Add a way to create a DeseqDataSet object from normalized count matrix / preprocessed adata object
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- Dominant language
- Python
- Stars
- 761
- Forks
- 90
- Avg merge
- 25m
- Merged PRs (30d)
- 10
Description
Currently, the only way to initialize a DeseqDataSet object is to have a non-negative integers in adata.X. The AnnData object might have been normalized/preprocessed before-hand, so this limits the integration with other tools.
Describe the solution you'd like
-
Solution:
Instead of throwing an Exception, a Warning might be better in thetest_valid_countsfunction. -
Solution
Add a constructor flag that ignores the test.
I am not sure which solution might work better, I can't think of a case where a Warning wouldn't do the job, but I can take care of this one if there is one preferred fix for it.
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 reading the DeseqDataSet initialization path and the test_valid_counts function to understand where normalized AnnData inputs are rejected. Compare the warning and constructor-flag proposals, then clarify which behavior should be supported and how it should be tested. Done means a normalized count matrix or preprocessed AnnData object can be accepted without the current exception, with validation behavior covered.
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
- Needs clarification
- Newbie friendliness
- 35/100