Hi Aaron, Thanks for your response. So far my intention is to to plot them and I do not intend on performing any other operation. The first step would be read in the VCF file and transform it into a meaningful object and I was hoping there was a core package already taking care of that, but I get from your answer that there's no such functionality implemented.
Thanks again Bernat El 5/18/19 a las 4:47 AM, Aaron Lun escribió: > I would say that it depends on what operations you intend to perform > on them. You can _store_ things any way you like, but the trick is to > ensure that operations and manipulations on those things are > consistent and meaningful. It is not obvious that there are meaningful > common operations that one might want to apply to all structural > variants. > > For example, translocations involve two genomic regions (i.e., the two > bits that get stuck together) and so are inherently two-dimensional. A > lot of useful operations will be truly translocation-specific, e.g., > calculation of distances between anchor regions, identification of > bounding boxes in two-dimensional space. These operations will be > meaningless to 1-dimensional variants on the linear genome, e.g., > CNVs, inversions. The converse also applies where operations on the > linear genome have no single equivalent in the two-dimensional case. > > So, I would be inclined to store them separately. If you must keep > them in one object, just lump them into a List with "translocation" > (GInteractions), "cnv" (GRanges) and "inversion" (another GRanges) > elements, and people/programs can pull out bits and pieces as needed. > > -A > > > On 5/17/19 4:38 AM, Bernat Gel Moreno wrote: >> Hi all, >> >> Is there any standard recommended container for genomic structural >> variants? I think InteractionSet would work fine for translocation and >> GRanges for inversions and copy number changes, but I don't know what >> would be the recommended way to store them all together using standard >> Bioconductor objects. >> >> And actually, is there any package that would load a SV VCF by lumpy or >> delly and build that object? >> >> Thanks! >> >> Bernat >> >> >> _______________________________________________ >> 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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel