[R-sig-genetics] Microsatellite analysis - Genetic Structure

[Jombart, Thibaut]

Dear Marcelo, 

numbers of alleles per locus and heterozygosity (expected, observed) are given by the summary function of genind objects in adegenet. Global F statistics can be computed using the function fstat, and pairwise Fst using pairwise.fst. You will find more information on the adegenet website:
http://adegenet.r-forge.r-project.org/

All the best,

Thibaut

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Dr Thibaut JOMBART
MRC Centre for Outbreak Analysis and Modelling
Department of Infectious Disease Epidemiology
Imperial College - Faculty of Medicine
St Mary’s Campus
Norfolk Place
London W2 1PG
United Kingdom
Tel. : 0044 (0)20 7594 3658
t.jombart at imperial.ac.uk
http://sites.google.com/site/thibautjombart/
http://adegenet.r-forge.r-project.org/

________________________________________
From: r-sig-genetics-bounces at r-project.org [r-sig-genetics-bounces at r-project.org] On Behalf Of Marcelo Laia [marcelolaia at gmail.com]
Sent: 22 March 2011 12:37
To: r-sig-genetics at r-project.org
Subject: [R-sig-genetics] Microsatellite analysis - Genetic Structure

Hi,

I would like to calculate genetic polymorphism for each population (mean number
of alleles per locus (A), the percentage of polymorphic loci (P), the mean
observed heterozygosity (HO) and the mean expected heterozygosity
under Hardy-Weinberg equilibrium (HE)), and population differentiation (analyzed
for polymorphic loci by F-statistics (Wright 1978)).

Please, could you point me out any paper or packages that do that?

Thank you very much!

Marcelo

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