Constructor for a bulk co-expression module result — new_bulk_module

Uniform container for the terminal output of every bulk co-expression method. Stores the module membership (gene to module_id assignment), the method-specific factor matrices (gene loadings, sample activities, eigengenes, dictionaries), the fit parameters, and method-specific diagnostics.

Usage

new_bulk_module_result(
  modules,
  factors = list(),
  method,
  params = list(),
  diagnostics = list()
)

Arguments

modules: data.table. Module membership. Must contain gene and module_id columns. Method-specific extras (sign, stability, loading, ...) are allowed.
factors: Named list of matrices. Method-agnostic keys shared across methods: gene_loadings, sample_activity, module_eigengenes, dictionary, loadings, gene_to_eigengene_cor. May be empty for methods that produce no factor matrices (e.g. Leiden).
method: String. One of c("correlation-based", "differential correlation-based", "ICA-based", "dgrdl-based", "nmf-based").
params: List. The params_xxx() list that produced the fit.
diagnostics: Named list. Method-specific diagnostics (stability data.table, resolution used, per-run losses, laplacians, ...).

Value

An object of class BulkModuleResult.