dha_ukbb_finemapping

dha_ukbb_finemapping.r

library(gwasglue)
library(ieugwasr)
library(tidyverse)
library(susieR)
library(glue)

# DHA fine mapping
temp <- associations("11:61200000-62100000", "met-d-DHA")
ggplot(temp, aes(x=position, y=-log10(p))) +
geom_point()


r <- extract_regional_data(chr=11, position=61650000, radius=500000, ids="met-d-DHA", bfiles <- "/Users/gh13047/data/ld_files/ldmat/EUR", plink = "plink")

ggplot(r[[1]]$x, aes(x=position.exposure, y=-log10(pval.exposure))) +
geom_point()


su <- susieR::susie_rss(z = r[[1]]$x$beta.exposure/r[[1]]$x$se.exposure, R = r[[1]]$ld, check_R=FALSE)

susie_plot(su, "PIP")

# took 3 days to run lol
paintor <- run_PAINTOR(r)