README.md

Analysis for MR Base methods paper

Run main MR analysis

Perform analysis of LDL, trigs, Lp(a) on all best outcomes

cd scripts
Rscript run_mr.R

This saves a file in results/lpa_ldl_trigs.RData which contains the instruments published by Willer et al, and those variants extracted from a large set of disease and risk factor GWASs.

Generate graphs

LDL-CHD plots

Rscript ldl-chd.R

Sensitivity analyses for all exposure - outcome pairs with p < 0.05:

Rscript figure_sensitivity_boxes.R

Volcano plots:

Rscript figure_volcano_plots.R

Create tables

Rscript tables.R

PheWAS scripts

Rscript PheWAS.R