[adegenet-forum] Combining SNP and microsatellites markers in a single DAPC

[Thibaut Jombart]

Hi again,

the annoying answer is: yes, and no. Several options you can explore:

1. extract tables using 'tab', cbind them, and run the analysis on the new
table: caveat: the table with the larger variance (typically the largest
one) will have a stronger weight in the analysis

2. do the above, but standardize the two tables before binding them, e.g.
by dividing them by the total inertia (sum of all variances)

3. before going for a single analysis, run separate analyses and look for
common structures using a coinertia. See ?ade4::cointertia for more
information.

Best
Thibaut






--
Dr Thibaut Jombart
Lecturer, Department of Infectious Disease Epidemiology, Imperial College
London
Head of RECON: repidemicsconsortium.org
sites.google.com/site/thibautjombart/
github.com/thibautjombart
Twitter: @TeebzR <http://twitter.com/TeebzR>
+44(0)20 7594 3658

On 24 April 2017 at 13:10, Adrien Rieux <adrien.rieux at cirad.fr> wrote:

> Hi there,
>
>
>
> Is there a way to combine microsatellite and SNP data in a single DAPC ? I
> do observe striking difference in the genetic structure independently
> measured by both type of markers and I’d be keen, if possible, to see what
> I get when both information are combined. I should tell that I only have
> SNP data for a subset of the samples that were genotyped with
> microsatellites.
>
>
>
> Cheers,
>
>
>
> Adrien
>
> --
>
> Adrien RIEUX
> CIRAD - Dpt BIOS - UMR PVBMT
> Tel: 0262499219
> https://adrienrieux.wordpress.com/home/
>
>
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