Download the CellPhoneDB ligand-receptor database
get_cellphonedb_db.RdFetches the CellPhoneDB v5.0.0 database from the
cellphonedb-data repository
and flattens it to one row per interaction. Each partner is resolved to
the gene symbols of its subunits: one gene for a single protein, several
for a complex. The download is cached in dir.
Usage
get_cellphonedb_db(dir = tempdir(), .verbose = TRUE)Arguments
- dir
String. Directory to store and look for
cellphonedb.zip. Defaults totempdir().- .verbose
Boolean. Controls verbosity of the download.
Value
A data.table with one row per interaction and the columns:
interaction_id - The CellPhoneDB interaction identifier.
partner_a, partner_b - The partner names: the gene symbol for a single protein, the complex name otherwise.
genes_a, genes_b - List columns with the gene symbols of the subunits.
is_complex_a, is_complex_b - Is the partner a complex.
directionality - E.g.
"Ligand-Receptor".classification - The signalling classification.