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

[Maria Guerrina]

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 alumni.UBC.ca,  Simon.Nadeau at canada.ca
> Tel: (604) 349-5196
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