feat: rename FDR params and expose matrix-level q-value controls#44
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feat: rename FDR params and expose matrix-level q-value controls#44
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Rename protein_level_fdr_cutoff -> precursor_qvalue to accurately reflect that DIA-NN's --qvalue controls precursor-level filtering, not protein-level FDR. Expose two new matrix-level FDR parameters: - matrix_qvalue (default 0.01): maps to --matrix-qvalue - matrix_spec_q (default 0.05): maps to --matrix-spec-q This enables proteogenomics workflows to independently control matrix filtering (e.g., matrix_spec_q=1.0 to retain variant proteins that lack sufficient unique peptides). Closes #42 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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Summary
protein_level_fdr_cutoff→precursor_qvalueto accurately reflect DIA-NN's--qvalue(precursor-level, not protein-level)matrix_qvalue(default 0.01, maps to--matrix-qvalue) andmatrix_spec_q(default 0.05, maps to--matrix-spec-q)--matrix-qvalueand--matrix-spec-qto blocked flags in FINAL_QUANTIFICATIONProteogenomics use case
Users can now set
--matrix_spec_q 1.0to retain variant proteins (e.g., COSMIC) that always have Protein.Q.Value = 1.0 due to insufficient unique peptides, without affecting precursor-level filtering.Closes #42
Test plan
--qvalue 0.01 --matrix-qvalue 0.01 --matrix-spec-q 0.05--matrix_spec_q 1.0— verify variant proteins are retained in pg_matrix--diann_extra_args '--matrix-qvalue 0.05'is stripped with a warning🤖 Generated with Claude Code