Package index • BREAD

Fit a BREAD model

The main entry point and the two backend fit helpers. Most users only call fit_bread(); backend-specific functions are exposed for power users.

fit_bread(): Fit a Bayesian region-specific methylation model
bread_prior(): Construct a BREAD prior for the summary-mode model

Pipeline building blocks

Exposed helpers for each stage of the pipeline — useful when you want to inspect intermediate output or plug BREAD into a larger workflow.

validate_bread_input(): Validate inputs to fit_bread()
map_probes_to_features(): Map probes to user-defined regions
summarize_features(): Summarize probe-level methylation into region-level values
posterior_summary(): Extract per-region posterior summaries
classify_regions(): Classify regions as hyper / hypo / inconclusive

Plotting and palette

plot_region_posterior(): Posterior density of the contrast coefficient per region
plot_region_data(): Raw region-level values by contrast group
plot_feature_set(): Feature-set classification summary
bread_colors(): BREAD color palettes (MetBrewer "Cross")

Enrichment

Post-hoc annotation of a BreadFit’s hyper / hypo regions against KnowYourCG reference databases (TFBS, chromHMM, CGI, tissue signatures, …).

bread_kycg(): Enrich BREAD classifications against KnowYourCG databases

Classes and methods

BreadFit BreadFit-class: The BreadFit S4 class
BreadResults BreadResults-class: The BreadResults S4 class
results(): Extract the region-level results table from a BreadFit
classifications(): Extract region classifications from a BreadFit
posterior_draws(): Draw from the posterior of a region's contrast coefficient