[R-sig-genetics] Linkage disequilibrium estimation

[Felipe Hernández]

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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