R/bed_to_granges.R

In davetang/bedr: BED to GRanges

#' BED to GRanges
#'
#' This function loads a BED-like file and stores it as a GRanges object.
#' The tab-delimited file must be ordered as 'chr', 'start', 'end', 'id', 'score', 'strand'.
#' The minimal BED file must have the 'chr', 'start', 'end' columns.
#' Any columns after the strand column are ignored.
#' 
#' @param file Location of your file
#' @param header Logical for whether file has a header (default = FALSE)
#' @keywords BED GRanges
#' @export
#' @examples
#' bed_to_granges('my_bed_file.bed')

bed_to_granges <- function(file, header = FALSE){
   df <- read.table(file,
                    header = header,
                    stringsAsFactors = FALSE)

   if(length(df) > 6){
      df <- df[,-c(7:length(df))]
   }

   if(length(df)<3){
      stop("File has less than 3 columns")
   }

   header <- c('chr','start','end','id','score','strand')
   names(df) <- header[1:length(names(df))]
   
   if('strand' %in% colnames(df)){
      df$strand <- gsub(pattern="[^+-]+", replacement = '*', x = df$strand)
   }
   
   library("GenomicRanges")

   if(length(df)==3){
      gr <- with(df, GRanges(chr, IRanges(start, end)))
   } else if (length(df)==4){
      gr <- with(df, GRanges(chr, IRanges(start, end), id=id))
   } else if (length(df)==5){
      gr <- with(df, GRanges(chr, IRanges(start, end), id=id, score=score))
   } else if (length(df)==6){
      gr <- with(df, GRanges(chr, IRanges(start, end), id=id, score=score, strand=strand))
   }
   return(gr)
}