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

[Rachel Turba]

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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