formatedMan.R

#!/usr/bin/env Rscript
```{r}
library(data.table)
library(dplyr)
library(qqman)
library(data.table)


getwd()
# ---- Input / Output ----
infile  <- "/wynton/group/andrews/users/rakshyasharma/PRS/MR/data/formated/BelloyAll_AD/BelloyAll_AD_formated.txt.gz"
outfile <- "/wynton/group/andrews/users/rakshyasharma/PRS/MR/results/BelloyAll_AD_Manhattan.png"

# ---- Read data ----
message("Reading: ", infile)
df <- fread(infile)
df
# ---- Standardize chromosome ----
df <- df %>%
  mutate(CHR = gsub("^chr", "", CHROM)) %>%          # remove 'chr' prefix if exists
  mutate(CHR = ifelse(CHR %in% c("X","Y","MT"), NA, as.numeric(CHR))) %>%
  filter(!is.na(CHR)) %>%
  rename(BP = POS)

# ---- Build qqman input ----
man_df <- df %>% select(SNP, CHR, BP, P)

# ---- Plot ----
png(outfile, width = 1600, height = 600)
manhattan(
  man_df,
  chr = "CHR",
  bp  = "BP",
  snp = "SNP",
  p   = "P",
  genomewideline = -log10(5e-8),
  suggestiveline = -log10(1e-5),
  cex = 0.6,
  cex.axis = 0.8,
  col = c("#4E79A7", "#E15759"),
  main = "Belloy ALL Alzheimer's GWAS (formatted)"
)
dev.off()

message("Saved: ", outfile)
```