# Preprocessing of the data file for the practical
# Use the files used in 2023 but make them smaller 

library(data.table)
setwd("/home/perline/2024/PGSpractical")
gwas <- fread("input/GIANT_HEIGHT_YENGO_2022_GWAS_SUMMARY_STATS_EAS")
head(gwas)

gwas_short <- gwas[gwas$P < 1e-2, ]

write.table(gwas_short, "input/GIANT_HEIGHT_YENGO_2022_GWAS_SUMMARY_STATS_EAS_1e-2",
            quote=F, row.names = F)