Dear Guidantonio, The function call you used is correct. The shortest distance 3103 is the shortest distance between the ends of the two ranges, not the same as the gap you are referring to. The example you gave shows that these two ranges overlap, i.e., gap of 0, therefore meets the criteria you set (maxgap =1000). FYI, in the next release, the function will no longer outputs the shortest distance. Best regards, Julie On 9/18/12 10:33 AM, "Guidantonio Malagoli Tagliazucchi" <guim86@gmail.com> wrote: Dear Julie Zhu, I'm Guidantonio Malagoli Tagliazucchi, an Italian PhD student. In these days I tried to use your package "ChipPeakAnno" to find the overlap between Chip-seq peaks and Cage Peaks. In particular I want annotate all cage peaks that distance at least one 1kb from chip-seq peaks. Then I tried to use the function findOverlappingPeaks in the follow way: table.annotate<-findOverlappingPeaks(data, dbcage, maxgap =1000, multiple = c(FALSE), NameOfPeaks1 = "Histone_modification", NameOfPeaks2 = "Cage_peak") But sometimes in the output I have that the shortestDistance are longest than the maxgap. for example: 198364499 198364696 - 198360400 198367799 + includeFeature 3103 Why the function report also these distances? Maybe I have not clear how to work the function. How can I do to obtain only the annotations of peaks cage that distance 1kb from chip-seq? Can I filter manually? Or is better using other functions? I hope you can help me. Best Regards, Guidantonio Malagoli Tagliazucchi [[alternative HTML version deleted]]