[R-sig-genetics] Linkage disequilibrium estimation

[Vikram Chhatre]

You should be able to compute LD between any two loci located anywhere in
the genome, including those on different chromosomes (although the latter
usually indicates other causes than linkage).  By 'contiguous', do you mean
'sequential' or 'consecutive'?  If so, that is not necessary.  Though I
will agree that from the Pegas documentation, it is not clear what numbers
the "locus=x:y" argument is referring to.  Is it an internal number?  Have
you tried computing another combination? locus=20:25, in case Pegas
starting the locus count at 0 and then 59 is non-existent?

V

On Mon, Nov 21, 2016 at 7:27 AM, Felipe Hernández <fhernandeu at uc.cl> wrote:

> Hello everyone,
>
> I would like to estimate if some of the alleles of my hog loci dataset (n=
> 59 loci) may be in linkage disequilibrium. I tried using the pegas package.
> I used the LD2 function (for unphased genotypes). In general, I got pretty
> low Delta correlation values for the loci pairwise-comparisons, but
> p-values associated with T2 were consistently significant (just trying a
> few loci comparisons). So, may I just conclude LD based on this p-value
> confidently? If that's the case, is it possible to compare loci that are
> not contiguous in the dataset? For example, when I tried comparing loci
> that are not contiguous (e.g., 50 and 59), I got this warning message:
> "Error in LD2(hogs, locus = 50:59, details = TRUE) : you must specify two
> loci to compute linkage disequilibrium"
>
> On the other hand, I wonder is there is another package to test LD between
> several multi-allelic loci at the same time (not only two loci)? Thanks for
> your feedback!
>
> Best,
> Felipe
>
> --
> Felipe Hernández
> Médico Veterinario (DVM), MSc.
> PhD. Candidate
> Interdisciplinary Ecology Program
> School of Natural Resources and Environment
> Wildlife Ecology and Conservation Department
> University of Florida
>
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