[BioC] "islands" and number of reads in the island in package chipseq/ShortRead

Kasper Daniel Hansen khansen at stat.berkeley.edu
Tue Dec 1 13:52:45 CET 2009

The best way to do this with IRanges is to make the reads into a set of IRanges with width 1, make your regions into IRanges as well and then use findOverlaps.  You need to do this by the chromosome, so you might want to use stuff like IRangesList and RangedData.  This is pretty fast but requires that all reads fit into memory.

An alternative is to use the Genominator package that was designed for this task.  That will require some overhead in learning how to use it (= reading the vignette).


On Dec 1, 2009, at 7:17 AM, Nora Rieber wrote:

> Dear all,
> I'm looking for a fast way of computing how many reads map into a
> certain location (e.g. between position 300 and 400 on chromosome 14).
> Is there any function to compute this in the packages chipseq or
> ShortRead? After reading the vignette for chipseq, I thought
> viewSums(islands) computes the number of reads, but it seems to compute
> the sum of the coverage.
> I've written my own code to do this but it is pretty slow and I wonder
> if there's a better way.
> Thanks,
> Nora
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