sc.tl.rank_genes_groups assumes the data is log(x+1) transformed
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Area – Differential Expression
- Dominant language
- Python
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Description
- [X ] Additional function parameters / changed functionality / changed defaults?
Could the function add a boolean parameter to make it work for non-log transformed data?
if [boolean depending on whether data is log transformed or not]:
foldchanges = (self.expm1_func(mean_group) + 1e-9) / (self.expm1_func(mean_rest) + 1e-9)
else:
foldchanges = (mean_group+ 1e-9) / (mean_rest + 1e-9)
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Research direction
Start at the sc.tl.rank_genes_groups entry point and trace how foldchanges are calculated from group and rest means. Add the requested option for non-log-transformed data while preserving the current behavior for log-transformed data, then verify both calculation paths against the issue's formulas.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100