[Bioc-devel] Base class for interaction data - expressions of interest

[Vincent Carey]

In our discussions of the multiassay object/analysis problem,

https://github.com/vjcitn/biocMultiAssay

Kasper Hansen has suggested elaborations of the Hits API (see for example
sec. 4 of

http://bioconductor.org/packages/release/bioc/vignettes/GenomicRanges/inst/doc/GenomicRangesIntroduction.pdf

,

more fully described in man pages in S4Vectors

http://bioconductor.org/packages/release/bioc/manuals/S4Vectors/man/S4Vectors.pdf
)

to manage work on general feature-feature relationships.  At present, the
Hits structures/methods
use a pair of integer vectors to collate elements of two objects.  Two
general problems that probably need more work are a) classes for feature
annotation elements and b) extensions to Hits that support R idioms for
subsetting collated objects at various points on an analysis path.

On Sun, Nov 8, 2015 at 8:05 AM, Laurent Gatto <lg390 at cam.ac.uk> wrote:

>
> On  7 November 2015 19:58, Ludwig Geistlinger wrote:
>
> > I agree with Martin, I would love to see something like that.
> > Especially if this would not be restricted to chromatin interactions, but
> > also allows to represent protein-protein, transcriptionFactor-targetGene,
> > miRNA-mRNA etc (e.g. via suitably tailored subclasses).
>
> I would be delighted to help out in PPI (or Protein-anything
> interactions) infrastructure development, if this is in scope.
>
> Best wishes,
>
> Laurent
>
> > This might nicely work together with bringing in existing regulatory
> > networks via AnnotationHub ...
> >
> > If help is needed, I'm happy to contribute ...
> >
> > Best,
> > Ludwig
> >
> >> Just to say that this is a great idea. If this starts as a github
> package
> >> (or in svn, we can create a location for you if you'd like) I and others
> >> would I am sure be happy to try to provide any guidance / insight. The
> >> main design principles are probably to reuse as much as possible from
> >> existing classes, especially the S4Vectors / GRanges world, and to
> >> integrate metadata as appropriate (like SummarizedExepriment, for
> >> instance).
> >>
> >> Martin
> >> ________________________________________
> >> From: Bioc-devel [bioc-devel-bounces at r-project.org] on behalf of Aaron
> Lun
> >> [alun at wehi.edu.au]
> >> Sent: Thursday, November 05, 2015 12:27 PM
> >> To: bioc-devel at r-project.org
> >> Subject: Re: [Bioc-devel] Base class for interaction data - expressions
> of
> >>      interest
> >>
> >> There's a growing number of Bioconductor packages dealing with
> >> interaction data; diffHic, GenomicInteractions, HiTC, to name a few (and
> >> probably more in the future). Each of these packages defines its own
> >> class to store interaction data - DIList for diffHic,
> >> GenomicInteractions for GenomicInteractions, and HTClist for HiTC.
> >>
> >> These classes seem to share a lot of features, which suggests that they
> >> can be (easily?) replaced with a common class. This would have two
> >> advantages - one, developers of new and existing packages don't have to
> >> continually write and maintain new classes; and two, it provides users
> >> with a consistent user experience across the relevant packages.
> >>
> >> My question is, does anybody have anything in the pipeline with respect
> >> to a base package for an interaction class? If not, I'm planning to put
> >> something together for the next BioC release. To this end, I'd welcome
> >> any ideas/input/code; the aim is to make a drop-in replacement (insofar
> >> as that's possible) for the existing classes in each package.
> >>
> >> Cheers,
> >>
> >> Aaron
> >>
> >> _______________________________________________
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> >>
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> >
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>
> --
> Laurent Gatto | @lgatt0
> http://cpu.sysbiol.cam.ac.uk/
> http://lgatto.github.io/
>
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