Builds signaling network for NicheNet using ConsensusPathDB

Builds signaling network prior knowledge using ConsensusPathDB (CPDB) data. Note, the interactions from CPDB are not directed and many of them comes from complex expansion. Find out more at http://cpdb.molgen.mpg.de/.

Usage

nichenet_signaling_network_cpdb(...)

Arguments

...

Passed to consensuspathdb_download.

Value

A network data frame (tibble) with signaling interactions suitable for use with NicheNet.

See also

• nichenet_signaling_network

• consensuspathdb_download

Examples

# use some parameters stricter than default:
cpdb_signaling_network <- nichenet_signaling_network_cpdb(
    complex_max_size = 2,
    min_score = .99
)
#> Error in map(., .uniprot_id_mapping_table, from, to): ℹ In index: 1.
#> ℹ With name: 1.
#> Caused by error in `.f()`:
#> ! Error at querying UniProt ID mapping: The parameter 'to' has an invalid value 'GENENAME'. The parameter 'from' has an invalid value 'ACC'. The combination of 'from=ACC' and 'to=GENENAME' parameters is invalid