[Feature request] one vs. all others
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- Dominant language
- Python
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Description
I'd like to be able to input a contrast design (or otherwise choose design factors), to do a one vs all comparison within in a particular "condition" that has more than two levels. If my column "condition" has levels A, B, C, and D, do a comparison of A vs B, C, D.
Something like these options in R deseq2:
design <- ~0 + condition
contrast = c(1, -1/3, -1/3, -1/3)
contrast=list(c("conditionA"),
c("conditionB","conditionC","conditionD"))
Would it be possible to do something where if you leave the second option blank in contrast, like:
contrast = ['condition', 'A', '']
it compares A with all other samples?
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by tracing how the existing contrast input is parsed and applied for multi-level conditions. Define the expected behavior for a blank second contrast option, including the A-versus-all-others example, then verify the resulting differential-expression output against the stated contrast semantics.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100