[adegenet-forum] Kmeans and DAPC on poolSeq data

[Benjamin Dauphin]

Hi Mark, 

Thanks for response. I’ve run find.clusters() with the matrix of allele frequencies as input file, and then run the DAPC using still the matrix (not the genind or genlight object) by assigning the group generated with kmeans (grp$grp). It works but I have a strange “inverted parabolic curve" for the kmean analysis. 
Is it a common picture for pooldseq data?

Thanks,
Ben

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> On 1 Feb 2018, at 18:01, 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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