Getting non-overlapping loci from GWAS for colocalization analysis

find_loci.R

disjoinGr <- function(df, chr = "CHR", bp = "BP", pval = "Pval", snp = "SNP", size = 5e5) {
  inGr <- GRanges(df[[chr]], IRanges(df[[bp]] - size, df[[bp]] + size - 1),
                   SNPID = df[[snp]], BP = df[[bp]], Pval = df[[pval]])
  
  disjointGr <- disjoin(inGr)
  ov <- findOverlaps(resize(inGr, 1, "center"), disjointGr)
  hitGr <- disjointGr[subjectHits(ov)]
  ovGr <- setdiff(disjointGr, hitGr)
  firstHalf <- resize(ovGr, width(ovGr) / 2 - 1, "start")
  secondHalf <- resize(ovGr, width(ovGr) / 2, "end")
  cmbGr <- c(hitGr, firstHalf, secondHalf) 
  cmbGr <- reduce(cmbGr)
  ov1 <- findOverlaps(resize(inGr, 1, "center"), cmbGr)
  inGr <- inGr[queryHits(ov1)]
  outGr <- cmbGr[subjectHits(ov1)]
  start(inGr) <- start(outGr)
  end(inGr) <- end(outGr)
  
  outDf <- as.data.frame(inGr) %>%
    dplyr::rename(CHR = seqnames) %>%
    mutate(start = ifelse(start > 0, start, 0))
  
  return(outDf)
}