Run the complete OmicsBraid workflow on sample-level data
Usage
run_omics_braid(
data,
group,
reference,
comparison,
omic_order = names(data$assays),
entities = NULL,
pathway_mapping = NULL,
pathway_method = "mean_z",
min_pathway_features = 3L,
bootstrap_B = 500L,
bootstrap_shrinkage = 0.05,
empirical_tests = FALSE,
empirical_B = 499L,
empirical_omnibus_method = c("permutation", "centered_bootstrap"),
empirical_heterogeneity_method = c("null_shift_bootstrap", "centered_bootstrap"),
empirical_use_as_primary = FALSE,
ci_method = c("analytic", "percentile", "basic", "bca"),
integrated_ci_method = c("analytic", "percentile", "basic"),
ci_conf_level = 0.95,
ci_min_boot = 100L,
orientation = NULL,
equivalence_margin = 0.3,
alpha = 0.05,
state_basis = c("local", "adjusted"),
equivalence_p_adjust = "BH",
trajectory_margin = 0.15,
trend_p_adjust = "BH",
min_slope = NULL,
pattern_draws = 2000L,
seed = 1L
)Arguments
- data
An `omics_braid_data` object.
- group
Metadata group column.
- reference
Reference group.
- comparison
Comparison group.
- omic_order
Biological/display order of omics. Defaults to assay order.
- entities
Optional entities to analyze.
- pathway_mapping
Optional mapping passed to `score_pathways()`; if supplied, analysis is performed on pathway scores.
- pathway_method
Pathway scoring method.
- min_pathway_features
Minimum pathway features per omic.
- bootstrap_B
Bootstrap replicates for cross-omic covariance. Set to 0 to assume independence.
- bootstrap_shrinkage
Correlation shrinkage.
- empirical_tests
Logical; if `TRUE`, calculate additional resampling- calibrated omnibus and heterogeneity p-values using `empirical_omics_tests()`.
- empirical_B
Number of empirical resampling replicates.
- empirical_omnibus_method
`"permutation"` or `"centered_bootstrap"`.
- empirical_heterogeneity_method
`"null_shift_bootstrap"` (recommended) or `"centered_bootstrap"`.
- empirical_use_as_primary
Logical; if `TRUE`, empirical p-values replace asymptotic p-values when available for downstream omnibus evidence. The original asymptotic p-values are retained in separate columns.
- ci_method
Layer-effect confidence interval method: `"analytic"`, `"percentile"`, `"basic"`, or `"bca"`. Bootstrap intervals change interval reporting only; analytic SEs and p-values remain available.
- integrated_ci_method
Consensus-effect confidence interval method: `"analytic"`, `"percentile"`, or `"basic"`.
- ci_conf_level
Confidence level for analytic/bootstrap intervals.
- ci_min_boot
Minimum finite bootstrap draws required before a bootstrap interval replaces the analytic interval.
- orientation
Optional named +1/-1 vector to harmonize omic effect directions.
- equivalence_margin
Smallest effect size of interest for practical equivalence.
- alpha
Significance level for local difference/equivalence and braid inference.
- state_basis
Use local or multiplicity-adjusted inferential states for deterministic braid labels.
- equivalence_p_adjust
Multiple-testing method retained for adjusted equivalence/difference evidence.
- trajectory_margin
Smallest meaningful standardized-effect change per one-layer transition.
- trend_p_adjust
Multiple-testing method retained for adjusted trajectory evidence.
- min_slope
Deprecated alias for `trajectory_margin`.
- pattern_draws
Monte Carlo draws for geometric uncertainty propagation.
- seed
Random seed.