[adegenet-forum] inbreeding coefficient with GBS-SNPs data

[Jombart, Thibaut]

Hi there, 

sorry but this question is too vague for me to answer properly. 

If the question is: 'do you think your inbreeding function works', my answer is yes, as it seems to work on data I tested it on.

If the question is: 'does it scale well', the answer is not too well. The more loci we have the more we bumped into numerical approximation problems - this issue has been documented on this forum before, worth checking the archives. Thing is, not so many loci are needed to estimate F, and ideally only unliked ones should be kept. 

The point of 0.5 estimate may be meaningless. If there is no information on inbreeding in the data, you expect a flat distribution for F and 0.5 to be the mean. Is it what you are seeing? Distributions peaking at 0.5 would be a different problem.

If you suspect the computations are wrong, please either check the code or come up with an example showing an issue.  

I will investigate the warning. The example currently fails in adegenet 2.0 and this needs fixing.

Cheers
Thibaut
==============================
Dr Thibaut Jombart
MRC Centre for Outbreak Analysis and Modelling
Department of Infectious Disease Epidemiology
Imperial College - School of Public Health
Norfolk Place, London W2 1PG, UK
Tel. : 0044 (0)20 7594 3658
http://sites.google.com/site/thibautjombart/
http://sites.google.com/site/therepiproject/
http://adegenet.r-forge.r-project.org/
Twitter: @thibautjombart



________________________________________
From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Julie Jacquemin [Julie.Jacquemin at uni-hohenheim.de]
Sent: 21 May 2015 13:09
To: adegenet-forum at lists.r-forge.r-project.org
Subject: [adegenet-forum] inbreeding coefficient with GBS-SNPs data

Hello,

I am trying to calculate inbreeding coefficients for each individual for
my different subpopulations. I have thousands of SNPs data, from
Genotyping-by-sequencing. I tried to use the function inbreeding in
Adegenet but i'm not certain about the results.
Here is the command i used and one of my structure file is attached.

genind_obj <-
read.structure(file="data.stru",n.ind=21,n.loc=6583,onerowperind=FALSE,col.lab=1,col.pop=2,row.marknames=1,NA.char="-9",missing="NA")

tempcebe <- inbreeding (genind_obj, N=300)
Fmeandistricebe <- sapply(tempcebe, mean)

#and to have the mean over the whole subpopulation
mean(Fmeandistricebe)

My problem is that i obtain, for all my subpopulations (i had three
differents) but also when i run it for the global population, always
values of F ~ 0,5, for all individuals and for the general mean of
course. Also two of my colleagues used the same procedure on their GBS
dataset for completely other species, and they also obtain always F very
close to 0,5. So i'm thinking they may be an artifact and 0,5 is not the
real value i should observe.

I also tried with different values for N (nothing changed) and with
returning the likelihood function
tempcebe <- inbreeding (genind_obj, N=100, res.type="function")
And here i only obtained warnings
(1: In mean.default(X[[1L]], ...) :
   argument is not numeric or logical: returning NA
2: In mean.default(X[[2L]], ...) :
   argument is not numeric or logical: returning NA
...)

and only NA values were returned for all individuals.

I would be glad to have your comments on this problem. Does this 0,5
recurrent value seem normal? Is the inbreeding function not adapted for
NGS data with big number of loci? Or is it a problem with the missing
values? Unfortunately with GBS i can not avoid those, i don't have any
locus with 0 missing values...Would you suggest anything?

Thanks in advance for your help

Best

Julie

?



--
Julie Jacquemin, PhD.
Post-doc
Crop Biodiversity and Breeding Informatics Group (350b)
Institute of Plant Breeding, Seed Science and Population Genetics
University of Hohenheim
Fruwirthstrasse 21, Room 0.25
D-70599 Stuttgart
Phone: +49-711-459 24437
jjacquem at uni-hohenheim.de