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