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datduong / RECOV

Meta analysis using explicit covariance matrix
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comparison between RECOV and RE2C #4

Open jackhump opened 3 years ago

jackhump commented 3 years ago

Dear Dr Duong,

I was excited to try using RECOV to perform a meta-analysis of eQTL summary statistics between a set of different tissues.

Because I want to generate meta-analysed P-values for every SNP-Gene association, this results in millions of tests, and unfortunately for this purpose RECOV is currently too slow - it's been 6 hours and chr1 is at < 1% of associations processed I'm thinking of trying the RE2C method instead, also from Buhm Han's group.

I don't have a strong statistical background so I'm not sure of the precise differences between the tools. Reading the papers they seem to be solving a similar problem. Can you advise on this?

best wishes,

Jack

datduong commented 3 years ago

Hi Jack, please call me Dat. I would recommend Prof. Buhm Han's method. I graduated recently and got a new job, not sure if I will have a lot of free time. When I ran Recov some years ago, I parallelized the code on multiple nodes at the school server. It does run very slow, I should have really written the code in Python which could have been faster. I can answer any other questions about this code/method if you like.

jackhump commented 3 years ago

Thanks for your quick reply Dat! I understand about your time commitments.

I'll check out RE2C.

datduong commented 3 years ago

Thanks. Let me know if you have problem reaching out to Buhm.