[adegenet-forum] problem with DAPC/find clusters analyses with rad seq data

[Thibaut Jombart]

Hello

if your computer can afford it, I would stick to genind objects and use
snapclust. The method is documented there:
tutorial: https://github.com/thibautjombart/adegenet/wiki/Tutorials
podcast: https://www.youtube.com/watch?v=Vl3cf0XHG7Q
paper:
https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.12968

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 16 April 2018 at 20:00, Lu Maffey <lucia.maffey at gmail.com> wrote:

> Hi Thibaut and everyone!
>
> I need some help with a DAPC analyses I'm trying to perform on my radseq
> data (whole genome for different mosquitoe samples, total of 65
> individuals). (I'm new with Adegenet so I apologize in advance if this
> question is quite basic!). The samples are from different locations and I'm
> trying to stablish if there is population structure within the data. I have
> previously performed analyses using Structure which showed that there are
> different clusters (of course using fewer SNPs than the total number
> available because of the panmixia assumption). So I've created the genlight
> object with all the SNPs(after filtering low frequencies in plink) but when
> I use find.clusters, the BIC against number of clusters graph only shows
> increasing values of BIC. It never decreases. So I know that it's not the
> only way to determine the number of clusters to perform the analysis but
> I'm not sure wether this means that the program doesn't recognize any
> clusters within the data or some other issue. I've tried using the same
> value I've obtained for this data in Structure and it shows a similar
> asignation but I'm not sure if thisis correct.
> If I perform a DAPC analyses, when I use the scatter function to show the
> results, the graph only shows the groups numbers, but no individual dots.
> Could you please give me some insight about what's going on here?
>
> Thank you very much in advance!
>
> cheers
>
> Lu
>
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