Argument assay.type.ref was not taken into account

[julien-roux]

This caused SingleR to fail if the normalized assay was not called logcounts in the reference dataset.

I simply added it in the trainSingleR() call

[Copilot]

🟡 Changes recommended

A regression test covering the assay.type.ref behavior should be added (and the introduced tab indentation fixed) to prevent future breakage.

Once you've addressed the issues Copilot identified, you can request another Copilot review.

Pull request overview

This PR fixes a bug in SingleR() where the reference assay selection (assay.type.ref) was not propagated into the internal trainSingleR() call, causing failures when the normalized assay in the reference dataset was not named "logcounts".

Changes:

• Pass assay.type.ref into trainSingleR() via its assay.type argument.
• Minor formatting change in the trainSingleR() argument list (indentation).

File summaries

File	Description
R/SingleR.R	Ensures assay.type.ref is respected when training on reference objects with non-default assay names.

Review details

• Files reviewed: 1/1 changed files
• Comments generated: 2
• Review effort level: Lite

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[LTLA]

Thanks for the fix. Looks mostly good, though I would use assayNames() in the tests instead of names(assays(...)).

Did Copilot invite itself in? I don't remember enabling this.

[julien-roux]

I would use assayNames() in the tests instead of names(assays(...)).

Sure, should I make the change, or do you take care of this?

Did Copilot invite itself in?

Yes 😂

[LTLA]

I'll take care of it, I need to do a little administrivia anyway (e.g., NEWS, DESCRIPTION).

Also need to figure out how to kick copilot out of this repo. Its involvement here is pretty innocuous but you never know when it'll slip in some proprietary code.