Re: [Bioc-devel] Base class for interaction data - expressions of interest
amework (one row per interaction).
With regards to the methods, most of the low-hanging fruit has
been
implemented, courtesy of inheriting from SummarizedExperiment0.
I'll add
proper unit tests over the coming week. It currently passes
through R
CMD check okay, except for a warning about ":::" in the
cbind/rbind
definitions (callNextMethod() didn't seem to work inside those
methods,
and I didn't want to rewrite the SE0 'binding methods).
Any thoughts appreciated.
- Aaron
On 07/11/15 19:33, Morgan, Martin wrote:
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-boun...@r-project.org
<mailto:bioc-devel-boun...@r-project.org>] on behalf of Aaron
Lun [a...@wehi.edu.au <mailto:a...@wehi.edu.au>]
Sent: Thursday, November 05, 2015 12:27 PM
To: bioc-devel@r-project.org
<mailto:bioc-devel@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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Re: [Bioc-devel] Base class for interaction data - expressions of interest
Hello all, I thought I might give an update on the state of affairs for the InteractionSet package. Currently, there's three classes: - the GInteractions class, inheriting from Vector and intended to represent pairwise interactions between genomic regions (based on suggestions from Malcolm Perry and Liz Ing-Simmons). - the InteractionSet class, inheriting from SummarizedExperiment0 and containing a GInteractions object; intended to store experimental data about pairwise interactions (one interaction per row). - the ContactMatrix class, inheriting from Annotated and storing data in matrix form (where rows/columns represent genomic regions). Getters, setters, conversion methods between classes, distance calculation methods and overlap methods have been implemented. Man pages and "testthat" scripts have also been written. Still missing a vignette, though it should be easy enough to write one. All in all, I think it's a solid first draft. Any comments would be appreciated. Cheers, Aaron On 08/11/15 19:31, Aaron Lun wrote: Okay, some meat and bones are on GitHub now: https://github.com/LTLA/InteractionSet The idea is to represent genomic interactions as pairs of genomic regions, using indices to point to a common GRanges object (a la Hits, though I haven't used that explicitly due to the presence of additional constraints on the indices). Data for each interaction is stored using a SummarizedExperiment framework (one row per interaction). With regards to the methods, most of the low-hanging fruit has been implemented, courtesy of inheriting from SummarizedExperiment0. I'll add proper unit tests over the coming week. It currently passes through R CMD check okay, except for a warning about ":::" in the cbind/rbind definitions (callNextMethod() didn't seem to work inside those methods, and I didn't want to rewrite the SE0 'binding methods). Any thoughts appreciated. - Aaron On 07/11/15 19:33, Morgan, Martin wrote: 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-boun...@r-project.org] on behalf of Aaron Lun [a...@wehi.edu.au] Sent: Thursday, November 05, 2015 12:27 PM To: bioc-devel@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 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. ___ 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
Re: [Bioc-devel] Base class for interaction data - expressions of interest
Our package, GenomicInteractions, was designed partly with this goal in mind. The latest version is in Bioc release and on github ( https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions). We've represented interactions using two different sets of anchors, with an additional 'counts' label, and the class is based around Vector since it was intended as a rough equivalent to GRanges. All of the usual methods (subsetting, sorting, mcols, overlaps etc.) are there as well as export and import for a number of interaction file formats and some functions for analysis. Malcolm On Sun, Nov 8, 2015 at 7:31 PM, Aaron Lun <a...@wehi.edu.au> wrote: > Okay, some meat and bones are on GitHub now: > > https://github.com/LTLA/InteractionSet > > The idea is to represent genomic interactions as pairs of genomic regions, > using indices to point to a common GRanges object (a la Hits, though I > haven't used that explicitly due to the presence of additional constraints > on the indices). Data for each interaction is stored using a > SummarizedExperiment framework (one row per interaction). > > With regards to the methods, most of the low-hanging fruit has been > implemented, courtesy of inheriting from SummarizedExperiment0. I'll add > proper unit tests over the coming week. It currently passes through R CMD > check okay, except for a warning about ":::" in the cbind/rbind definitions > (callNextMethod() didn't seem to work inside those methods, and I didn't > want to rewrite the SE0 'binding methods). > > Any thoughts appreciated. > > - Aaron > > On 07/11/15 19:33, Morgan, Martin wrote: > >> 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-boun...@r-project.org] on behalf of Aaron >> Lun [a...@wehi.edu.au] >> Sent: Thursday, November 05, 2015 12:27 PM >> To: bioc-devel@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 >> >> ___ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> >> This email message may contain legally privileged and/or confidential >> information. If you are not the intended recipient(s), or the employee or >> agent responsible for the delivery of this message to the intended >> recipient(s), you are hereby notified that any disclosure, copying, >> distribution, or use of this email message is prohibited. If you have >> received this message in error, please notify the sender immediately by >> e-mail and delete this email message from your computer. Thank you. >> >> > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Base class for interaction data - expressions of interest
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-boun...@r-project.org] on behalf of Aaron Lun >> [a...@wehi.edu.au] >> Sent: Thursday, November 05, 2015 12:27 PM >> To: bioc-devel@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 >> >> ___ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> >> This email message may contain legally privileged and/or confidential >> information. If you are not the intended recipient(s), or the employee or >> agent responsible for the delivery of this message to the intended >> recipient(s), you are hereby notified that any disclosure, copying, >> distribution, or use of this email message is prohibited. If you have >> received this message in error, please notify the sender immediately by >> e-mail and delete this email message from your computer. Thank you. >> ___ >> 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 -- Laurent Gatto | @lgatt0 http://cpu.sysbiol.cam.ac.uk/ http://lgatto.github.io/ ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Base class for interaction data - expressions of interest
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 <lg...@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-boun...@r-project.org] on behalf of Aaron > Lun > >> [a...@wehi.edu.au] > >> Sent: Thursday, November 05, 2015 12:27 PM > >> To: bioc-devel@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 > >> > >> ___ > >> Bioc-devel@r-project.org mailing list > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > >> > >> > >> This email message may contain legally privileged and/or confidential > >> information. If you are not the intended recipient(s), or the employee > or > >> agent responsible for the delivery of this message to the intended > >> recipient(s), you are hereby notified that any disclosure, copying, > >> distribution, or use of this email message is prohibited. If you have > >> received this message in error, please notify the sender immediately by > >> e-mail and delete this email message from your computer. Thank you. > >> ___ > >> 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 > > -- > Laurent Gatto | @lgatt0 > http://cpu.sysbiol.cam.ac.uk/ > http://lgatto.github.io/ > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Base class for interaction data - expressions of interest
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 <st...@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 <lg...@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-boun...@r-project.org] on behalf of >> Aaron Lun >> >> [a...@wehi.edu.au] >> >> Sent: Thursday, November 05, 2015 12:27 PM >> >> To: bioc-devel@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 >> >> >> >> ___ >> >> Bioc-devel@r-project.org mailing list >> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> >> >> &
Re: [Bioc-devel] Base class for interaction data - expressions of interest
Thanks for the interest, everyone. I'll try to put up what I've currently got onto my GitHub page, sometime over the week. Currently, I'm calling it an "InteractionSet" object; it builds off the SummarizedExperiment0 class and adds some stuff to handle pairwise genomic interactions. - Aaron On 07/11/15 19:33, Morgan, Martin wrote: 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-boun...@r-project.org] on behalf of Aaron Lun [a...@wehi.edu.au] Sent: Thursday, November 05, 2015 12:27 PM To: bioc-devel@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 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Base class for interaction data - expressions of interest
Okay, some meat and bones are on GitHub now: https://github.com/LTLA/InteractionSet The idea is to represent genomic interactions as pairs of genomic regions, using indices to point to a common GRanges object (a la Hits, though I haven't used that explicitly due to the presence of additional constraints on the indices). Data for each interaction is stored using a SummarizedExperiment framework (one row per interaction). With regards to the methods, most of the low-hanging fruit has been implemented, courtesy of inheriting from SummarizedExperiment0. I'll add proper unit tests over the coming week. It currently passes through R CMD check okay, except for a warning about ":::" in the cbind/rbind definitions (callNextMethod() didn't seem to work inside those methods, and I didn't want to rewrite the SE0 'binding methods). Any thoughts appreciated. - Aaron On 07/11/15 19:33, Morgan, Martin wrote: 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-boun...@r-project.org] on behalf of Aaron Lun [a...@wehi.edu.au] Sent: Thursday, November 05, 2015 12:27 PM To: bioc-devel@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 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Base class for interaction data - expressions of interest
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-boun...@r-project.org] on behalf of Aaron Lun [a...@wehi.edu.au] Sent: Thursday, November 05, 2015 12:27 PM To: bioc-devel@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 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Base class for interaction data - expressions of interest
Metoo. This is becoming an item of major interest for some treatment biomarkers we are studying. --t > On Nov 7, 2015, at 11:33 AM, Morgan, Martin <martin.mor...@roswellpark.org> > wrote: > > 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-boun...@r-project.org] on behalf of Aaron Lun > [a...@wehi.edu.au] > Sent: Thursday, November 05, 2015 12:27 PM > To: bioc-devel@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 > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. > ___ > 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
Re: [Bioc-devel] Base class for interaction data - expressions of interest
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). 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-boun...@r-project.org] on behalf of Aaron Lun > [a...@wehi.edu.au] > Sent: Thursday, November 05, 2015 12:27 PM > To: bioc-devel@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 > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. > ___ > 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
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 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
