[Bioc-sig-seq] Operations between sets of ChIP-seq peak locations

Ivan Gregoretti ivangreg at gmail.com
Thu Jan 28 16:46:40 CET 2010

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

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 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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