min_in_group_fraction in filter_rank_genes_groups doesn't work as expected
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Description
the default value of min_in_group_fraction is 0.25, which I understand is filter those genes that has less than 25 percent present in the group.
I use min_in_group_fraction = 0, max_in_group_fraction=1.01 to try to filter everything just by foldchange and adj_p value, but it doesn't add any gene when comparing to min_in_group_franction=0.25,
in my test, if I filter on rank_gene_groups by foldchange and adj_p, I got 87 genes back. but if I try mini_in_group_franction=0 in filter_ranK_gene_groups, I only get 25 back.
I notice an issue https://github.com/theislab/scanpy/issues/863 that mentionthat rank_gene_groups and filter_rank_gene_groups calculate fold change differently, was wondering
- why
- this doesn't explain the huge difference between numbers of gene returned by different filter method.
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Research direction
Start with the filter_rank_genes_groups and rank_gene_groups entry points described in the issue, reproducing the comparison with min_in_group_fraction=0 and max_in_group_fraction=1.01. Trace how fold change, adjusted p-values, and group fractions are calculated; done means the filtering behavior matches the documented parameter semantics and the discrepancy is explained or corrected.
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Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 32/100