Compute Metacells

Compute Metacells

Usage

compute_metacells(
  clean,
  forbidden_gene_names,
  cell_type_col,
  target_size = 160000,
  abundance_score = 0.9,
  n_cores = NULL,
  seed = 12345
)

Arguments

clean

anndata object

forbidden_gene_names

list of genes names that are not used as metacell base

cell_type_col

cell type column of cleaned anndata, used for reannotation

target_size

target UMI count per metacells

abundance_score

metacell celltype purity score

n_cores

number of cores to use

seed

seed