bed_to_granges.r

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)
}