[adegenet-forum] How to get observed heterozygosity per population

[Simon Nadeau]

Hi Thibault,

     Thank you very much for your help. I just downloaded the dev version
but I get the same results using summary(x) than with the previous version.
summary gives me expected and observed heterozygosity but per loci:

summary(x)$Hobs

     What I would like to have is Hobs *per population* instead. Something
similar to the function Hs but for Hobs. Is there anything like that in
adegenet? I tried basic.stats from Hierfstat as Maria suggested, but I got
an error message, probably due to something wrong in the way I formatted
the data.

Simon

On Mon, Nov 23, 2015 at 6:58 AM, Maria Guerrina <maria.guerrina at edu.unige.it
> wrote:

> Hi Thibaut!
> I have a problem similar to Simon.
> I have tried to use the function 'summary', but I get 0 both for the
> observed heterozigosity both for the expected one...
> I have tried to use the function 'basic.stats' in hierfstat, but it
> doesn't give a result for Ho, in my case with my data.
>
> any idea?
> Thanks!
> Maria
> --
> Maria Guerrina PhD
> Università di Genova
> DISTAV
> Corso Dogali 1M
> I - 16136 GENOVA (Italy)
> maria.guerrina at edu.unige.it
>
>
>
>
>
> On 23/nov/2015, at 13.11, Jombart, Thibaut wrote:
>
> Hello,
>
> have you tried 'summary'? Note, the current devel version is better
> (previous summary was returning invisibly a list).
>
> Cheers
> Thibaut
>
>
> ------------------------------
> *From:* adegenet-forum-bounces at lists.r-forge.r-project.org [
> adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Simon
> Nadeau [simon.nadeau.ubc at gmail.com]
> *Sent:* 19 November 2015 23:00
> *To:* adegenet-forum at lists.r-forge.r-project.org
> *Subject:* [adegenet-forum] How to get observed heterozygosity per
> population
>
> Hi,
>
>       I have recently been using the various features of adegenet unsing
> genind objects and I works great so far. However, I can't seem to be able
> to find easy summary stats:
>
> Observed heterozygosity per population: this would be very handy but I
> only found the function Hs (expected heterozygosity).
>
> Global allele frequencies per loci: there is a nice histogram of minor
> allele frequencies on page 30 of the adegenet genomic tutorial, but I can't
> find how to generate the same plot using genind objects.
>
> Thank you very much for your help,
>
> Simon
>
> --
> Simon Nadeau, M. Sc.
> Biologiste / Biologist
>
> Ressources naturelles Canada, Service canadien des forêts, Centre de
> foresterie des Laurentides / Natural Resources Canada, Canadian Forest
> Service, Laurentian Forestry Centre
> 1055 rue du P.E.P.S., C.P. 10380 succ. Sainte-Foy, Québec (Québec), Canada
> G1V 4C7
> Simon.Nadeau at a <Simon.Nadeau.UBC at gmail.com>lumni.UBC.ca
> <http://lumni.ubc.ca>,
> * Simon.Nadeau at canada.ca <Simon.Nadeau at RNCan-NRCan.gc.ca>*
> Tel: (604) 349-5196
> _______________________________________________
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> adegenet-forum at lists.r-forge.r-project.org
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>
>
>


-- 
Simon Nadeau, M. Sc.
Biologiste / Biologist

Ressources naturelles Canada, Service canadien des forêts, Centre de
foresterie des Laurentides / Natural Resources Canada, Canadian Forest
Service, Laurentian Forestry Centre
1055 rue du P.E.P.S., C.P. 10380 succ. Sainte-Foy, Québec (Québec), Canada
G1V 4C7
Simon.Nadeau at a <Simon.Nadeau.UBC at gmail.com>lumni.UBC.ca
<http://lumni.ubc.ca>,
*Simon.Nadeau at canada.ca <Simon.Nadeau at RNCan-NRCan.gc.ca>*
Tel: (604) 349-5196
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