comparing_packages

comparing_packages.r

library(TwoSampleMR)
library(RadialMR)
library(MendelianRandomization)

# Read in example data
a <- extract_instruments(2)
b <- extract_outcome_data(a$SNP, 7)
ab <- harmonise_data(a,b)
ab$SNP <- as.character(ab$SNP)
# IVW in TwoSampleMR package
TwoSampleMR::mr(ab, method_list="mr_ivw")

# IVW in MendelianRandomization package
ab2 <- dat_to_MRInput(ab)[[1]]
MendelianRandomization::mr_ivw(ab2)

# IVW in RadialMR package
ab3 <- format_radial(ab$beta.exposure, ab$beta.outcome, ab$se.exposure, ab$se.outcome, ab$SNP)
RadialMR::ivw_radial(ab3, weights=1)
RadialMR::ivw_radial(ab3, weights=2)
RadialMR::ivw_radial(ab3, weights=3)

# Manually do radial regression
w <- 1/ab$se.outcome^2
wr <- ab$beta.outcome / ab$beta.exposure
y <- wr * sqrt(wr)
x <- sqrt(w)
summary(lm(y ~ 0 + x))