[adegenet-forum] proportion of shared alleles

[jombart at biomserv.univ-lyon1.fr]

Quoting Grant Gillis <grant.j.gillis at gmail.com>:

> List and Thibaut,
>
> I posted this question on the R-sig-phylo list and Thibaut suggested that
> this is a more appropriate list.  Great looking package by the way.   I am
> looking for a way to calculate the proportions of shared alleles between
> individuals.  I have been looking through the documentation but am having a
> hard time getting started (a result of my lack of familiarity with R).  Any
> ideas or nudges in the right direction are appreciated.
>
> Grant
>

Dear Grant,

here is a function that should do what you want (called propShared), and that
will eventually become a part of adegenet.

I am out for vacations until tuesday, and all I have here is an old mac with
R 2.2 installed... So I could not test the function
as much as I would have liked to, but this is a start. The input is a genind
object, i.e. the representation of a set of genotypes in adegenet. It computes
the proportions of shared alleles for each locus, (function f1) and then
averages theses proportions over loci to get the overall measure. The handling
of missing data as it is here inderestimates the proportion of shared alleles.
I'll fix this in the final implementation of the method in the package, which
will likely be in C anyway.

Best,

Thibaut.



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