Dear R helpers,
I am trying to test for linkage disequilibrium (LD) in R between all pairs
of loci. Importantly, my loci are microsatellites and have up to 30
alleles per locus. Do you know of any R packages that can either (1)
calculate measures of LD directly or (2) test for the presence of LD within
a statistical framework? Every package I have run across seems to be only
able to handle biallelic (e.g., SNP) data. I have
searched unsuccessfully both at CRAN and Bioconductor.
Many thanks for any help you can provide,
Mark Christie
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