R/joinRegions.R

In bernatgel/regioneR: Association analysis of genomic regions based on permutation tests

#' Join Regions
#' 
#' @description 
#' Joins the regions from a region set A that are less than \code{min.dist} bases apart.
#' 
#' @note 
#' All metadata (additional columns in the region set in addition to chromosome, start and end) will be ignored and not present in the returned region set.
#' 
#' The implementation relies completely in the \code{\link{reduce}} function from \code{IRanges} package.
#' 
#' @usage 
#' joinRegions(A, min.dist=1)
#' 
#' @param A   a region set in any of the accepted formats by \code{\link{toGRanges}} (\code{\link{GenomicRanges}}, \code{\link{data.frame}}, etc...)
#' @param min.dist  an integer indicating the minimum distance required between two regions in order to not fuse them. Any pair of regions closer than \code{min.dist} bases will be fused in a larger region. Defaults to 1, so it will only join overlapping regions.
#' 
#' @return
#' It returns a \code{\link{GenomicRanges}} object with the regions resulting from the joining process.
#' 
#' @seealso \code{\link{plotRegions}}, \code{\link{toDataframe}}, \code{\link{toGRanges}}, \code{\link{subtractRegions}}, \code{\link{splitRegions}}, \code{\link{extendRegions}}, \code{\link{commonRegions}}, \code{\link{mergeRegions}}, \code{\link{overlapRegions}}
#' 
#' @examples
#' A <- data.frame("chr1", c(1, 10, 20, 30), c(12, 13, 28, 40))
#' 
#' join1 <- joinRegions(A)
#' 
#' join2 <- joinRegions(A, min.dist=3)
#' 
#' join3 <- joinRegions(A, min.dist=10)
#' 
#' plotRegions(list(A, join1, join2, join3), chromosome="chr1", regions.labels=c("A", "join1", "join2", "join3"), regions.colors=4:1)
#' 
#' @export joinRegions
#' 
#' @importFrom GenomicRanges reduce



#The implementation relies completely in the reduce function from IRanges
joinRegions <- function(A, min.dist=1) {
  
  if(!hasArg(A)) stop("A is missing")
  if(!is.numeric(min.dist)) stop("min.dist must be numeric")

  A <- toGRanges(A)
  
  return(GenomicRanges::reduce(A, min.gapwidth=min.dist))
  
}