From eaba1a324336a61bd70b4be811daf5f4552c9e63 Mon Sep 17 00:00:00 2001 From: "M.E. Ketelaar" Date: Mon, 17 Feb 2020 19:35:06 +0000 Subject: [PATCH] --- Home.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Home.md b/Home.md index b35d43f..fd75088 100644 --- a/Home.md +++ b/Home.md @@ -9,14 +9,14 @@ Due to ethical restrictions we can only share code and summary statistics, no ra Version of PLINK: PLINK v1.90b3.32 64-bit (24 Feb 2016) -### #Step 1: load PLINK module: + #Step 1: load PLINK module: - module load plink/v1.90b3.32 + --module load plink/v1.90b3.32 # Step 2: Perform association analyses between IL33 (imputed) genotype (400kb region, defined by start/stop SNP) and phenotype: ## 2a LIFELINES/DAG?GASP individual cohorts: Binary or continous phenotype: - plink --noweb --fam "file.fam" --allow-no-sex --dosage "imputedgenofile.dose" noheader format=2 Zin --map "file.bim" --from rs61134586 --to rs73639329 --pheno "phenofile.dat" --missing-phenotype -9 --covar "covarfile.dat" --out "outfile.txt" --ci 0.95 + --plink --noweb --fam "file.fam" --allow-no-sex --dosage "imputedgenofile.dose" noheader format=2 Zin --map "file.bim" --from rs61134586 --to rs73639329 --pheno "phenofile.dat" --missing-phenotype -9 --covar "covarfile.dat" --out "outfile.txt" --ci 0.95 ###The phenotype is in the *.fam files. In the cov_XXX.txt files the covariates gender and age are included