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3.2 years ago
hyekyung.hkj
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0
Hello
I am studying gwas research and genetic-environment interaction.
plink --bfile myfile--pheno diz.txt --pheno-name diz--logistic --ci 0.95 --covar diz.txt --covar-name AGE,SEX,BMI --allow-no-sex --interaction --parameters 1,2,3,4,5,6,7,8 --snps-only just-acgt --out result.
In this case, none of the analyzed values of the variables appear, and the covariate also appears as NA.
- I dont know how to set the order of parameters
- How is 1,2,3,4,5,6,7,8 determined?
- How to write the header of environment variable when 1,2.3.4.5.6.7.8 of parameters is determined
- How to make the structure of the txt file?
- I don't know how to write environment variable headers, etc..
Hi, you posted this question already. Can you confirm that you have read the PLINK documentation? The functioning of
--parametersis explained —with examples— here: https://www.cog-genomics.org/plink/1.9/assocHi, I read the plink description below, but I dont understand. I want to analyze the interaction of genome x environmental variable and genome x covariate.
Which option formula to use
Great. By the way, these are the same thing:
genome x environmental variable == genome x covariateYou are already specifying covariates via:
--covar-name AGE,SEX,BMIYour covariates file (diz.txt) is the same as your phenotype file (diz.txt)?
The order of the sample entries in diz.txt must be the exact same as the order of sample entries in myfile