Package index
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run_omics_braid() - Run the complete OmicsBraid workflow on sample-level data
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run_omics_braid_summary() - Run OmicsBraid from externally estimated summary statistics
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braid_results_table() - Create a one-row-per-entity master result table
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write_omics_braid() - Export OmicsBraid results
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omics_braid_data() - Construct an OmicsBraid data object
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as_omics_braid_data() - Coerce supported objects to OmicsBraid data
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validate_omics_braid_data() - Validate an OmicsBraid data object
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read_omics_braid() - Read OmicsBraid input files
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harmonize_entities() - Harmonize assay-specific feature identifiers to common entities
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score_pathways() - Score pathways within each omic layer
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orient_omics() - Harmonize the sign orientation of omic-layer effects
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estimate_effects() - Estimate layer-specific standardized effects
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bootstrap_effect_covariance() - Estimate cross-omic effect covariance by matched-subject bootstrap
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bootstrap_effect_intervals() - Bootstrap confidence intervals for layer-specific standardized effects
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bootstrap_consensus_intervals() - Bootstrap confidence intervals for GLS consensus effects
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integrate_effects() - Integrate effects across omic layers and quantify heterogeneity
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empirical_omics_tests() - Empirically calibrate OmicsBraid omnibus and heterogeneity tests
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test_equivalence() - Test practical equivalence to a negligible effect region
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test_braid_trend() - Test ordered cross-omic effect trajectories with generalized least squares
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classify_braids() - Classify cross-omic braid patterns using inferential evidence
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braid_pattern_probabilities() - Quantify uncertainty in effect-braid geometry
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plot_evidence_forest() - Plot an Omics Evidence Forest
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plot_effect_braid() - Plot an Effect Braid
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plot_concordance_map() - Plot concordance versus integrated significance
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plot_braid_heatmap() - Plot a braid heatmap across entities and omics
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simulate_braid_data() - Simulate multi-omics data with known braid patterns