[R-sig-genetics] R Package to compute observed heterozygosity within a population

[Bhuller, Ravneet]

Many thanks, Thibaut.

I will try the way you have suggested.

Kind regards,

Rav

On 16 Jan 2017, at 12:03, Thibaut Jombart <thibautjombart at gmail.com<mailto:thibautjombart at gmail.com>> wrote:

Hello,

Hs(x) in adegenet will do this for the expected heterozygosity. You can use 'summary' combined with seppop to get the average Hobs per population; example with sim2pop:

> lapply(seppop(sim2pop), function(e) mean(summary(e)$Hobs, na.rm = TRUE))
$P01
[1] 0.755

$P02
[1] 0.77


Cheers
Thibaut


--
Dr Thibaut Jombart
Lecturer, Department of Infectious Disease Epidemiology, Imperial College London
Head of RECON: repidemicsconsortium.org<http://repidemicsconsortium.org/>
sites.google.com/site/thibautjombart/<http://sites.google.com/site/thibautjombart/>
github.com/thibautjombart<http://github.com/thibautjombart>
Twitter: @TeebzR<http://twitter.com/TeebzR>
+44(0)20 7594 3658

On 12 January 2017 at 13:19, Bhuller, Ravneet <ravneet.bhuller13 at imperial.ac.uk<mailto:ravneet.bhuller13 at imperial.ac.uk>> wrote:
Dear Members,

Is there any suitable package to compute observed heterozygosity within a population?

I am interested to compute observed heterozygosity for a population using genind object, rather than at a locus.

Many thanks for all your time.

Kind regards,

Rav

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