In lorenzoFabbri/exposome-challenge: Code For The ISGlobal Exposome Challenge 2021

library(exposomeChallenge)
library(ggplot2)

Load datasets:

dat <- exposomeChallenge::loadExpData()

exposome <- dat$exp
met_serum <- dat$serum
met_urine <- dat$urine

Perform MWAS:

res <- exposomeChallenge::runMulRegressionSig(signatures = met_serum, 
                                              exposome = exposome, 
                                              formula = "hs_zbmi_who ~", 
                                              family = "gaussian")
# Apply correction for multiple testing
p.adjusted <- as.data.frame(p.adjust(res[, 1], method = "bonferroni"))
names(p.adjusted) <- "p.adjusted"
rownames(p.adjusted) <- rownames(res)

to_keep <- p.adjusted %>%
  filter(p.adjusted <= 0.05)
print(dim(to_keep))
print(to_keep)

lorenzoFabbri/exposome-challenge documentation built on March 13, 2021, 1:50 p.m.