[R-sig-genetics] LD calculation question

[Emmanuel Paradis]

Hi Felipe,

The only thing I can think of is that, if all loci are biallelic (eg, 
SNPs), to use LDscan and LDmap. Otherwise, you'll have to do pairs by 
pairs as you describe.

Best,

Emmanuel

Le 30/03/2017 à 21:47, Felipe Hernández a écrit :
> Hi everyone,
>
> I have been using the pegas package (function LD2) to calculate LD among a
> set of loci (52 loci) across 29 populations. I would like to do the same,
> but within each population this time. However, because all the multiple
> comparisons between loci pairs (considering the number of loci and
> populations), that would take a lot of time. Any suggestion about how to
> make it faster? Sorry if the question is really basic, but I would
> appreciate any helpful advice, thanks!
>
> Best,
> Felipe
>