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

[Thibaut Jombart]

Hello,

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.

Best
Thibaut

--
Dr Thibaut Jombart
Lecturer, Department of Infectious Disease Epidemiology, Imperial College London
Head of RECON: repidemicsconsortium.org
WHO Consultant - outbreak analysis
sites.google.com/site/thibautjombart/
Twitter: @TeebzR
+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.
>
>
>
> Mark
>
>
>
>
>
> 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.
>
>
>
> Thanks
>
>
>
> --
> Angela P. Fuentes-Pardo. Biologist, Ph.D. candidate
> Ruzzante Lab, Department of Biology
> Dalhousie University, Halifax, Canada, B3H 4R2
> http://fuentespardo.weebly.com
>
> 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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