Sorry it took so long but I just checked this in for version 1.7.8 On Tue, Jun 8, 2010 at 8:27 PM, Michael Lawrence <michafla@gene.com> wrote: > > > On Tue, Jun 8, 2010 at 8:00 PM, Kasper Daniel Hansen < > kasperdanielhansen@gmail.com> wrote: > >> On Tue, Jun 8, 2010 at 9:53 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote: >> > On 06/09/2010 02:36 AM, Kasper Daniel Hansen wrote: >> >> Hi Michael >> >> >> >> Michael, >> >> >> >> Thanks for pointing out nearest and friends; I agree that this >> >> function should address my question. >> >> >> >> Reading the man page for nearest function, might I suggest an >> >> additional argument like >> >> multihits = c("arbitrary", "all") >> > >> > yes thanks for the timely nearest hint; for me I was hoping that ties >> > could be decided based on maximum overlap (though ties might still >> > occur, and perhaps I could break ties myself if 'all' were returned >> > without too much difficulty). >> >> I would strongly advocate just returning the multiple hits and let the >> user decide how to break ties. While I certainly see use cases where >> Martin's suggestion is reasonable, what happens if a range overlap two >> different ranges, which have very different width. Should "maximum >> overlap" be counted in number of integers (in which case you might be >> biased towards the longer of the two ranges) or should it be in >> %-length or ? I think allowing for all these possibilities would make >> for a very complicated interface with little gain. >> >> One might conceive of a filter function on top of the return object >> (which could work for findOverlaps as well), but as the filtering in >> some cases would depend on additional metadata (say the ranges are of >> different type and there is an ordering on the type so an overlap with >> a certain type trumps another type), it might be a lot of >> infrastructure with very little gain. And really, the filtering would >> just be an apply over the sparse matrix. >> >> > I agree that returning "all" is a good option to have, and it is consistent > with the functionality of findOverlaps. If compelling common use cases > emerge for tie resolution, the number of multihits options can be expanded. > > Thanks for the suggestion, > Michael > > >> Kasper >> >> >> > >> > Martin >> > >> >> with the intention that a user can get full information in case one >> >> range overlaps (or ties in distance) with multiple other ranges. The >> >> return value could be a sparse matrix, findOverlaps-like. I find it >> >> important to know about multiple hits, especially in the case when a >> >> range has multiple overlaps. >> >> >> >> Thanks, >> >> Kasper >> >> >> >> On Tue, Jun 8, 2010 at 1:25 PM, Michael Lawrence >> >> <lawrence.michael@gene.com> wrote: >> >>> For all pairwise distances, something simple based on outer() should >> >>> suffice. It might not be very space efficient, but speed should be >> somewhat >> >>> close to optimal. >> >>> >> >>> What is the end goal of this? For example, the nearest() function >> finds >> >>> nearest neighbors efficiently. >> >>> >> >>> You might be able to leverage findOverlaps(). For example, one can set >> the >> >>> maximum gap between ranges to be considered overlapping. That could be >> set >> >>> to a non-zero value representing some maximum allowable distance. The >> sparse >> >>> doublet matrix from as.matrix() would be pretty efficient for distance >> >>> calculation, via the pgap() function. >> >>> >> >>> Michael >> >>> >> >>> On Tue, Jun 8, 2010 at 8:51 AM, Kasper Daniel Hansen >> >>> <kasperdanielhansen@gmail.com> wrote: >> >>>> >> >>>> Assuming I have two IRanges, each with multiple ranges, like >> >>>> ir1 = IRanges(start = 3:6, width = 2) >> >>>> ir2 = IRanges(start = 10:17, width = 2) >> >>>> >> >>>> Is there a fast way to compute a pairwise distance matrix between the >> >>>> two sets, by which I mean >> >>>> ii = 1 >> >>>> jj = 2 >> >>>> width(gaps(c(ir1[ii], ir2[jj]))) >> >>>> where ii, jj would index into a result matrix. Essentially this >> would >> >>>> be an expanded version of findOverlaps, since any two ranges with >> >>>> distance = 0, have an overlap. >> >>>> >> >>>> Is such functionality available in IRanges, in an efficient >> >>>> implementation (think of the case where the two IRanges have - say - >> >>>> 10,000 ranges or more)? >> >>>> >> >>>> Kasper >> >>>> >> >>>> _______________________________________________ >> >>>> Bioconductor mailing list >> >>>> Bioconductor@stat.math.ethz.ch >> >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >>>> Search the archives: >> >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >>> >> >>> >> >> >> >> _______________________________________________ >> >> Bioconductor mailing list >> >> Bioconductor@stat.math.ethz.ch >> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > >> > >> > -- >> > Martin Morgan >> > Computational Biology / Fred Hutchinson Cancer Research Center >> > 1100 Fairview Ave. N. >> > PO Box 19024 Seattle, WA 98109 >> > >> > Location: Arnold Building M1 B861 >> > Phone: (206) 667-2793 >> > >> > > [[alternative HTML version deleted]]