[Bioc-devel] InteractionSet for structural variants

[Sean Davis]

On Tue, May 21, 2019 at 2:54 AM Aaron Lun <
infinite.monkeys.with.keyboards using gmail.com> wrote:

> > 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.
>
> Not to my knowledge... but if you're planning on writing some relevant
> functions, I'm sure we could find a home for it somewhere.
>

I do have a couple of simple functions in VCFWrenchR (not in Bioc), but
like much VCF code, it probably misses a bunch of edge cases. The functions
target VRanges, not interactionsets.

https://github.com/seandavi/VCFWrenchR

Sean


> -A
>
> > 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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