[adegenet-forum] Could adegenet be modified to accept allele frequencies as input data?

Mark Coulson Mark.Coulson.ic at uhi.ac.uk
Tue Oct 31 10:24:45 CET 2017

Hi Angela,

I've done something similar with a data set for ~900,000 SNPs where I only had allele frequencies per each of my 'populations'. I simply imported this as a matrix where each value was the 'A' allele frequency and did my dapc etc from there. Not sure if this will work well given the much larger number of SNPs you have but worth a try.


From: adegenet-forum-bounces at lists.r-forge.r-project.org [mailto:adegenet-forum-bounces at lists.r-forge.r-project.org] On Behalf Of Angela Fuentes Pardo
Sent: 30 October 2017 15:24
To: adegenet-forum at lists.r-forge.r-project.org
Subject: [adegenet-forum] Could adegenet be modified to accept allele frequencies as input data?

Hi there,

My dataset consists of allele frequencies of millions of SNPs for >10 populations (I don't have individual genotype data). adegenet requires individual genotypes as input data, but considering many population genetic tests are based on allele frequencies, I wanted to ask if there is any possibility that adegenet could have a function that accepts population allele frequencies as input data. I am mostly interested on conducting PCA and DAPC tests.


Angela P. Fuentes-Pardo. Biologist, Ph.D. candidate
Ruzzante Lab, Department of Biology
Dalhousie University, Halifax, Canada, B3H 4R2

Inverness College UHI, a partner in the University of the Highlands and Islands www.inverness.uhi.ac.uk Board of Management of Inverness College (known as Inverness College UHI), Scottish Charity No SC021197.
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