commit 2d7386444dba47448a8feabca0596983ad4399c2
Author: M.E. Ketelaar <m.e.ketelaar@rug.nl>
Date:   Mon Feb 17 19:33:49 2020 +0000

    AssociationScripts_Phenotype_Ketelaaretal JACI

diff --git a/Home.md b/Home.md
new file mode 100644
index 0000000..ef14704
--- /dev/null
+++ b/Home.md
@@ -0,0 +1,26 @@
+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
\ No newline at end of file