LD in genlight objects

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Marcela Rodriguero

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Jul 6, 2021, 10:06:25 AM7/6/21

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Dear All, I have a vcf file with 68290 SNPs. I converted this into a genlight object to run poppr. However, when trying to estimate LD, I converted it to genind in order to use the ia test I have found in https://grunwaldlab.github.io/Population_Genetics_in_R/Linkage_disequilibrium.html

since this cannot use genlight objects as input. But whenever I intend to run the analysis, R aborts the session. Maybe this is a too much big file to be converted in genind?

I tried to run ia with a genlight object and replaced “ia(data, sample = 999)” by “samp.ia(data, n.snp = XXX, reps = 999, threads = 0, quiet = FALSE)”

My question is, how many loci should I try? I am trying 10000. Is this enough, is this not enough? How many should I try? Any other suggestions t estimate LD? Thanks in advance. Kindest regards,