M.E. Ketelaar 2020-02-17 19:36:54 +00:00
parent eaba1a3243
commit a5d28ace7b

@ -11,12 +11,12 @@ 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: # 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: ## 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 ###The phenotype is in the *.fam files. In the cov_XXX.txt files the covariates gender and age are included