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

[Simon Nadeau]

Hi,

     This worked. I could not figure out how to access $Hobs for each
population without using a for loop.

x.pop = seppop(x)
summary.by.pop = lapply(x.pop, summary)
Hobs.ls = rep(NA, length(summary.by.pop))
for (i in 1:length(summary.by.pop)){
  Hobs.ls[i] = mean(summary.by.pop[[i]]$Hobs)
}
barplot(Hobs.ls, names.arg = levels(pop(x)), las = 2, main = "Observed
heterozygosity", ylab = "Ho")

Thank you very much for your help,

Simon

On Mon, Nov 23, 2015 at 10:38 AM, Jombart, Thibaut <t.jombart at imperial.ac.uk
> wrote:

> 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> 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
>> _______________________________________________
>> adegenet-forum mailing list
>> 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 <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
>



-- 
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20151123/e1be5a9b/attachment-0001.html>