Hi,
I don't know about a specific function (maybe there is) so I use the following
code to simulate ranges.
I simplified it a bit so it might not directly run but shows the concept.
simulate.GRanges <- function (n, mean.length, genome.size ){
# assuming read lengths are poisson distributed around the mean length, you
could use a different random function
# assuming reads are uniformly distributed wrt. start position
ir = IRanges(start=as.integer(runif(n, min=1, max=genome.size)),
width=rpois(n, mean.length))
ir = restrict(ir, 1, genome.size) # cut off reads at the end, not perfect
strand = Rle(sample(x=c("+","-", "*"), size=n, replace=TRUE)) # make some
strand information
gr = GRanges(ir , seqnames="chr1",
seqlengths=genome.size,
strand=strand, universe="Mygenome")
return(gr)
}
You just need to get an estimate of read-length distribution from somewhere
then.
Hope this is useful
Michael
On Dec 2, 2010, at 4:06 PM, Anna Terry wrote:
> Hi,
>
> Is there any function in GenomicRanges (or other package) for getting a set
> of random ranges based on size distribution of a sample set?
> Similar functions are available in bedTools(
> http://code.google.com/p/bedtools/wiki/Usage#shuffleBed) and Random Intervals
> from the ENCODE tools on Galaxy.
>
> Many Thanks
> Anna
>
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