Use Plink to calculate OR for homozygous ?

Question

[lmobuchon]

Hi everyone,

I would like to calculate OR for heterozygous and homozygous for the risk allele of the SNP I identified by GWAS. I only succeed in calculating OR for heterozygous using logistic regression. Does anyone know how to do it for homozygous using Plink ? Thanks a lot in advance ! Best,

Lenha

Answer 1

[chrchang523]

plink's logistic regression normally uses the assumption that OR(homozygous for risk allele) is the square of OR(heterozygous for risk allele). You can use "--logistic hethom" instead of --logistic to tell plink to treat homozygous calls and heterozygous calls independently, but prepare to see many more "NA" results when the minor allele frequency is low.

Answer 2

[lmobuchon]

Thank you so much ! I am going to try --logistic hethom !

[lmobuchon]

It's worked with --logistic --genotypic --hethom ! Thanks !