P252222/IL33_Ketelaaretal_JACI2020
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AssociationScripts_Phenotype_Ketelaaretal JACI

M.E. Ketelaar 2020-02-17 19:33:49 +00:00
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This script belongs to the paper of Ketelaar, Portelli, Dijk et al.
Entitled 'Phenotypic and functional translation of IL33 genetics in asthma', submitted to JACI
Below example scripts of the association analyses between IL33 gemotype and phenotypes are shown, written for PLINK
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, et al. Am J Hum Genet 2007 Sep;81(3):559-575.
PLINK: a tool set for whole-genome association and population-based linkage analyses.'
Due to ethical restrictions we can only share code and summary statistics, no raw input data files
Version of PLINK: PLINK v1.90b3.32 64-bit (24 Feb 2016)
# #Step 1: load PLINK module:
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
###The phenotype is in the *.fam files. In the cov_XXX.txt files the covariates gender and age are included
## 2b DAG/GASP Meta-analysis on the association files from 2a:
--meta-analysis DAG_IL33_eosgt.assoc.dosage GASP_IL33_eosgt.assoc.dosage --out IL33_eosgt_meta