A[!ranges(A) %in% ranges(B),]

On Thu, Jan 28, 2010 at 7:46 AM, Ivan Gregoretti <ivangreg@gmail.com> wrote:

> Hi everybody,
>
> I have two sets of ChIP-seq peaks: A and B.
> How do I select the peaks in A that are not overlapped by any peak in B?
>
>
> Now in more detail:
>
> I do
>
> library(rtracklayer)
> A <- import('condition_A.bed', 'bed')
> B <- import('condition_B.bed', 'bed')
>
> they are both RangedData instances.
>
> I need to compute A - B.
>
> How do you guys do it?
>
> Thank you,
>
> Ivan
>
>
> Ivan Gregoretti, PhD
> National Institute of Diabetes and Digestive and Kidney Diseases
> National Institutes of Health
> 5 Memorial Dr, Building 5, Room 205.
> Bethesda, MD 20892. USA.
> Phone: 1-301-496-1592
> Fax: 1-301-496-9878
>
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