R/reCenterPeaks.R

In ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges

#' re-center the peaks
#' 
#' Create a new list of peaks based on the peak centers of given list.
#' 
#' 
#' @param peaks An object of \link[GenomicRanges:GRanges-class]{GRanges} or
#' \link{annoGR}.
#' @param width The width of new peaks
#' @param ... Not used.
#' @return An object of GRanges.
#' @author Jianhong Ou
#' @keywords misc
#' @export
#' @examples
#' 
#'     reCenterPeaks(GRanges("chr1", IRanges(1, 10)), width=2)
#' 
reCenterPeaks <- function(peaks, width=2000L, ...){
    stopifnot(inherits(peaks, c("annoGR", "GRanges")))
    peaks.center <- start(peaks) + floor(width(peaks)/2)
    peaks.recentered <- peaks
    start(peaks.recentered) <- peaks.center - floor(width/2)
    width(peaks.recentered) <- width
    if(any(start(peaks.recentered)<1)){
      warning("Some start position of the peaks are less than 1!")
    }
    seqLen <- seqlengths(peaks)
    seqLen <- seqLen[!is.na(seqLen)]
    if(length(seqLen)>0){
      peaks.subset <- 
        peaks.recentered[seqnames(peaks.recentered) %in% names(seqLen)]
      if(any(end(peaks.subset)>seqLen[as.character(seqnames(peaks.subset))])){
        warning("Some end position of the peaks are out of bound!")
      }
    }
    peaks.recentered
}