Compute exact p-values for small null configurations #114
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When the number of possible rankings C(total, num_pos) is less than or equal to null_size, compute exact null distribution by enumerating all combinations instead of random sampling. This provides exact p-values for small configurations like (5 replicates, 20 negcon) where C(20, 5) = 15,504 < 10,000. Closes #105 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
johnarevalo
requested changes
Dec 8, 2025
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Thanks for the PR!
Shouldn't this be C(25, 5)? 😄 |
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Ah yes :) I've updated the example (and with a smaller one fwiw) |
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Summary
C(total, num_pos) <= null_size, compute exact null distribution by enumerating all possible rankings instead of random samplingexact_ap()function to enumerate all combinationsnull_dist_cached()to use exact computation when feasiblenull_sizefor consistent interfaceCloses #105
Example
For a small configuration with
num_pos=3positives andtotal=10items:C(10, 3) = 120If
null_size=10,000, all 120 exact AP scores are computed and tiled to fill 10,000 slots, giving exact p-values.Test plan
uv run pytestpasses (65 tests)uv run ruff check src/ tests/passesexact_ap, exact/random switching logic🤖 Generated with Claude Code