Instrument strength of pQTLs

pqtl_inst_strength.r

library(readxl)
library(dplyr)

download.file("https://www.biorxiv.org/content/biorxiv/early/2022/06/18/2022.06.17.496443/DC2/embed/media-2.xlsx?download=true", here("data", "media-2.xlsx"))
a <- read_xlsx(here("data", "media-2.xlsx"), sheet="ST6", skip=2) %>% 
  dplyr::select(
    exposure="Assay Target",
    id.exposure="Assay Target",
    SNP="rsID", 
    beta.exposure="BETA (discovery, wrt. A1)", 
    se.exposure="SE (discovery)", 
    pval.exposure="log10(p) (discovery)", 
    eaf.exposure="A1FREQ (discovery)", 
    snpid="Variant ID (CHROM:GENPOS (hg37):A0:A1:imp:v1)",
    cistrans.exposure=`cis/trans`) %>% 
  mutate(pval.exposure = 10^-pval.exposure) %>%
  tidyr::separate(snpid, sep=":", into=c("chr.exposure","pos.exposure","other_allele.exposure", "effect_allele.exposure", "imp", "v"))
a$n <- 35571
a$F <- a$beta.exposure^2 / a$se.exposure^2
a$r2 <- a$F / (a$F + a$n-1)
write.csv(a, file="~/Downloads/pqtl_instrument_strength.csv")