AlexsLemonade / AlexsLemonade/scpcaTools

Allow `include_altexps` to take a vector in `merge_sce_list`

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Description

For the future, part of me wonders if we should allow `include_altexps` to be a vector of `altExps` to include. This would be a change in `scpcaTools`, and for backward compatibility we should allow a `TRUE/FALSE` to mean keep all or keep none, with a vector meaning (implicitly) keep some.

_Originally posted by @jashapiro in https://github.com/AlexsLemonade/scpca-nf/pull/666#discussion_r1465705567_

The idea here is that we could allow
```
merge_sce_list(sce_list, include_altexp = c("adt"))
```
to keep only the `adt` altExp, even if there were also a `cellhash` altExp that we wanted to exclude.

```
merge_sce_list(sce_list, include_altexp = FALSE)
```
would still work as before and not include any altExps, and `TRUE` would include all altExps.

This does not need to be implemented until we think we will have data that actually does contain more than one altExp.

Contributor guide

Open the contributing guide

Research direction

Start by locating the merge_sce_list entry point in scpcaTools and review how include_altexp currently handles TRUE and FALSE. Check whether tests cover alternate experiments, then define completion as accepting a vector of altExp names while preserving TRUE as all and FALSE as none.

Written by the indexing model from the issue text.

Assessment

Tech stack
r
Domain
data
Issue type
Feature
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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