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

[Jombart, Thibaut]

You can use 'seppop' to split your data by population, and then lapply over it to get population specific summaries (averaging over loci if you need).

Makes sense?

Cheers
Thibaut


________________________________
From: Simon Nadeau [simon.nadeau.ubc at gmail.com]
Sent: 23 November 2015 18:19
To: Maria Guerrina
Cc: Jombart, Thibaut; adegenet-forum at lists.r-forge.r-project.org
Subject: Re: [adegenet-forum] How to get observed heterozygosity per population

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<mailto: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<mailto: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<mailto:adegenet-forum-bounces at lists.r-forge.r-project.org> [adegenet-forum-bounces at lists.r-forge.r-project.org<mailto:adegenet-forum-bounces at lists.r-forge.r-project.org>] on behalf of Simon Nadeau [simon.nadeau.ubc at gmail.com<mailto:simon.nadeau.ubc at gmail.com>]
Sent: 19 November 2015 23:00
To: adegenet-forum at lists.r-forge.r-project.org<mailto: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<mailto:Simon.Nadeau.UBC at gmail.com>lumni.UBC.ca<http://lumni.ubc.ca>,
Simon.Nadeau at canada.ca<mailto:Simon.Nadeau at RNCan-NRCan.gc.ca>
Tel: (604) 349-5196<tel:%28604%29%20349-5196>
_______________________________________________
adegenet-forum mailing list
adegenet-forum at lists.r-forge.r-project.org<mailto:adegenet-forum at lists.r-forge.r-project.org>
https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum




--
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<mailto:Simon.Nadeau.UBC at gmail.com>lumni.UBC.ca<http://lumni.ubc.ca>,
Simon.Nadeau at canada.ca<mailto:Simon.Nadeau at RNCan-NRCan.gc.ca>
Tel: (604) 349-5196
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20151123/948337bf/attachment.html>