[adegenet-forum] Kmeans and DAPC on poolSeq data

[Mark Coulson]

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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