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" <[email protected]> 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 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
