mrcieu / mr-maternal-smoking

Analysis code for proxy gene-by-environment Mendelian randomization of maternal smoking on offspring health

Proxy gene × environment Mendelian randomization study

This study uses UK Biobank participants' 'smoking heaviness' SNP rs16969968 in gene CHRNA5 as a proxy of their mother's rs16969968.

This repository accompanies the paper:

Yang Q, et al. A proof of principle proxy gene × environment Mendelian randomization study: Testing causal effects of maternal smoking heaviness during pregnancy. bioRxiv (2019).

Our analyses mainly have 5 steps:

(1) Extract genotype information

(2) Extract phenotype information

(3) Conduct MR analyses

(4) Visualize MR results

(5) Compare statistical power of G-by-E MR with that of proxy G-by-E MR in the simulation

Set enviromental variables

To extract genotype information from UKB shared data using Linux, we set the following environment variable:

export UKB_DATA="/path/to/ukb/data"

We run all R scripts in Windows by setting the folders containing extracted input data, output results and UKB shared data in R (version 3.5.1) as below:

Sys.setenv(Mydata="/path/to/extracted/input/data")
Sys.setenv(Myresults="/path/to/output/results")
Sys.setenv(UKB_DATA="/path/to/ukb/data")

mr-maternal-smoking's Issues

Running the analysis on local computer

Hi I am new to the MR analysis and in need to conduct GXE and I am wondering for step 1 can I use my computer, I guess that will require a lot of computational power right? what do you advise?