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Test preservation of reference WGCNA modules in another cohort

Source: R/network.R
coexpr_preservation.Rd

The two cohorts remain explicit MAE inputs. Features are intersected and ordered identically before constructing the multiData and multiColor lists required by WGCNA::modulePreservation().

Usage

coexpr_preservation(
  reference,
  reference_experiment,
  test,
  test_experiment,
  module_colors,
  reference_assay,
  test_assay,
  permutations = 200,
  network_type = "signed",
  seed = 1,
  verbose = 2,
  save_permuted_statistics = FALSE,
  ...
)

Arguments

reference, test

Reference and test MultiAssayExperiment objects.

reference_experiment, test_experiment

Experiment names.

module_colors

Named vector assigning every reference feature to a WGCNA module color or label.

reference_assay, test_assay

Assays on comparable transformed scales.

permutations

Number of permutations.

network_type

WGCNA network type.

seed

Random seed passed to WGCNA.

verbose

Backend verbosity.

save_permuted_statistics

Save permutation statistics to a file. The default avoids hidden filesystem output.

...

Additional arguments passed to WGCNA::modulePreservation().

Value

The native WGCNA module-preservation result list, augmented with a bulkMAEInputQuality element documenting feature intersections and automatic sample/feature filtering.