pairFST: Pairwise FST among populations

In poolABC: Approximate Bayesian Computation with Pooled Sequencing Data

Pairwise FST among populations

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

pairFST(nPops, Pop_pi, coverage)

Arguments

nPops	is an integer indicating how many populations are present in the data.
Pop_pi	is a matrix of allele frequencies. Each row of that matrix should correspond to a different population and each column to a different site.
coverage	is a matrix containing depths of coverage. 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. However, this function computes FST for a single locus.

Value

a upper triangular matrix with the pairwise FST values between each population.

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