[adegenet-forum] Retrieving population allele frequencies of SNPs using HGDP file

[Thibaut Jombart]

Hi Davide,

I am not entirely sure what you need, so sorry if I miss the point.
adegenet cannot make up for absent population information, but you can
try to identify clusters of course, e.g. using find.clusters.

eHGDP is not a file (at least not in the sense you probably mean), but
a genind object. If the question is how you can get a file looking
like the one you link into a genind object, you probably want to use
something like read.csv and then df2genind. Imports should be detailed
in the basics tutorial:
https://github.com/thibautjombart/adegenet/wiki/Tutorials

Best
Thibaut

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


On 4 October 2017 at 14:08, Davide Piffer <pifferdavide at gmail.com> wrote:
> Hello,
>
> I am new to Adegenet. I would like to retrieve population frequencies of
> SNPs (using rsID) from the HGDP file "HGDP_FinalReport_Forward.txt" :
> http://www.hagsc.org/hgdp/files.html
>
> However, the file lacks population information. It contains SNPs x
> individuals.
> I need a file structured like the eHGDP (except with SNPs and not
> microsatellite data) file provided with the package, that can be easily
> converted into genpop file and then compute the frequencies via makefreq.
> Do you know if there is any such file downloadable on the internet?
> i guess there must be a way to produce such a file using ADEGENET starting
> from raw data. but my knowledge of this package is not advanced enough yet.
>
> Best wishes,
>
> Davide
>
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