[adegenet-forum] Could adegenet be modified to accept allele frequencies as input data?
thibautjombart at gmail.com
Tue Oct 31 13:02:40 CET 2017
you can create a genpop object from a matrix of allele counts, so this
should be fairly straightforward. It is documented in section 4.7 of
the basics tutorial.
Dr Thibaut Jombart
Lecturer, Department of Infectious Disease Epidemiology, Imperial College London
Head of RECON: repidemicsconsortium.org
WHO Consultant - outbreak analysis
+44(0)20 7594 3658
On 31 October 2017 at 09:24, Mark Coulson <Mark.Coulson.ic at uhi.ac.uk> wrote:
> 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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