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Apply per-gene multiple testing correction for site selection metrics#460

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FerriolCalvet merged 5 commits into
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copilot/apply-multiple-testing-correction
Jun 1, 2026
Merged

Apply per-gene multiple testing correction for site selection metrics#460
FerriolCalvet merged 5 commits into
devfrom
copilot/apply-multiple-testing-correction

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Copilot AI commented May 21, 2026 •
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Site selection p-values must be corrected per gene (not across the full panel). The site comparison output should include both raw and adjusted p-values for downstream consumers.

  • Per-gene multiple testing
    • Apply Benjamini–Hochberg correction within each GENE group in omega_comparison_per_site.py.
  • Output surface
    • Emit p_value_adj alongside p_value for each site/AA grouping.
result["p_value_adj"] = np.nan
for gene, gene_df in result.groupby("GENE", dropna=False):
    valid_mask = gene_df["p_value"].notna()
    if not valid_mask.any():
        continue
    adjusted = benjamini_hochberg(gene_df.loc[valid_mask, "p_value"].to_numpy())
    result.loc[gene_df.index[valid_mask], "p_value_adj"] = adjusted

Copilot AI linked an issue May 21, 2026 that may be closed by this pull request
Apply multiple testing correction for site selection analysis #459
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@FerriolCalvet
Add per-gene multiple testing correction for site comparisons
829e06c 
Agent-Logs-Url: https://github.com/bbglab/deepCSA/sessions/78cc6f96-7594-4d38-93df-622555a78ba3

Co-authored-by: FerriolCalvet <38539786+FerriolCalvet@users.noreply.github.com>
Copilot AI changed the title [WIP] Add multiple testing correction for site selection analysis Apply per-gene multiple testing correction for site selection metrics May 21, 2026
Copilot AI requested a review from FerriolCalvet May 21, 2026 07:43
@FerriolCalvet FerriolCalvet marked this pull request as ready for review June 1, 2026 09:54
@FerriolCalvet

FerriolCalvet commented Jun 1, 2026 •
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tested and works well!

  • pending to remove genes that are not in the panel from the results

@FerriolCalvet FerriolCalvet requested a review from Copilot June 1, 2026 11:00
Copilot AI reviewed Jun 1, 2026
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Pull request overview

This PR updates the per-site positive selection (“site comparison”) outputs to include per-gene multiple-testing correction (Benjamini–Hochberg) and surfaces the adjusted p-values to downstream consumers (notably saturation plots). It also wires an optional gene subset parameter through the Nextflow module invocation.

Changes:

  • Add p_value_adj to omega_comparison_per_site.py by applying Benjamini–Hochberg correction within each GENE group, after flooring underflowed p_value == 0.
  • Update saturation plotting logic to use adjusted p-values (p_value_adj / pvalue_adj) for significance decisions and adjust default significance threshold to 0.05.
  • Pass an optional --genes subset from Nextflow config/module into omega_comparison_per_site.py, and include compiled global-local omega results in summary inputs when enabled.

Reviewed changes

Copilot reviewed 3 out of 6 changed files in this pull request and generated 1 comment.

Show a summary per file
File Description
workflows/deepcsa.nf Adds compiled global-local omega results into the positive selection result bundle for downstream summary/plotting.
modules/local/bbgtools/sitecomparison/main.nf Adds optional --genes argument plumbing to the site comparison process (currently introduces a command construction bug).
conf/tools/omega.config Wires params.selected_genes into the site comparison module via ext.genes_subset.
bin/utils.py Introduces shared MIN_NONZERO_PVALUE constant for p-value underflow flooring.
bin/plot_gene_saturation.py Switches significance logic to adjusted p-values and aligns defaults/inputs for global-local omega table usage.
bin/omega_comparison_per_site.py Implements per-gene BH correction and emits p_value_adj alongside raw p_value; adds --genes option.

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Comment thread modules/local/bbgtools/sitecomparison/main.nf
@FerriolCalvet FerriolCalvet merged commit d012b74 into dev Jun 1, 2026
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@FerriolCalvet FerriolCalvet deleted the copilot/apply-multiple-testing-correction branch June 1, 2026 11:58
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Apply multiple testing correction for site selection analysis

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