`?SummarizedExperiment` redirects to the docs for `RangedSummarizedExperiment`

[lazappi]

I have just noticed (for me at least) that using ?SummarizedExperiment opens the docs for RangedSummarizedExperiment as does using any links etc. Possibly I'm doing something stupid but I've tried with devel, the current release and previous release in RStudio and on the command line and I haven't had any luck accessing the SummarizedExperiment page interactively. It is still included in the manual on website though.

[PeteHaitch]

I haven't had any luck accessing the SummarizedExperiment page interactively

This will do it:

?`SummarizedExperiment-class`

R at the terminal, R.app, and RStudio should show this in the autocomplete dropdown menu if you type ?Summ or similar and hit tab at the command line (provided SummarizedExperiment is attached) but my experience is that RStudio does a better job of inserting the ` characters needed to handle the hyphen in the name.

[lazappi]

Ok, that works. But I still think it's not ideal that ?SummarizedExperiment doesn't take you to the correct object (or a package page) and the links between the RangedSummarizedExperiment page (or anything else) and the SummarizedExperiment page don't work.

[vjcitn]

This package was not documented with roxygen. So the man pages are composed manually. For some reason the \alias{SummarizedExperiment} entry is in RangedSummarizedExperiment-class.Rd ... and

## Constructor

# See ?RangedSummarizedExperiment for the constructor function.

is present in SummarizedExperiment-class.Rd. I would wonder what @hpages would think about moving the \alias{SummarizedExperiment} to the SummarizedExperiment-class.Rd, and adding a note to the RangedSE doc to indicate where the basic constructor is found, indicating that the rowRanges argument, when used, will produce a RangedSE.

I seem to remember some discussion about deprecating RangedSummarizedExperiment as it isn't really needed? An SE may or may not have non-null rowRanges.

[hpages]

I would wonder what @hpages would think about moving the \alias{SummarizedExperiment} to the SummarizedExperiment-class.Rd, and adding a note to the RangedSE doc to indicate where the basic constructor is found

Done in SummarizedExperiment 1.35.1 (see commit c5b7ca2f8d975af13a18b3b5931449f092657f5c).

I seem to remember some discussion about deprecating RangedSummarizedExperiment as it isn't really needed? An SE may or may not have non-null rowRanges.

Agreed that it would kind of make sense to collapse RangedSummarizedExperiment and SummarizedExperiment into a single class. Not an easy/light thing to do at this point though with so many classes that extend RangedSummarizedExperiment.

[hpages]

I'm closing this.

@vjcitn Please open a new issue to request/discuss deprecation of RangedSummarizedExperiment if you feel this is worth pursuing.