cytomining / cytomining/copairs

compute exact p-value for small null configs

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Dominant language
Python
Stars
24
Forks
11
PR merge metrics
No merged PRs in 30d

Description

When num_pos and num_total is relatively small, e.g. (5 replicates, 20 negcon), total combinations is 4845. Here, instead of building `null_size=10,000` random ranks, p_val should be estimated by computing the 4,845 average precision scores.

In general, if `math.comb(num_total, num_pos)

Contributor guide

Open the contributing guide

Research direction

Start by locating the code that uses num_pos, num_total, null_size, and p_val, then inspect how average precision scores are generated for random null ranks. Use math.comb(num_total, num_pos) as the branch condition; done means configurations below null_size use all combinations and produce the exact p-value, with existing behavior preserved otherwise.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data
Issue type
Feature
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
48/100

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