[Bioc-devel] How best to remap S4Vectors::Hits indices?

[Pariksheet Nanda]

Hi folks,

I'm working on a package that does some trivial GRanges position
classifications; primarily to standardize nomenclature according to the
literature in workflows.

The API for S4Vectors::Hits() generally doesn't seem amenable to modify
Hits objects, except for the remapHits() feature (which I see underneath
the covers really generates a new Hits object).

I was hoping someone could take a quick look at a short function I'm using
to subset and reindex Hits in the da_tss() function:
https://github.com/coregenomics/nascentrna/blob/a2d9d10564c3a88759237b56ec49d0d3e73f6d16/R/classify.R#L70
Yes, to illustrate the problem I'm having, I've directly used the @-style
S4 access which is, of course, a terrible thing to do because it defeats
the purpose of S4 object validation, which is why I'm e-mailing the list
for an alternative.  I feel like casting to something like a data.frame,
changing the indices, and changing back to Hits would be wasteful and
improperly using the Bioconductor framework?

Here are the corresponding tests that run the da_tss() function:
https://github.com/coregenomics/nascentrna/blob/a2d9d10564c3a88759237b56ec49d0d3e73f6d16/tests/testthat/test-classifiers.R

What it comes down to is this:
I want to compare a subset of GRanges for hits, but revert to the original
GRanges indices when returning the results.

Thanks for any advice!
Pariksheet

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