Hi Ivan,

The findOverlappingPeaks function in ChIPpeakAnno package (dev version 1.3.8) might be what you are looking for. Please let me know if it works out for you. Thanks!

AoverlapBCD = findOverlappingPeaks(findOverlappingPeaks(peaks1, peaks2, maxgap=100, multiple=F, NameOfPeaks1="A", NameOfPeaks2="B")$Peaks1withOverlap, peaks3, maxgap=100, multiple=F, NameOfPeaks1="AB", NameOfPeaks2="C")$Peaks1withOverlap, peaks4, maxgap=100, multiple=F, NameOfPeaks1="ABC", NameOfPeaks2="D")$Peaks1withOverlap

Best regards,

Julie


*******************************************
Lihua Julie Zhu, Ph.D
Research Associate Professor
Program Gene Function and Expression
University of Massachusetts Medical School
364 Plantation Street, Room 613
Worcester, MA 01605
508-856-5256
http://www.umassmed.edu/pgfe/faculty/zhu.cfm
*******************************************



On 3/16/10 2:34 PM, "Ivan Gregoretti" <ivangreg@gmail.com> wrote:

Hello everybody,

Say A, B, C, D, .... are all RangedData instances.

How do you come up with the list of ranges in A that have at least
some overlap with B, C, D, ...?

I want to calculate the multiple intersection ignoring the extent of
the overlap.

?findOverlaps does not hint how to recover the ranges from A.

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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