Does PLINK 2.0 perform genotype-environment interactions?

Hasnat A

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Aug 5, 2018, 8:44:41 AM8/5/18

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Hi,

A quick question to check that the results I'm getting are what I think they are.

plink2 --pfile called --pheno cognition.pheno --covar pcs.age.covar --glm interaction --out results1

The cognition.pheno files contains 1 continuous phenotype and the pcs.age.covar contains 11 continuous covariates and the last of these 11 is labelled age. In the results file, there are lines containing ADDxage. Am I correct in thinking that the statistics reported in these lines refer to a linear regression model with a genotype*age interaction term along with 10 covariates?

Thank you,

Hasnat

Christopher Chang

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Aug 6, 2018, 11:43:44 AM8/6/18

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No, there should be 11 interaction terms and 11 covariates. To cherry-pick interaction terms and covariates, use the --parameters flag.

Hasnat A

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Aug 6, 2018, 4:13:11 PM8/6/18

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Thank you.

Hasnat A

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Aug 6, 2018, 4:36:22 PM8/6/18

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cognition = PC1 + PC2 + PC3 + PC4 + PC5 + PC6 + PC7 + PC8 + PC9 + PC10 + age + genotype + age*genotype

Is the above model possible to run in PLINK 2.0?

Christopher Chang

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Aug 6, 2018, 5:07:05 PM8/6/18

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Yes; read the --parameters documentation under http://www.cog-genomics.org/plink/1.9/assoc#linear .

Sanjeev Sariya

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Jun 19, 2019, 3:55:42 PM6/19/19

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Sorry Chris the documentation is absolutely confusing for new entrant.

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