Zepeng-Mu

ggQQplot <- function(pList, colVec = c("black", "orange", "red", "purple"),
                     legendLabel = NULL, title = "", openRange = F, sampling = 1) {

  if (is.null(legendLabel)) {
    legendLabel = colVec
  }

  if (length(pList) > length(colVec)) {
    stop("pList needs to be shorter than colVec!!!")
  }

Zepeng-Mu

getFDR <- function(Stat, Stat0) {
  m <- length(Stat)
  n <- length(Stat0)
  v <- c(rep(T, m), rep(F, n))
  v <- v[order(c(Stat, Stat0), decreasing = T)]
  vSumT <- (m - cumsum(v == T)[v == T] + 1) / m
  vSumF <- (n - cumsum(v == F)[v == T]) / n
  fdr <- cummin(pmin(1, vSumF / vSumT))
  fdr <- fdr[rank(-Stat)]
  return(fdr)

Zepeng-Mu

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")