Apply BH multiple-testing correction to omega outputs#454
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- select the correct gene column - remove '-' as a gene missing: - check if there is an additional ',' at the end
- new container for query independent from dNdS Missing: - container dependencies should be installed but are not found
- Merge remote-tracking branch 'origin/custom-refcds' into feat/dynamic-refcds - add script from intogen repo
- add automatic querying to Ensembl biomart - filter regions based on consensus panel - output dNdS: cv, loc and global - output warning of false splicesites
-not tested
- testing pending
-species and genome were not used
…ts (#439) * Initial plan * feat: add depth-vs-metrics QC module and workflow wiring Agent-Logs-Url: https://github.com/bbglab/deepCSA/sessions/a3d27832-9c45-4e45-8f40-3262358fa1f2 Co-authored-by: FerriolCalvet <38539786+FerriolCalvet@users.noreply.github.com> * refactor: remove test-data coupling from optional QC placeholders Agent-Logs-Url: https://github.com/bbglab/deepCSA/sessions/a3d27832-9c45-4e45-8f40-3262358fa1f2 Co-authored-by: FerriolCalvet <38539786+FerriolCalvet@users.noreply.github.com> * fix: harden optional input handling for metrics-vs-depth QC Agent-Logs-Url: https://github.com/bbglab/deepCSA/sessions/a3d27832-9c45-4e45-8f40-3262358fa1f2 Co-authored-by: FerriolCalvet <38539786+FerriolCalvet@users.noreply.github.com> * style: tighten metrics-vs-depth QC output globs Agent-Logs-Url: https://github.com/bbglab/deepCSA/sessions/a3d27832-9c45-4e45-8f40-3262358fa1f2 Co-authored-by: FerriolCalvet <38539786+FerriolCalvet@users.noreply.github.com> * fix: create metrics-vs-depth stub output directory Agent-Logs-Url: https://github.com/bbglab/deepCSA/sessions/a3d27832-9c45-4e45-8f40-3262358fa1f2 Co-authored-by: FerriolCalvet <38539786+FerriolCalvet@users.noreply.github.com> * fix: plot and focus the analysis within each gene - sample comparisons are relevant within a gene - comparisons between genes of the same sample are not that relevant - add FIXME for defining command line arguments properly * update depth plots * update depth qcs plot working * exclude subgenic elements from depth qc * cleanup workflow - activate the use of all groups * restrict number of genes plotted to 200 --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: FerriolCalvet <38539786+FerriolCalvet@users.noreply.github.com> Co-authored-by: FerriolCalvet <ferriolcalvet@gmail.com>
* implement optional gff3 local file * allow local gff3 definition * small suggested update * minor fixes in config * fix bug in processing of non-human genomes
* Initial plan * Add VAF distortion threshold parameter Agent-Logs-Url: https://github.com/bbglab/deepCSA/sessions/401bf46f-f988-4886-945d-ddca759982d1 Co-authored-by: FerriolCalvet <38539786+FerriolCalvet@users.noreply.github.com> --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: FerriolCalvet <38539786+FerriolCalvet@users.noreply.github.com>
- not tested
- updated profile_all logic
add dynamic RefCDS definition for dNdScv
* remove computation of simple mutdensity_adjusted - omega not working * provide adjusted mutation density to omega - not tested, but should work - NOT CORRECT * rename and reorganize mutdensity files * update adjusted mut density with sample values - add drop duplicates with potential fix * add adjusted mut density variability plots - not tested * fix bug after upstream change * fix error in computation of adjusted mutation density * fix bug in synonymous mut. density selection * add dndsproxy computation * fix dnds proxy computation * update 0 handling and output * run omega preprocessing once * update omega execution to a single case * fix merge remainders * temporary fix coexistent synmutdensity modes - this results in - a correct omega computation (consistent with the current implementation of the method) - the computation of the dnds proxy value that has remained hidden for too long - not tested * fix bugs - tested * mutation densities working - omega still to be recovered * undo all changes in omega * apply suggested from review
Agent-Logs-Url: https://github.com/bbglab/deepCSA/sessions/0dc29618-9415-4b29-8cfd-475121150c33 Co-authored-by: FerriolCalvet <38539786+FerriolCalvet@users.noreply.github.com>
Agent-Logs-Url: https://github.com/bbglab/deepCSA/sessions/0dc29618-9415-4b29-8cfd-475121150c33 Co-authored-by: FerriolCalvet <38539786+FerriolCalvet@users.noreply.github.com>
Agent-Logs-Url: https://github.com/bbglab/deepCSA/sessions/0dc29618-9415-4b29-8cfd-475121150c33 Co-authored-by: FerriolCalvet <38539786+FerriolCalvet@users.noreply.github.com>
Co-authored-by: FerriolCalvet <38539786+FerriolCalvet@users.noreply.github.com>
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[WIP] Apply multiple-testing correction to omega outputs
Apply BH multiple-testing correction to omega outputs
May 13, 2026
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Omega and omegagloballoc outputs require independent multiple-testing correction across cohort/group/sample slices, applied separately at gene and subgenic levels. This change adds those corrections and ensures corrected outputs are published.
omega_multiple_testing.pyto compute BH-adjusted p-values per{all_samples|group|sample} × {gene|subgenic}slice and emitpvalue_adj.OMEGA_MULTITESTmodule wired intoOMEGA_ANALYSISto replace compiled omega outputs for both omega and omegagloballoc before publish.pvalue_adjin outputs.Example usage: