ComputeModuleEigengene: ComputeModuleEigengene

In smorabit/scWGCNA: hdWGCNA

ComputeModuleEigengene

Description

Internal helper function that computes module eigengene for a single module.

Usage

ComputeModuleEigengene(
  seurat_obj,
  cur_mod,
  modules,
  group.by.vars = NULL,
  verbose = TRUE,
  vars.to.regress = NULL,
  scale.model.use = "linear",
  pc_dim = 1,
  assay = NULL,
  wgcna_name = NULL,
  ...
)

Arguments

seurat_obj	A Seurat object
cur_mod	name of a module found in seurat_obj@misc[seurat_obj@misc$active_wgcna]$wgcna_net$colors
modules	table containing module / gene assignments, as in GetModules(seurat_obj).
group.by.vars	groups to harmonize by
verbose	logical indicating whether to print messages
vars.to.regress	character vector of variables in [e-mail] to regress when running ScaleData
scale.model.use	model to scale data when running ScaleData choices are "linear", "poisson", or "negbinom"
pc_dim	Which PC to use as the module eigengene? Default to 1.
assay	Assay in seurat_obj to compute module eigengenes. Default is DefaultAssay(seurat_obj)
wgcna_name	name of the WGCNA experiment

smorabit/scWGCNA documentation built on April 4, 2024, 10:32 a.m.