Hi Steve, Michael and Malcolm, Thanks very much for your suggestions. I'd need to think about how to deal with these overlapping signals as well before I give Steve's suggestion a go! Thanks again for your kind advice and guidance! Jeremy On Sat, Mar 22, 2014 at 6:02 AM, Michael Lawrence <lawrence.michael@gene.com> wrote: > It could be that Steve's suggestion solves your problems, but you might > want to clarify how you want to merge the data. It looks like > gsm97tf.ranges has internal overlaps (e.g., the first two ranges), so it's > not obvious which signal should be assigned to the intersection. > > > On Fri, Mar 21, 2014 at 1:50 PM, Jeremy Ng <jeremy.ng.wk1990@gmail.com>wrote: > >> Hi there, >> >> I'm relatively new to the GRanges class of objects, and have some >> questions; and hopefully, I'd be able to better understand what's going on >> here. >> >> I have 2 Granges objects, which are data from GEO. I want to find where >> the >> overlap, and then after that, the signals from each set. Here's what I >> have >> so far: >> >> >gsm97tf.ranges >> GRanges with 171378 ranges and 1 metadata column: >> seqnames ranges strand | signal >> <rle> <iranges> <rle> | <numeric> >> [1] chr10 [54828986, 54829035] + | 0.79 >> [2] chr10 [54829024, 54829073] + | 0.05 >> [3] chr10 [54829176, 54829225] + | 0.04 >> [4] chr10 [54829746, 54829795] + | 0.15 >> [5] chr10 [54829898, 54829947] + | 0.24 >> ... ... ... ... ... ... >> > gsm94tf.ranges >> GRanges with 171249 ranges and 1 metadata column: >> seqnames ranges strand | signal >> <rle> <iranges> <rle> | <numeric> >> [1] chr10 [54828834, 54828883] + | 0.65 >> [2] chr10 [54828986, 54829035] + | 0.73 >> [3] chr10 [54829024, 54829073] + | 0.33 >> [4] chr10 [54829138, 54829187] + | 0.02 >> [5] chr10 [54829176, 54829225] + | 0.02 >> >> In order to find the regions of the genome where both sets overlap, I use >> the following: >> >> overlaps<-intersect(gsm94tf.ranges,gsm97tf.ranges) >> >> This will give me a GRanges object containing the coordinates where both >> sets intersect. The result looks like this: >> >overlaps >> GRanges with 72012 ranges and 0 metadata columns: >> seqnames ranges strand >> <rle> <iranges> <rle> >> [1] chr1 [148374757, 148374806] + >> [2] chr1 [148374833, 148374996] + >> [3] chr1 [148375061, 148375148] + >> [4] chr1 [148375821, 148375870] + >> [5] chr1 [148376087, 148376212] + >> >> My next question seems pretty trivial, but I'm stuck on what to go on >> next. >> I want to map back the overlaps to the original sets, to find their signal >> values. I was wondering, how do I do this? >> >> Sorry if this question is pretty simple - I'm trying to get a better >> handle >> of the GRanges classes! >> >> Thanks for any pointers! >> >> Jeremy >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]