SPONGEffects enrichment_modules uses outdated software
- Dominant language
- R
- Stars
- 14
- Forks
- 9
- PR merge metrics
- No merged PRs in 30d
Description
This function of SPONGEffects uses outdated software from the `GSVA` package.
Since Bioconductor 3.18 this has changed (copied from [documentation](https://www.rdocumentation.org/packages/GSVA/versions/1.20.0)):
Instead of gsva(expr=., gset.idx.list=., method=., ...), use a method-specific parameter object, see [plageParam](http://127.0.0.1:38211/help/library/GSVA/help/plageParam) [zscoreParam](http://127.0.0.1:38211/help/library/GSVA/help/zscoreParam) [ssgseaParam](http://127.0.0.1:38211/help/library/GSVA/help/ssgseaParam) [gsvaParam](http://127.0.0.1:38211/help/library/GSVA/help/gsvaParam), followed by a call to the new gsva() function, see [gsva](http://127.0.0.1:38211/help/library/GSVA/help/gsva).
Probably the corresponding function in `SPONGE::enrichment_modules()` has to be replaced, the functionality should be identical.
Contributor guide
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Research direction
Locate SPONGE::enrichment_modules() and compare its GSVA call with the linked GSVA documentation for Bioconductor 3.18. Verify the replacement preserves the existing enrichment functionality and outputs, then test the function with the project's available checks or examples.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- r
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 48/100