R: Verifiable FDR Diagnostics for Proteomics

# Verifiable FDR Diagnostics for Proteomics

## Documentation for package ‘diagFDR’ version 0.1.1

- DESCRIPTION file
- User guides, package vignettes and other documentation

## Help Pages

as_dfdr_tbl | Create a 'dfdr_tbl'
dfdr_bh_diagnostics | BH diagnostics at a headline alpha (threshold, discoveries, boundary support)
dfdr_bh_elasticity | BH list elasticity (Jaccard) across alpha values
dfdr_curve_stability | Stability curve across alpha values
dfdr_elasticity | Threshold elasticity (list stability to cutoff perturbation)
dfdr_equal_chance_qbands | Equal-chance plausibility by q-value bands
dfdr_headline | Headline stability diagnostics at a given alpha
dfdr_local_tail | Local tail support near the cutoff
dfdr_pep_decoy_sanity | Decoy PEP sanity checks
dfdr_pep_reliability | Posterior Error Probability (PEP) reliability and internal PEP calibration error (IPE)
dfdr_pep_reliability_tdc | Target-focused PEP reliability using a TDC-style error proxy
dfdr_pi0_storey | Storey pi_0(lambda) tail-uniformity diagnostic
dfdr_plot_bh_elasticity | Plot BH elasticity (Jaccard) vs alpha
dfdr_plot_cv | Plot 'CV_hat' versus 'alpha'
dfdr_plot_dalpha | Plot decoy support D_alpha versus 'alpha'
dfdr_plot_dwin | Plot local decoy support 'D_alpha_win' versus 'alpha'
dfdr_plot_elasticity | Plot threshold elasticity (Jaccard) versus 'alpha'
dfdr_plot_equal_chance | Plot equal-chance plausibility by q-value bands
dfdr_plot_fdrhat_pi0 | Plot Storey-style estimated FDR curve: \hatpi_0 m t / R(t)
dfdr_plot_pep_density_by_decoy | Plot PEP density by decoy/target
dfdr_plot_pep_reliability | Plot PEP reliability
dfdr_plot_pep_reliability_tdc | Plot target-focused PEP reliability (TDC-style)
dfdr_plot_pi0 | Plot Storey pi_0(lambda) curve
dfdr_plot_p_calibration | Plot p-value calibration (ECDF minus uniform)
dfdr_plot_p_calibration2 | P-value calibration plot (cp4p-style), with multiple pi0 reference curves
dfdr_plot_p_density_by_decoy | Plot (pseudo-)p-value density by decoy/target
dfdr_plot_scope_disagreement_matrix | Plot scope disagreement as a Jaccard overlap heatmap
dfdr_plot_score_distributions | Plot target vs decoy score distributions
dfdr_p_calibration | P-value calibration diagnostic (ECDF vs uniform; stratified)
dfdr_render_report | Render a human-readable HTML report from 'dfdr_run_all' output
dfdr_run_all | Run a standard set of FDR QC diagnostics
dfdr_run_jaccard | Inter-run Jaccard overlap matrix at a fixed threshold
dfdr_scope_disagreement | Scope disagreement between two lists
dfdr_summary_headline | Build a headline summary table (one row per list)
dfdr_sumpep | Expected number of false targets among accepted identifications
dfdr_write_manifest | Write a manifest file describing parameters, list metadata, and warnings
dfdr_write_readme | Write a human-readable 'README.md' report
dfdr_write_report | Write diagnostic outputs to a folder
diann_global_minrunq | DIA-NN: global precursor list built by minimum run-wise q across runs
diann_global_precursor | DIA-NN -> global precursor universe (deduplicated by 'Precursor.Id')
diann_runxprecursor | DIA-NN -> run-by-precursor universe (deduplicated within run)
flag_headline | Flag diagnostic values based on heuristic thresholds
mokapot_competed_universe | Create a competed-winner universe from mokapot PSM outputs
print.dfdr_tbl | Print a 'dfdr_tbl'
read_dfdr_maxquant_msms | Read MaxQuant 'msms.txt' into a 'dfdr_tbl' (PSM-level; reconstructed TDC q-values)
read_dfdr_mzid | Read mzIdentML into a 'dfdr_tbl' (generic; score-based TDC q-values)
read_diann_parquet | Read a DIA-NN 'report.parquet'
read_mokapot_psms | Read mokapot PSM text outputs (targets + decoys) and combine
read_spectronaut | Read a Spectronaut TSV report
read_spectronaut_efficient | Read Spectronaut efficiently with column selection
score_to_pvalue | Convert identification scores to p-values or pseudo-p-values
spectronaut_runxprecursor | Spectronaut -> run-by-precursor universe (deduplicated within run by 'EG.PrecursorId')