diagFDR

• dfdr_alert_basis(): evidential basis of each alert (derived check, simulation-informed alert, heuristic alert, descriptive).
• dfdr_p_summary() / dfdr_p_interpretation(): pi0 by the eight cp4p estimators on targets + decoys, targets and decoys, grouped into a converging set (consensus value) and the others; p-value threshold, and score or PEP threshold, giving an estimated FDR of alpha on targets with the consensus pi0 and with pi0 = 1 (Benjamini-Hochberg); comparison with target-decoy counting; pooled targets + decoys check; caveats.
• dfdr_pep_summary() / dfdr_pep_interpretation(): whether PEPs agree with, under- or overestimate the decoy-derived reference, and the sum of the PEPs of the accepted targets against the number of accepted decoys.

Inputs

• as_dfdr_tbl() and the DIA-NN builders take two_pass (set TRUE for --reanalyse / match-between-runs reports); the DIA-NN builders say once per session when it is not given.
• dfdr_run_all(compute_pseudo_pvalues = TRUE) warns, and records the reason in the list metadata (p_source), when a list has no score column (DIA-NN 2.x reports carry no CScore). pseudo_pvalue_score = "pep" uses -PEP as an approximate surrogate score.
• mokapot_competed_universe(q_mode = c("as_exported", "recount")): mokapot computes q-values over all PSMs it receives; "recount" recomputes (D+1)/T q-values on the competed winners.
• DIA-NN builders keep the largest score of a collapsed unit (higher is better), and the smallest q-value and PEP.

HTML report

• Executive summary with alerts to review, each tagged with its evidential basis; lists without alert shown as "no internal alert"; checks that are not evaluable shown as "n/e".
• Every table is followed by a legend of its columns; small values are shown in scientific notation; formulas are written in HTML (no MathJax needed).
• "What the p-value diagnostics say" and a PEP interpretation, written from the summaries above.
• The recomputed decoy ratio is labelled D/T; the Jaccard guide treats overlap as descriptive.
• dfdr_render_report() accepts a relative out_dir and renders from a temporary copy of the template.
• A plot that cannot be built for a list (e.g. too few p-values) is skipped with a warning.