[adegenet-forum] Kmeans and DAPC on poolSeq data

[Thibaut Jombart]

Hi there

find.clusters is implemented for matrices as well, and should deal nicely
with any kind of quantitative data. So it should apply readily to your
data. Same for DAPC.

Best
Thibaut


--
Dr Thibaut Jombart
Lecturer, Department of Infectious Disease Epidemiology, Imperial College
London
Head of RECON: repidemicsconsortium.org
WHO Consultant - outbreak analysis
https://thibautjombart.netlify.com
Twitter: @TeebzR
+44(0)20 7594 3658

On 1 February 2018 at 17:01, Mark Coulson <Mark.Coulson.ic at uhi.ac.uk> wrote:

> Hi Ben,
>
> I have used allelotype data with the input as a matrix of the frequency of
> the A allele in each group to run DAPC and it worked well. However, my
> groups were defined already but could the same type of input not be used to
> find.clusters?
>
> Mark
>
>
> -----Original Message-----
> 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 Benjamin
> Dauphin
> Sent: 31 January 2018 09:18
> To: adegenet-forum at lists.r-forge.r-project.org
> Subject: [adegenet-forum] Kmeans and DAPC on poolSeq data
>
> Dear all,
>
> I am newly working on pool sequencing data and I simply wonder if I can
> use kmeans (find.cluster) and DAPC to investigate population structure from
> poolseq data (allele frequencies)? How find.clusters can deal with allele
> frequencies?
>
> Dataset: 7 pools and 100’000 SNPs
>
> Any comment or help would be much appreciated.
> Best regards
> Ben
>
>
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