[adegenet-forum] inbreeding coefficient

Jombart, Thibaut t.jombart at imperial.ac.uk
Thu Dec 18 16:39:11 CET 2014

Hi Marina,
'inbreeding' in adegenet will estimate the likelihood function of the inbreeding coefficient (F), which is a richer result than a mere test of significance: you get the full distribution of F, that is, which values of F are most likely given your data.
Note that 0.5 does not have any specific meaning here (did you mean 5%?), but it is actually quite a strong inbreeding already. F=0.5 means there are 50% chances of being homozygote through shared ancestry only.

From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Marina Mergey [mergey_marina at yahoo.fr]
Sent: 17 December 2014 09:29
To: adegenet-forum at lists.r-forge.r-project.org
Subject: [adegenet-forum] inbreeding coefficient

Hi everybody,
i'm sending a message for the first time on the forum and i would like to take this opportunity to thank all of you and your messages for their interesting help .
At the moment, i'm trying to understand significant positive Fis in many study sites. I checked for null alleles first and it's ok for the set of loci. Then i would like to discriminate inbreeding consequences and wahlund effect. So i would like to know if i can use the mean inbreeding coefficient for each study site (from the inbreeding function in the adegenet package) to validate or not the inbreeding hypothesis. Is it enough to reject it since all the values are under 0.5 ?
Thanks for your help,
All the best,

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