Detect co-expression modules with WGCNA

Usage

coexpr_wgcna(
  x,
  experiment,
  assay,
  power,
  top_n = NULL,
  network_type = "signed",
  tom_type = NULL,
  min_module_size = 30,
  merge_cut_height = 0.25,
  numeric_labels = TRUE,
  seed = 1,
  verbose = 2,
  ...
)

Arguments

x: A MultiAssayExperiment object.
experiment: Optional experiment name.
assay: Assay name or one-based assay index.
power: Soft-thresholding power chosen for the dataset.
top_n: Optional number of most variable genes.
network_type: WGCNA network type. Use the same value for module preservation.
tom_type: Optional topological-overlap type. By default it follows network_type (unsigned stays unsigned; signed variants use signed TOM).
min_module_size: Minimum module size.
merge_cut_height: Module merging threshold.
numeric_labels: Return numeric module labels.
seed: Random seed used by WGCNA without changing the caller's random number generator state.
verbose: Backend verbosity.
...: Additional arguments passed to WGCNA::blockwiseModules().

Value

The native WGCNA module result list, augmented with bulkMAEQuality, bulkMAERemovedSamples, and bulkMAERemovedFeatures elements documenting automatic quality filtering.