ReassignModules

Reassigns features to different modules

Usage

ReassignModules(
  seurat_obj,
  harmonized = TRUE,
  features = NULL,
  new_modules = NULL,
  ignore = FALSE,
  wgcna_name = NULL
)

Arguments

seurat_obj

A Seurat object

harmonized

logical indicating whether or not to use harmonized MEs

features

character vector containing features for manual module reassignment,

new_modules

character vector containing modules to reassign the genes

ignore

logical indicating whether or not to ignore error message about reassigning non-grey features

wgcna_name

The name of the hdWGCNA experiment in the seurat_obj@misc slot

Value

seurat_obj with the an updated modules table for the selected wgcna experiment

Details

ReassignModules reassigns features with negative kMEs in their assigned module to the module that had the highest kME for that feature. Alternatively, this function can manually assign features to different modules, which can be helpful if certain genes of interest are assigned to the grey module. We generally do not advise reassigning features to new modules if they are in non-grey modules, but the user can do so at their own risk by setting ignore=TRUE.