CodeToRun.R

rm(list = ls())
library(magrittr)
library(dplyr)
library(ggplot2)
library(here)
library(flextable)
source(here("Functions","Functions.R"))

pathData <- 'D:/Projects/PDE5_AD_MendelianRandomisation/'
dir.create(paste0(pathData,"Results/"))
pathResults <- paste0(pathData,"Results/")
pathUKB <- paste0(pathData,"UKBiobank/")

# Instrument selection
source(here::here("Scripts/1-InstrumentSelection.R"))

# Mendelian randomisation
dir.create(paste0(pathResults,"MR_Results"))
source(here::here("Scripts/2-MendelianRandomisation.R"))

# Mendelian randomisation - sex stratified
dir.create(paste0(pathResults,"MR_Results"))
source(here::here("Scripts/2-MendelianRandomisation.R"))

# Colocalisation
dir.create(paste0(pathResults,"Colocalisation"))
source(here::here("Scripts/3-Colocalisation.R"))

# Two-step mendelian randomisation
dir.create(paste0(pathResults,"TwoStepMR"))
source(here::here("Scripts/4-TwoStepMR.R"))

# Leave-one-out analysis
dir.create(paste0(pathResults,"LeaveOneOutAnalysis"))
source(here::here("Scripts/4-LeaveOneOutAnalysis.R"))

# Sex-specific
dir.create(paste0(pathResults,"SexSpecific"))
source(here::here("Scripts/5-UKBiobank.R"))

# Figures and tables from the article
dir.create(paste0(pathResults,"TablesAndFigures"))
source(here::here("Scripts/TablesAndFigures.R"))