Dear All,
How do I interpret the results from PLINK2.0 when generating haplotype frequencies for three variants?
plink2 --bfile mydata --ld 12439 12340 --out gene_12439_12340
This generates the following results:
Solution #3 (best likelihood):
r^2 = 0.624219 D' = 1
Frequencies : 12439
(expectations under LE) MAJOR MINOR
---------- ----------
MAJOR 0.599307 0
(0.422837) (0.176470)
12340
MINOR 0.106236 0.294457
(0.282706) (0.117987)
Major alleles are in phase with each other.
Specifically, I obtained three solutions with different D' and R-squared values, where the first and third solutions had D' = 1, while the second had D' = 0.593841. Similarly, the R-squared values also varied.
Although I understand that an R-squared value of 0.624219 suggests moderate correlation between the two SNPs, and a D' value of 1 indicates perfect LD.
I am still struggling to interpret the frequencies given for the major and minor alleles in the 2X2 table. Additionally, I do not understand why these three solutions have different D' and R-squared values. Can anyone provide guidance on how to interpret these results?
