[Bioc-devel] [question about class extension]

[Sean Maden]

 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
>
>
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

	[[alternative HTML version deleted]]