#' Title
#'
#' Description
#'
#' @usage get_peaks(data, quantile = 0.999, snp.annot = TRUE, rm.loc = TRUE)
#'
#' @param data description
#' @param quantile description
#' @param snp.annot description
#' @param rm.loc description
#'
#' @return description
#'
#' @import data.table
#' @export
get_peaks <- function(data, quantile = 0.999, snp.annot = TRUE, rm.loc = TRUE) {
# Managing arguments
data <- copy(data)
qtl <- quantile(x = data[, PBS], quantile)
# Getting desired peaks
data <- data[data[, .I[PBS >= qtl], by = CHR]$V1]
# SNP Annotation
if(snp.annot) {
data[, GENE := snp.annot(SNP)][]
setcolorder(data, c("CHR","CM","POS","SNP","GENE","PBS"))
if(rm.loc) {
data[, GENE := sapply(GENE, function(.) {
genes <- unlist(strsplit(., ","))
genes <- genes[!grepl("LOC", genes)]
paste(genes, collapse = ",")
})]
}
data[GENE == "", GENE := NA][]
}
return(data)
}
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