Should I perform eQTL colocalization for just one of eGenes at a time?
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11 weeks ago
maximal_life ▴ 20

Thank you for reading and answering in advance.

Hello, now I want to do GWAS-eQTL colocalization analysis and I'm totally new to colocalization. I'm planning to use coloc or eCaviar. But, according to the manual, It seems that I should manually divide genomic regions for colocalization and should input one region at a time.

I want to perform colocalization for all of eGenes from my three eQTL results. Also, I have three GWAS summary stats for colocalization. (thus, 3 GWAS X 3 eQTL -> 9 Coloc.) I will set each of several thousand of eGene as a region for colocalization. If I have to perform colocalization for a region at a time, It will be extremely hard work.

Is there any way to do genome-widely? Or I just should deal with each eGene at a time?

colocalization coloc eCaviar eQTL • 196 views
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