[adegenet-forum] Per locus pairwise Fst

Jombart, Thibaut t.jombart at imperial.ac.uk
Sat Sep 13 20:20:39 CEST 2014

Hi there,

yes, this function is not optimized for large datasets. You can use the same approach but using functions from the hierfstat package. 

From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Vikram Chhatre [crypticlineage at gmail.com]
Sent: 12 September 2014 18:31
To: adegenet-forum at lists.r-forge.r-project.org
Subject: Re: [adegenet-forum] Per locus pairwise Fst

I am revisiting this topic due to some technical problems.

The task at hand is to estimate pairwise Fst matrices for each locus separately.

# Genind object is stored in:

# Use seploc to separate loci:
gen100_seploc <- seploc(gen100_genind, truenames=TRUE, res.type=c('genind', 'matrix')

# Calculate pairwise Fst:
gen100_perLocusPWFst <- lapply(gen100_seploc, pairwise.fst, res.type=c('dist', 'matrix'), trunames=TRUE)

For a data set consisting of 30 populations, 20 individuals each, 1000 loci and 2 alleles per locus (1.2 million data points), it takes up to 6 hours to estimate the pairwise Fst matrix with this method.

Is there any way to speed this up?  Should I look into any other packages?

Many thanks for your time and help.

On Mon, Jul 14, 2014 at 9:16 AM, Vikram Chhatre <crypticlineage at gmail.com<mailto:crypticlineage at gmail.com>> wrote:
Perfect!  Thank you for both solutions.


On Mon, Jul 14, 2014 at 9:13 AM, Jombart, Thibaut <t.jombart at imperial.ac.uk<mailto:t.jombart at imperial.ac.uk>> wrote:

Hi there,

you can use seploc to separate loci, and lapply over the resulting list using your prefered fst function.

From: adegenet-forum-bounces at lists.r-forge.r-project.org<mailto:adegenet-forum-bounces at lists.r-forge.r-project.org> [adegenet-forum-bounces at lists.r-forge.r-project.org<mailto:adegenet-forum-bounces at lists.r-forge.r-project.org>] on behalf of Vikram Chhatre [crypticlineage at gmail.com<mailto:crypticlineage at gmail.com>]
Sent: 14 July 2014 14:01
To: adegenet-forum at lists.r-forge.r-project.org<mailto:adegenet-forum at lists.r-forge.r-project.org>
Subject: [adegenet-forum] Per locus pairwise Fst

Good morning.

I would like to estimate per locus pairwise Fst for populations, but it appears that Adegenet only estimates this over all loci (i.e. single matrix).  What I would like is one matrix per locus.  Has anyone modified the functions or know of alternative programs that can do this?


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