Function to convert labelled seurat object to avg expression matrix — seurat_ref (original) (raw)

Function to convert labelled seurat object to avg expression matrix

Usage

seurat_ref(seurat_object, ...)

# S3 method for class 'Seurat'
seurat_ref(
  seurat_object,
  cluster_col = "classified",
  var_genes_only = FALSE,
  assay_name = NULL,
  method = "mean",
  subclusterpower = 0,
  if_log = TRUE,
  ...
)

Arguments

seurat_object

seurat_object after tsne or umap projections and clustering

...

additional arguments

cluster_col

column name where classified cluster names are stored in seurat meta data, cannot be "rn"

var_genes_only

whether to keep only var_genes in the final matrix output, could also look up genes used for PCA

assay_name

any additional assay data, such as ADT, to include. If more than 1, pass a vector of names

method

whether to take mean (default) or median

subclusterpower

whether to get multiple averages per original cluster

if_log

input data is natural log, averaging will be done on unlogged data

Value

reference expression matrix, with genes as row names, and cell types as column names

Examples

so <- so_pbmc()
ref <- seurat_ref(so, cluster_col = "seurat_clusters")