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MRCIEU / TwoSampleMR

R package for performing 2-sample MR using MR-Base database
https://mrcieu.github.io/TwoSampleMR
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Bug with the GWAS summary data #210

Open QinFinn opened 4 years ago

QinFinn commented 4 years ago

Dear Developing Team

Great thanks for this beautiful package and all the efforts in harmonising the GWAS summary data as well integrating the MR methods.

I have recently noticed there are some bugs with the harmonised GWAS data; e.g the GWAS summary data for the UKBB biomarker data released by Neale Lab. For example, the sample size in the database for HDL GWAS (id = ukb-d-30760_irnt) was set to NA but this was reported in the original GWAS summary data, also the P-values for some variants were wrongly reported (e.g. for rs12720922, the P-value in the original summary data was P=0, but in the TwoSampleMR package it was reported as P=1), P= 0 or 1 is hugely different and may lead to really wrong conclusions. Of course, we could estimate the correct P using beta and se, but I think at least I would let you know these bugs.

Best wishes, Qin

explodecomputer commented 4 years ago

Many thanks for this Qin, looking into it and will hopefully be able to fix soon