Handling NaN counts
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- Dominant language
- Python
- Stars
- 761
- Forks
- 90
- Avg merge
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- Merged PRs (30d)
- 10
Description
Currently, PyDESeq2 throws an error when trying to initialise a DeseqDataSet with a count matrix that contains NaNs – this is to reproduce DESeq2's behaviour.
As pointed out by @arthurPignetOwkin, it seems like it would make sense to simply raise a warning instead and carry on with the analysis, and return NaNs for dispersions, LFCs, and p-values of genes that have NaN counts (as we already do for genes whose counts are all-zero).
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 at DeseqDataSet initialization and trace the existing handling for genes whose counts are all-zero. Follow how dispersions, LFCs, and p-values are produced for those genes, then verify that NaN-count genes emit a warning, analysis continues, and those outputs are NaN.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100