Negative and positive linkage disequilibrium

Question

[fatima]

Hello everyone,

Could you explain me what is exactly the meaning of Negative and positive LD which mentioned in Plink "-flip-scan"?

The result fo the "--flip-scan" is plink.fipscan and I have nan for all elements of R_NEG column. What is the problem for that?

Thank you.

Answer 1

[seta]

Although it's late, as far as I know, under linkage disequilibrium, haplotypes do not occur at the frequencies expected when the alleles were independent. Positive linkage disequilibrium exists when two alleles occur together on the same haplotype more often than expected, and negative LD exists when alleles occur together on the same haplotype less often than expected.