R/motifClassCount.R

In takahirosuzuki1980/InfiniumDiffMetMotR: Motif Overrepresentation analysis for Illumina Methylation Arrays

#' PWM Count
#' 
#' cunting PWMs in a window, sliding the window.
#'
#' @param motifPosi relative position of identified PWM from probe
#' @param windowSize window size
#' @param slide length of window sliding
#' @param seq_range range from probe position to be analyze
#'
#' @return a data frame of class and number of PWM.
#' 
#' @keywords count of PWM

motifClassCount <- function(motifPosi, windowSize, slide, seq_range){
  relativePosi <- 0
  freqs <- NULL
  class <- NULL
  windowStr <- seq_range[1] + relativePosi    #intitial start position
  windowEnd <- windowStr + windowSize    #intial end position
  while(windowEnd <= seq_range[2]){    #sliding
    windowStr <- seq_range[1] + relativePosi    #5' of window end
    windowEnd <- windowStr + windowSize    #3' of window end
    class <- c(class, windowStr+(windowSize/2))    #class (center of window)
    freqs <- c(freqs,sum((motifPosi >= windowStr) & (motifPosi <= windowEnd)))    #counting of motif frequency
    relativePosi <- relativePosi+slide    #Window sliding
  }
  freqs <- freqs
  motifCounts <- cbind(class, freqs)
  return (motifCounts)
}