.