ComputeModuleEigengene: ComputeModuleEigengene
In smorabit/hdWGCNA: hdWGCNA

ComputeModuleEigengene

R Documentation

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 seurat_obj@meta.data 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