chr1swallace/coloc

Using coloc for conditionally independent eQTLs in the HLA region

joycekang opened this issue · 3 comments

joycekang commented

Hi Chris,

Thanks for making this fantastic package!

I had a conceptual question - I performed an eQTL analysis within the HLA region, and also did multiple rounds of conditional analysis to find additional independent signals (conditioning on the top variant in each round(s) before). I also did this in 3 cell types. So for example for each gene, I have potentially multiple conditionally independent eQTLs in 3 cell types.

What I'd like to do is compare the eQTLs across cell types to see if any overlap, for example maybe for a given gene, the secondary eQTL signal in cell type 1 colocalizes with the tertiary eQTL signal in cell type 3. Do you think coloc.abf would be appropriate since at each round, I've residualized out the effect of previous round(s)?

Thanks for your advice!
Joyce

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