Covariance-Aware Inference of Cross-Omic Effect Trajectories

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Documentation for package ‘OmicsBraid’ version 0.2.3

• DESCRIPTION file.
• Package NEWS.

Help Pages

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