[Bioc-devel] InteractionSet for structural variants

Bernat Gel Moreno bge| @end|ng |rom |gtp@c@t
Mon May 20 10:14:36 CEST 2019

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


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
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