Plink 1.9 --ld and --r2/r
2
0
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5.4 years ago
Kousik ▴ 10

Hello, I am unable to understand that with respect to which allele plink (plink-1.90b3w) calculates the --r/r2. Although, it is written that it is based on the non-reference allele , but when I use major allele in A2 in the bim file, it gives the same matrix as it gives for when A2 is the reference allele.

Does --r/r2 option follow:

0 = both ref allele 1 = one ref and one alt allele 2 = both alt allele

OR

0 = both major allele 1 = one major and one minor allele 2 = both minor allele

OR

something else

I found --keep-allele-order and/or a2-allele do not have any effect on the r/r^2 matrix for a set of SNPs. Is this true or I am doing something wrong?

--ld option is based on haplotype frequency, which is different that --r/r2 option. But my question is the same as above. Which allele they follow (0,1, and 2).

Any help would be highly appreciated. Thank you very much.

plink SNP linkage disrqulibrium • 3.2k views
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5.4 years ago
mastal511 ★ 2.1k

The reference allele is usually the major allele.

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5.4 years ago
Kousik ▴ 10

Yes, but not always the case. I need to know how PLINK handles this.

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