The BreadFit S4 class — BreadFit • BREAD

Main fitted object returned by fit_bread(). Thin S4 wrapper with stable slots that downstream packages can depend on.

Slots

call: The original fit_bread() call.
params: List of parameters used (delta, prob_cutoff, summary_fun, mode, backend, contrast, min_probes, feature_class_col, iter, chains, cores, seed).
mode: "summary" or "hierarchical".
assay_name: Assay name used from se.
input_scale: "M" or "Beta".
mapping: Probe-to-region data frame from map_probes_to_features().
features: GRanges of regions that survived min_probes filtering.
model: Internal fit object from fit_bread_summary().
posterior: Per-region posterior summary data frame.
results: Per-region data frame with classification column.
diagnostics: List with backend, seed, feature counts, failure counts.