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RitchieLab / eQTpLot

Visualization of Colocalization Between eQTL and GWAS Data
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congruence or not? #20

Closed yqhu96 closed 9 months ago

yqhu96 commented 9 months ago

Considering that the positive or negative direction of the beta values for SNPs in GWAS can be achieved by swapping the effect allele and other allele, while in eQTL, there seems to be only one beta value, does this congruence still make sense?

TGDrivas commented 9 months ago

Thank you for pointing this out. Yes this is true -- this R package does not check to make sure that, for a given SNP, the effect allele is the same between the eQTL and GWAS data. We recommend that you ensure that your data are harmonized with regard to SNP identifier and effect allele before running eQTpLot. We will consider adding a harmonization step to future releases.