R/write.bed.R

In robinweide/RHWlib: Simple functions to make life... simpler.

#' Write bed
#'
#' DF in, bed written
#'
#' @param df A dataframe with bed-like first three columns
#' @param path Full path for output
#' @param chromSizesPath The path to a chrom.sizes file
#' @param chr Prepend chr to chromosome-names
#' @param sort Do you want a sorted df?
#' @return A genomicRanges-object
#' @export
write.bed <- function(df, path, chromSizesPath, chr = T, sort = F){
  require(data.table)
  chromSizes <- data.table::fread(chromSizesPath, data.table = F)

  for(chromosome in unique(df[,1])){
    currChromDF <- df[df[,1] == chromosome,]
    chromSize <- chromSizes[chromSizes[,1] == chromosome,2]

    bigger <- currChromDF[,3] > chromSize
    df[bigger,3] <- chromSize
  }

  if(sort == T){
    # Sort
    o = order(df[, 1])
    bed = df[o,]

    od = 1:ncol(bed)
    chroms <- unique(df[,1])
    for (i in chroms)
    {
      chr.bed = bed[bed[, 1]==i,]
      o = order (as.integer(as.character(chr.bed[,2])))
      od = rbind (od, chr.bed[o, ])
    }
    od = od [-1,]
    colnames (od)= colnames(bed)

    options(scipen = 99999999)

    write.table(od, file = path, quote = F, sep = "\t", row.names = F, col.names = F)

    invisible(od)
  } else {

    write.table(df, file = path, quote = F, sep = "\t", row.names = F, col.names = F)

    invisible(df)

  }


}