nichenet_gr_network_omnipath: Builds gene regulatory network for NicheNet using OmniPath

In saezlab/OmnipathR: OmniPath web service client and more

Builds gene regulatory network for NicheNet using OmniPath

Description

Retrieves network prior knowledge from OmniPath and provides it in a format suitable for NicheNet. This method never downloads the 'ligrecextra' dataset because the ligand-receptor interactions are supposed to come from nichenet_lr_network_omnipath.

Usage

nichenet_gr_network_omnipath(min_curation_effort = 0, ...)

Arguments

min_curation_effort	Lower threshold for curation effort
...	Passed to import_transcriptional_interactions

Value

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

See Also

• nichenet_gr_network_evex

• nichenet_gr_network_harmonizome

• nichenet_gr_network_htridb

• nichenet_gr_network_omnipath

• nichenet_gr_network_pathwaycommons

• nichenet_gr_network_regnetwork

• nichenet_gr_network_remap

• nichenet_gr_network_trrust

Examples

# use interactions up to confidence level "C" from DoRothEA:
op_gr_network <- nichenet_gr_network_omnipath(
    dorothea_levels = c('A', 'B', 'C')
)

saezlab/OmnipathR documentation built on Nov. 10, 2024, 11:02 p.m.