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Use Plink to calculate OR for homozygous ?

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
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updated by lmobuchon • lmobuchon • written by lmobuchon • lmobuchon

2 answers

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.

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written by chrchang523 chrchang523

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

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written by lmobuchon • lmobuchon

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

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written by lmobuchon • lmobuchon

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