inst/analysis/tg.R

In Chris1221/pRs: Polgenic Risk Score Toolkit in R

library(data.table)
library(dplyr)
library(magrittr)


tg <- fread("/scratch/hpc2862/lshtm/aprs/summary_data/jointGwasMc_LDL.txt", h = T)

tg <- tg[tg$P < 0.05,]

cad <- fread("~/cad.add.fixrand.dgc.anno.160614.out.txt", h = T)

cad %<>% select(legendrs, beta) %>% mutate(rsid = legendrs) %>% select(-legendrs)
tg %<>% select(rsid, A2)

tg <- merge(tg, cad, by = "rsid")

tg %>% select(rsid, A2, beta) %>% mutate(A2 = toupper(A2)) %>% write.table(file = "~/repos/aprs/data-raw/tg_0.05.raw", col.names = F, row.names = F, quote = F)