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: dataframe or file path to table of gene names in uniprot, hgnc_symbol, or ensembl format in cellphonedb database format
proteins: dataframe or file path to table of protein features in cellphonedb format
interactions: dataframe or file path to table of protein-protein interactions in cellphonedb format
complexes: optional: dataframe 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

rl_map_tiny <- create_rl_map_cellphonedb(genes = dominoSignal:::genes_tiny, 
 proteins = dominoSignal:::proteins_tiny, interactions = dominoSignal:::interactions_tiny, 
 complexes = dominoSignal:::complexes_tiny)