R/makeAccMatrix.R

In FabianErdel/RWire: Identification of co-regulated genomic regions based on correlation analysis

#' This function makes accessibility matrices from a set of BED files
#'
#' @param path Path to BED files
#' @param rois GRanges object containing ROIs
#' @param nmax Number of cells used for the analysis. When set to 0, all cells will be considered.
#' @return Accessibility matrix
#' @export

makeAccMatrix<-function(path, rois, nmax = 0) {
  # check input arguments
  if(!file.exists(path)) stop("file not found")
  if(!is.numeric(nmax)) stop("nmax must be a number")

  # determine number of ROIs
  nrois <- length(rois)

  # determine number of BED files in path
  files <- list.files(path, "*.bed")
  ncells <- length(files)

  # reduce ncells if applicable
  if((nmax > 0) & (ncells > nmax)) {ncells = nmax}

  # initialize data frame
  am <- new("AccMatrix",
            coord = data.frame(chr = as.character(seqnames(rois)), start = start(rois), end = end(rois), stringsAsFactors=F),
            accmat = data.frame(rep(0,length(rois))))

  # loop through BED files
  for(i in 1:ncells) {
    # print progress
    print(paste0(i,"/",ncells,":   ",path,"/",files[i]))

    # read BED file
    data <- readBed(paste0(path,"/",files[i]))

    # count reads in ROIs
    cnt <- countReads(data, rois)

    # write counts in accessibility matrix
    am@accmat[,i] <- cnt
  }

  # add column names
  colnames(am@accmat) <- c(paste0(path,"/",files[1:ncells]))

  # return accessibility matrix
  return(am)
}