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

[Vincent Carey]

It also seems worth mentioning that the graph package (
http://bioconductor.org/packages/release/bioc/html/graph.html)
has reasonable numbers of dependers and importers and could
undoubtedly play a role in feature-feature management.

On Sun, Nov 8, 2015 at 8:49 AM, Vincent Carey <stvjc at channing.harvard.edu>
wrote:

> 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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>
>

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