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

[brian knaus]

Hi Rachel,

I believe that the statement for why DAPC can not be scripted is because
the steps to determine the number of principal components and discriminant
functions are interactive. If you know this information you can send the
DAPC step to a server without a monitor. Not sure DAPC is going to help you
find SNPs associated with phenotypes though.

Good luck!
Brian

On Wed, Mar 6, 2019 at 11:14 AM Rachel Turba <rturba at outlook.com> wrote:

> 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> 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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>>
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