R/bed_to_granges.R

In KSheu/ksheu.lib: KSheu Library1

#' 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
#' @keywords BED GRanges
#' @export
#' 


# bed_to_granges('my_bed_file.bed')

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