Update CellPhoneDB — update_cpdb_db • scrnaseq.cellcomm

Update CellPhoneDB and generate required files

Usage

update_cpdb_db(
  source_cpdb_dir,
  db,
  gene_info_table,
  output_dir,
  return_list = FALSE
)

Arguments

source_cpdb_dir: directory with CellPhoneDB files
db: database with at least 'source_genesymbol' and 'target_genesymbol' and their subunits starting with 'source_genesymbol_subunit' or 'target_genesymbol_subunit'
gene_info_table: dataframe with uniprot, protein name, genesymbol and ensembl
output_dir: path to directory for saving the generated CellPhoneDB files
return_list: return list with generated dataframes (default = FALSE)

Value

if return_list = TRUE, return list with complex_input, gene_input, interaction_input and protein_input