On Thu, May 22, 2014 at 6:14 AM, Julian Gehring <julian.gehring@embl.de>wrote: > Hi Michael, > > In my use case, the individual entries of the GRanges object define > regions of interest. For each ROI, I want to extract data from multiple > sources and perform a analysis on those. > > Failing a better algorithm, the only real possibility would be to rely on some assumptions to optimize the construction of new GRanges when iterating. For example, lapply,CompressedList turns off validation when extracting each element, so GRangesList might offer some slight benefits. It would still be helpful to see a concrete example of this, because it may be possible to use some tricks to improve performance, and then we can think about ways to make those tricks easier / more intuitive. In this case, I cannot think of a way to avoid the looping over the > entries. For a few large regions, this is fine. With increasing length of > the GRanges object, most time is spent in extracting the indivdual ranges. > > An alternative solution would be to convert the columns of the GRanges > object into a data frame or a set of vectors, and loop over this. But if > you want to use some bioc standard functions (e.g. getSeq), you would have > to contruct the GRanges every time (also slow). > > Best wishes > Julian > > > > On 22.05.2014 15:06, Michael Lawrence wrote: > >> Hi Julian, >> >> What sort of operations need to be implemented this way? I'm usually >> able to avoid them somehow. As a last resort, reducing the complexity of >> the object helps. For example, you could operate over ranges(gr) if all >> you need are the starts and ends. >> >> Michael >> >> >> On Thu, May 22, 2014 at 5:56 AM, Julian Gehring <julian.gehring@embl.de>> <mailto:julian.gehring@embl.de>> wrote: >> >> Hi, >> >> Is there a fast way of looping over/extracting the entries of a >> 'GRanges' object individually? Due to the complex structure of a >> GRanges object, a simple solution like >> >> library(GenomicRanges) >> n = 1e4 >> gr = GRanges(1, IRanges(1:n, width = 1)) >> >> for(i in seq_along(gr)) { >> x = gr[i] >> ## more complex code acting on 'x' >> } >> >> takes notably long. Converting to a 'GRangesList' or >> 'GenomicRangesList' does obviously not improve the situation. I was >> wondering if there is some dedicated functionality which would allow >> this in a faster manner, in cases where simple vectorized operations >> are not applicable. >> >> Best wishes >> Julian >> >> _________________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org <mailto:bioconductor@r-project.org> >> https://stat.ethz.ch/mailman/__listinfo/bioconductor >> >> <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: >> http://news.gmane.org/gmane.__science.biology.informatics.__conductor< >> http://news.gmane.org/gmane.science.biology.informatics.conductor> >> >> >> [[alternative HTML version deleted]]

Hi Julian, I believe that some of the functions can be applied to the entire GRanges object without looping. For example you can try getSeq(BSgenome_object,GRanges_object) and this will output the sequences for each region of interest. Hopefully this still works, it has been a while since I have tried this. Brian On Thu, May 22, 2014 at 9:14 AM, Julian Gehring <julian.gehring@embl.de>wrote: > Hi Michael, > > In my use case, the individual entries of the GRanges object define > regions of interest. For each ROI, I want to extract data from multiple > sources and perform a analysis on those. > > In this case, I cannot think of a way to avoid the looping over the > entries. For a few large regions, this is fine. With increasing length of > the GRanges object, most time is spent in extracting the indivdual ranges. > > An alternative solution would be to convert the columns of the GRanges > object into a data frame or a set of vectors, and loop over this. But if > you want to use some bioc standard functions (e.g. getSeq), you would have > to contruct the GRanges every time (also slow). > > Best wishes > Julian > > > > On 22.05.2014 15:06, Michael Lawrence wrote: > >> Hi Julian, >> >> What sort of operations need to be implemented this way? I'm usually >> able to avoid them somehow. As a last resort, reducing the complexity of >> the object helps. For example, you could operate over ranges(gr) if all >> you need are the starts and ends. >> >> Michael >> >> >> On Thu, May 22, 2014 at 5:56 AM, Julian Gehring <julian.gehring@embl.de>> <mailto:julian.gehring@embl.de>> wrote: >> >> Hi, >> >> Is there a fast way of looping over/extracting the entries of a >> 'GRanges' object individually? Due to the complex structure of a >> GRanges object, a simple solution like >> >> library(GenomicRanges) >> n = 1e4 >> gr = GRanges(1, IRanges(1:n, width = 1)) >> >> for(i in seq_along(gr)) { >> x = gr[i] >> ## more complex code acting on 'x' >> } >> >> takes notably long. Converting to a 'GRangesList' or >> 'GenomicRangesList' does obviously not improve the situation. I was >> wondering if there is some dedicated functionality which would allow >> this in a faster manner, in cases where simple vectorized operations >> are not applicable. >> >> Best wishes >> Julian >> >> _________________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org <mailto:bioconductor@r-project.org> >> https://stat.ethz.ch/mailman/__listinfo/bioconductor >> >> <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: >> http://news.gmane.org/gmane.__science.biology.informatics.__conductor< >> http://news.gmane.org/gmane.science.biology.informatics.conductor> >> >> >> > _______________________________________________ > 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 > -- Brian Herb, Ph.D. Johns Hopkins School of Medicine Dr. Andrew Feinberg Laboratory Rangos 580 855 N. Wolfe St. Baltimore, MD 21205 Phone:410-614-3478 Fax: 410-614-9819 [[alternative HTML version deleted]]