Question: Use Plink to calculate OR for homozygous ?
0
gravatar for lmobuchon
3.0 years ago by
lmobuchon40
lmobuchon40 wrote:

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

snp plink odd ratio • 1.1k views
ADD COMMENTlink modified 3.0 years ago by lmobuchon0 • written 3.0 years ago by lmobuchon40
0
gravatar for chrchang523
3.0 years ago by
chrchang5235.6k
United States
chrchang5235.6k wrote:

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.

ADD COMMENTlink written 3.0 years ago by chrchang5235.6k
0
gravatar for lmobuchon
3.0 years ago by
lmobuchon0
lmobuchon0 wrote:

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

ADD COMMENTlink written 3.0 years ago by lmobuchon0

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

ADD REPLYlink written 3.0 years ago by lmobuchon40
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