[adegenet-forum] Kmeans and DAPC on poolSeq data

Mark Coulson Mark.Coulson.ic at uhi.ac.uk
Thu Feb 1 18:01:46 CET 2018


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


_______________________________________________
adegenet-forum mailing list
adegenet-forum at lists.r-forge.r-project.org
https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum
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.


More information about the adegenet-forum mailing list