R/15.get_PAscore.R

In haibol2016/InPAS: Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data

#' Calculate the CP score
#'
#' Calculate the CP score by using PWM of polyadenylation signal with sequence
#' around given position
#'
#' @param seqname a character(n) vector, the chromosome/scaffold' name
#' @param pos genomic positions
#' @param str DNA strand
#' @param idx offset position
#' @param PWM An R object for a position weight matrix (PWM) for a hexamer
#'   polyadenylation signal (PAS), such as AAUAAA.
#' @param genome an object of [BSgenome::BSgenome-class]
#' @param ups the number of upstream bases for PAS search.
#' @param dws the number of downstream bases for PAS search.
#' @return A list containing offset positions after PA score-based filtering
#' @import GenomicRanges
#' @seealso [get_PAscore2()]
#' @keywords internal
#' @author Jianhong Ou

get_PAscore <- function(seqname,
                        pos,
                        str,
                        idx,
                        PWM,
                        genome,
                        ups = 50,
                        dws = 50) {
  pos <- pos[!is.na(pos)]
  if (length(pos) < 1) {
    return(NULL)
  }
  start <- pos - ups
  start[start < 1] <- 1
  end <- pos + dws
  gr <- GRanges(seqname, IRanges(start, end,
    names = as.character(pos)
  ),
  strand = str
  )
  seq <- getSeq(genome, gr)

  mT <- future_lapply(seq, matchPWM,
    pwm = PWM,
    min.score = "70%", with.score = TRUE
  )

  hits <- sapply(mT, function(.ele) {
    if (!is(.ele, "XStringViews")) {
      return(FALSE)
    }
    if (length(.ele) == 0) {
      return(FALSE)
    }
    TRUE
  })
  idx[hits]
}