I want to perform colocalization analysis between an eqtl- and a GWAS-dataset.
For this I want to use the
coloc.abf function from R coloc package.
Now the question is, which window size to define for this analysis.
My plan would be, to simply take as my "window" all SNPs, which are reported in the GWAS and which have an eqtl with the specific gene in gtex. What do you think about this?