Question: Plink 1.9 --ld and --r2/r
0
gravatar for Kousik
3.1 years ago by
Kousik10
Germany
Kousik10 wrote:

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.

ADD COMMENTlink modified 15 months ago by Biostar ♦♦ 20 • written 3.1 years ago by Kousik10
0
gravatar for mastal511
3.1 years ago by
mastal5112.0k
mastal5112.0k wrote:

The reference allele is usually the major allele.

ADD COMMENTlink written 3.1 years ago by mastal5112.0k
0
gravatar for Kousik
3.1 years ago by
Kousik10
Germany
Kousik10 wrote:

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

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by Kousik10
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