Create a receptor - ligand map from a CellPhoneDB signaling database — create_rl_map

Generates a data frame of ligand-receptor interactions from a CellPhoneDB database annotating the genes encoding the interacting ligands and receptors to be queried in transcriptomic data.

Usage

create_rl_map_cellphonedb(
  genes,
  proteins,
  interactions,
  complexes = NULL,
  database_name = "CellPhoneDB",
  gene_conv = NULL,
  gene_conv_host = "https://www.ensembl.org",
  alternate_convert = FALSE,
  alternate_convert_table = NULL
)

Arguments

genes: data frame or file path to table of gene names in uniprot, hgnc_symbol, or ensembl format in CellPhoneDB database format
proteins: data frame or file path to table of protein features in CellPhoneDB format
interactions: data frame or file path to table of protein-protein interactions in CellPhoneDB format
complexes: optional: data frame or file path to table of protein complexes in CellPhoneDB format
database_name: name of the database being used, stored in output
gene_conv: a tuple of (from, to) or (source, target) if gene conversion to orthologs is desired; options are ENSMUSG, ENSG, MGI, or HGNC
gene_conv_host: host for conversion; default ensembl, could also use mirrors if desired
alternate_convert: boolean if you would like to use a non-ensembl method of conversion (must supply table; not recommended, use only if ensembl is down)
alternate_convert_table: supplied table for non-ensembl method of conversion

Value

Data frame where each row describes a possible receptor-ligand interaction

Examples

data(CellPhoneDB)
rl_map_tiny <- create_rl_map_cellphonedb(genes = CellPhoneDB$genes_tiny,
 proteins = CellPhoneDB$proteins_tiny,
 interactions = CellPhoneDB$interactions_tiny,
 complexes =CellPhoneDB$complexes_tiny)