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

Davide Piffer pifferdavide at gmail.com
Fri Oct 6 11:24:18 CEST 2017

Dear Thibaut,

thanks for answering my question. I will try to reformulate my question
differently, stating the assumptions:
1)  I assume that the eHGDP object was made into a genpop object from some
raw .txt file, like the HGDP file I linked to in the previous email.
2) I need an object that looks exactly like the eHGDP object, but with SNPs
instead of microsatellite alleles.
3) Since it's gonna be a rather complex task, I asked if any of you knows
if someone has already done this job before and published it (e.g. as
supplementary file).
4) Otherwise, I would like to know how to produce such a file myself,
starting from a version of the HGDP file with population information. If
this was done for microsatellites, surely it can be done for the SNPs as
well? I assume they rely on the same raw HGDP file.

Many thanks!


On 6 October 2017 at 10:56, Thibaut Jombart <thibautjombart at gmail.com>

> 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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