R Package to compute observed heterozygosity within a population
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 _______________________________________________ R-sig-genetics mailing list R-sig-genetics at r-project.org<mailto:R-sig-genetics at r-project.org> https://stat.ethz.ch/mailman/listinfo/r-sig-genetics