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 >> > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
