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yuanzhongshang / PMR

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Real data usage (moPMR-Egger) #4

Open PoojaMiddha opened 2 years ago

PoojaMiddha commented 2 years ago

Hi, Thank you for developing this interesting method for TWAS analysis of multiple correlated outcomes. I looked at the example provided based on simulation data. I have GWAS summary data (also have access to individual level data) and I want to use GTEx eQTL models. It is not very clear how to use this method for real data. Could you maybe share a more detailed description file or some suggestions? Thanks!

Best, Pooja.

yuanzhongshang commented 5 months ago

Hi Pooja,

Thank you for your patience. I apologize for the delayed response; I only recently came across your message.

Regarding your inquiry, moPMR-Egger is a joint likelihood-based method, which differs from the traditional two-stage TWAS method. Consequently, it cannot utilize existing eQTL weights from GTEx. The inputs for the summary verison of moPMR-Egger are the summary statistics from both GWAS and eQTL data.

Currently, we provide summary statistics from the GEUVADIS dataset for your use.

Thank you for your understanding. Please let me know if you have any further questions.

Best, Zhongshang