It's possible that you could vectorize this code. Maybe open an issue on the support site.
On Mon, May 14, 2018 at 7:56 AM, Jack Fu <jf...@jhu.edu> wrote: > Hi Michael, > > Mostly for sending each element of the GRanges object to a custom function > that runs an identical analysis on each element. > I have some functions that take as input a single range -> calculate number > of reads that overlap the range -> subset the range into K number of > segments based on coverage patterns across the range. > > Thanks! > Jack > > > Michael Lawrence wrote: > > Just out of curiosity, why are you looping over a GRanges in the first > place? > > On Mon, May 14, 2018 at 7:28 AM, Jack Fu <jf...@jhu.edu> wrote: > > Hey all, > > I think some of the recent changes to GRanges has affected using the > apply class functions with GRanges objects: > > o GenomicRanges now is a List subclass. This means that GRanges objects > and their derivatives are now considered list-like objects (even > though > [[ don't work on them yet, this will be implemented in Bioconductor > 3.8). > > > The following code will throw: > gr <- GRanges(1, IRanges(1:2, 3:4)) > sapply(gr, print) > > Error in (function (classes, fdef, mtable) : > unable to find an inherited method for function 'getListElement' for > signature '"GRanges"' > > Access using gr[1], gr[1:2] still works normally. > Are there any recommendations on a workaround for this issue without > resorting back to for loops? > > Thanks all, > Jack > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel