[adegenet-forum] Scripting adegenet with whole-genome data

[brian knaus]

Hi Rachel,

Demographic patterns are generally thought to occur throughout the genome.
In which case you shouldn't need the entire genome but can use a
representative subset of your variants. We've demonstrated how to
accomplish this at the below link.

https://grunwaldlab.github.io/Population_Genetics_in_R/gbs_analysis.html#subsetting-a-vcfr-object-to-200-random-variants

Good luck!
Brian

On Tue, Mar 5, 2019 at 11:24 AM Rachel Turba <rturba at outlook.com> wrote:

> Hi all,
>
>
>
> I have researched this on the forum but was not successful in finding
> help, so I apologize in advance if this has been addressed already.
>
>
>
> In this tutorial (
> https://grunwaldlab.github.io/Population_Genetics_in_R/DAPC.html) it says
> that adegenet cannot be scripted a priori, but my data has 6Gb and takes a
> very long time to generate the DAPC object. So I have to submit it as a
> script to the university cluster. I get the plot of variance explained by
> PC but then everything halts because I do not provide the number of PCs to
> be retained for continuing the analysis. Is there a way around this? How
> does anyone handle large datasets?
>
>
>
> Thank you in advance,
>
> Rachel
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