ProjectModules: ProjectModules

In smorabit/hdWGCNA: hdWGCNA

ProjectModules

Description

Project a set of co-expression modules from a reference to a query dataset

Usage

ProjectModules(
  seurat_obj,
  seurat_ref,
  modules = NULL,
  group.by.vars = NULL,
  gene_mapping = NULL,
  genome1_col = NULL,
  genome2_col = NULL,
  overlap_proportion = 0.5,
  vars.to.regress = NULL,
  scale.model.use = "linear",
  wgcna_name = NULL,
  wgcna_name_proj = NULL,
  ...
)

Arguments

seurat_obj	A Seurat object where the modules will be projected to
seurat_ref	A Seurat object containing the co-expression modules to be projected
modules	optionally provide a dataframe containing gene-module information to bypass seurat_ref
group.by.vars	groups to harmonize by
gene_mapping	dataframe to map gene names between genomes
genome1_col	column in gene_mapping containing the genes for seurat_ref (reference)
genome2_col	column in gene_mapping containing the genes for seurat_obj (query)
overlap_proportion	the proportion of genes that must be present in seurat_obj for a given module to be projected. Default = 0.5 (50% of genes)
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"
wgcna_name	The name of the hdWGCNA experiment in the seurat_ref@misc slot
wgcna_name_proj	The name of the hdWGCNA experiment to be created for the projected modules in seurat_obj

Examples

ProjectModules

smorabit/hdWGCNA documentation built on Oct. 23, 2024, 11:19 p.m.