Step 6. Collect Information About the Current R Session.
Contact
The Centre for Artificial Intelligence Driven Drug Discovery (AIDD) at Macao Polytechnic University.
Location:
匯智樓 (WUI CHI)-4/F, N46B, Rua de Luís Gonzaga Gomes, Macau
Email:
kefengl@mpu.edu.mo
Call:
(+853) 8599 6883
Open Hours:
Mon-Fri: 10AM - 16PM
Two sample Mendelian randomization (2SMR)
Two sample Mendelian randomization (2SMR) is a method to estimate the causal effect of an exposure on an outcome using only summary statistics from genome wide association studies (GWAS).
The TwoSampleMR package aims to make this easy by combining three important components.
Click here for a demo:
The general principles (G. Davey Smith and Ebrahim 2003; George Davey Smith and Hemani 2014), and statistical methods (Pierce and Burgess 2013; Bowden, Davey Smith, and Burgess 2015) can be found elsewhere, here we will just outline how to use the application base on the TwoSampleMR R package.
The workflow for performing 2SMR is as follows:
- Select instruments for the exposure (perform LD clumping if necessary).
- Extract the instruments from the IEU GWAS database for the outcomes of interest.
- Harmonise the effect sizes for the instruments on the exposures and the outcomes to be each for the same reference allele.
- Perform MR analysis, sensitivity analyses, create plots, compile reports.
A diagrammatic overview is shown here:
