[Bioc-devel] [question about class extension]

[migdal migdal]

Hi Delphine,

I had a similar dilemma while developing midasHLA
<https://github.com/Genentech/midasHLA> package. There, we wanted to have
unique features names across all experiments and colData as well as
mandatory metadata. To this end I wrote a new class specific to my package
that extends MAE. I had some negative comments
<https://github.com/Genentech/midasHLA/issues/5#issue-727826240> regarding
this solution (see R code section of the comment by LTLA; it might help you
decide how to approach your particular case), but IMO it works nicely.

Best Maciek

On Wed, 24 Jan 2024 at 14:43, Sean Maden <maden.sean using gmail.com> wrote:

>  There aren't strict standards imposed on many of the packages in
> Bioconductor introducing classes, but many other packages extend and impose
> standards and constraints for given areas/fields/subjects.
>
> If you are considering this route, something like the following could work
> to determine if introducing metadata features and restrictions is the route
> to take:
>
> libraryVector <-
>   c("MultiAssayExperiment", "SummarizedExperiment",
>     "SingleCellExperiment", "SpatialExperiment")
>
> # Try something like this to test your candidate data classes:
>
> testClass <- function(libraryName, functionString){
>   # libraryName : valid class library
>   eval(parse(text = paste0(functionString,"(",libraryName,")")))
> }
>
> for(libraryName in libraryVector){
>   testClass(libraryName, "library")
>   testClass(libraryName, "new <- ")
>
>   metadata(new) #
>
>   testClass("new", "rm")
>   testClass(libraryName, "detach")
> }
>
> There may be better ways to harmonize and share the data with collaborators
> as a flat table.
>
> MAE has extensive documentation and there is also a cheatsheet provided to
> help out with tasking.
>
> See also: DOI: 10.18129/B9.bioc.MultiAssayExperiment
>
> Sean
>
> On Tue, Jan 23, 2024 at 5:45 AM Delphine Charif <delphine.charif using inrae.fr>
> wrote:
>
> > Dear Bioc developer,
> >
> > We are developing a package and have used the MultiAssayExperiment class
> > to manage our data.
> > We need to impose a particular structure on the slot metadata of the MAE
> > object (list => named list)
> > because we havec defined methods that depend on this named list.
> > Is it good practice to extend the MAE class for the specificity of our
> > metadata structure or is it better
> > to define new methods applying to a MAE object  (and check the metadata
> > structure )?
> >
> > Thanks in advance,
> >
> >
> >
> >
> >
> >
> > --------------------------------------
> > Delphine CHARIF
> > +33 (0)1 30 83 35 24
> >
> > IJPB<https://ijpb.versailles.inrae.fr/> - <https://www.inrae.fr/> INRAE<
> > https://www.inrae.fr/>
> > RD10 - Route de Saint-Cyr
> > 78026 Versailles
> > ---------------------------------------
> > En temps partiel le mercredi
> >
> >
> >
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> >
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> >
>
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