[BioC] Help with sliding window analysis on GRanges object

[Martin Morgan]

Hi Stefano --

On 03/08/2014 01:41 PM, Stefano Iantorno wrote:
> Hello
>
>
>
> I am trying to conduct a sliding window analysis on a GRanges object. My
> ranges are a list of 60272 single nucleotide positions representing high
> confidence SNPs stored as IRanges object. I would like to retrieve the
> list of GRanges row IDs for each  500bp window in the genome
> (overlapping windows).
>
>
>
> All the documentation I could find on sliding window functions such as
> runsum, runmean, etc are all for Rle objects.
>
>
>
> Any idea where to start from? I can't figure out a way to pick windows
> in the IRanges object across intervals, since each interval is
> represented by a start and end position (same genomic position since
> it's a single nucleotide long).
>
>

It's hard for me to figure out what you want to do? I guess you've got some SNPs

    snps = GRanges("chr1", IRanges(c(1000, 1200, 2000), width=1))

and you'd like to count the number of SNPs in a sliding window of width 500?

You can easily represent your SNPs as an Rle instead of a GRanges

 > (cvg <- coverage(snps))
RleList of length 1
$chr1
integer-Rle of length 2000 with 6 runs
   Lengths: 999   1 199   1 799   1
   Values :   0   1   0   1   0   1

and then calculate a running mean (or runsum) as I guess you've found

 > (r <- runmean(cvg, 500))
RleList of length 1
$chr1
numeric-Rle of length 1501 with 6 runs
   Lengths:   500   200   300   200   300     1
   Values :     0 0.002 0.004 0.002     0 0.002

The toy example could be visualized as

   plot(as.numeric(r[[1]]), type="l")

or perhaps ggbio::autoplot(r).

Is that something like what you're looking for? Or you'd like to take this a 
step further? Maybe you can construct a simple example like the one here to show 
what you're trying to do?

Martin

>
> Any help will be greatly appreciated.
>
>
>
> Thanks
>
>
>
> -          Stefano
>
>
>
>


-- 
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793