CRT: option to sample NTC null groups with replacement (as SCEPTRE does) - #16
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Add replace=False to make_ntc_groups_matched_by_freq / make_ntc_groups_ensemble, exposed as --ntc_replace, plus --max_ntc_groups to cap groups per ensemble. Without replacement, NTC guides are consumed as groups are built, so the null runs out after about n_ntc / --number_guide groups, and frequency-bin matching shrinks that further (e.g. ~200 NTC guides with 15 guides per target gave only 3-6 groups per ensemble). With replace=True each group is drawn without replacement but guides return to the pool, and identical groups are rejected, mirroring SCEPTRE's negative-control group construction (sample_combinations_v2, Katsevich-Lab/sceptre). With no cap, one group is built per real target. Default behavior is unchanged: replace=False reproduces the original groups exactly (checked against the unmodified function over 20 configurations). Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
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Builds on #13 (base:
crt-fixed-count-resampling).Why: Without replacement, NTC guides are used up as null groups are built, so the null runs out after about n_ntc /
--number_guidegroups, and frequency-bin matching cuts that further. With ~200 NTC guides and 15 guides per target we got only 3–6 null groups per ensemble.What:
replace=Falseoption onmake_ntc_groups_matched_by_freq/make_ntc_groups_ensemble, exposed as--ntc_replace. With it, each group is drawn without replacement, guides go back into the pool after each group, and identical groups are rejected. This follows SCEPTRE's negative-control group construction (sample_combinations_v2insrc/negative_control_functions.cpp, Katsevich-Lab/sceptre).--max_ntc_groupsto cap groups per ensemble. With--ntc_replaceand no cap, one group is built per real target (~10x the real-target CRT runtime at n_ensemble=10).CRT.sh/CRT_parallel.shcomments, runner-skill parameter references, CHANGELOG.tests/Script/Stage2_Evaluation/test_crt_ntc_replace.py.Default unchanged: with
replace=Falsethe groups are identical to the original code (checked over 20 configurations).One difference from SCEPTRE: groups are still matched to real-gene frequency-bin signatures, as elsewhere in this module.
Testing: new tests pass;
CRT.py --helpshows the new flags. Not yet run: the existingtest_crt_resampling.py, or CRT on real data with--ntc_replace.Note:
CRT.pyon this branch (and #13) imports the CRT package from a hard-coded path to ymo's checkout (line 28), which doesn't have #13's changes yet, so it fails withImportError: cannot import name 'OUTCOMES'from any other checkout. PR #14 on main already makes this path relative; merging main intocrt-fixed-count-resamplingshould fix it.🤖 Generated with Claude Code