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

[Rachel Turba]

Hi Brian,

Thank you for the help. I was avoiding to subset my data because I am interested in investigating SNPs that could be related to a change in morph between these populations.

Cheers,
Rachel

________________________________
From: brian knaus <briank.lists at gmail.com>
Sent: Tuesday, March 5, 2019 2:05:03 PM
To: Rachel Turba
Cc: adegenet-forum at lists.r-forge.r-project.org
Subject: Re: [adegenet-forum] Scripting adegenet with whole-genome data

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<mailto: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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