nichenet_signaling_network_pathwaycommons: NicheNet signaling network from PathwayCommons

In saezlab/OmnipathR: OmniPath web service client and more

NicheNet signaling network from PathwayCommons

Description

Builds signaling network prior knowledge for NicheNet using PathwayCommons.

Usage

nichenet_signaling_network_pathwaycommons(
  interaction_types = c("catalysis-precedes", "controls-phosphorylation-of",
    "controls-state-change-of", "controls-transport-of", "in-complex-with",
    "interacts-with"),
  ...
)

Arguments

interaction_types	Character vector with PathwayCommons interaction types. Please refer to the default value and the PathwayCommons webpage.
...	Ignored.

Value

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

Examples

# use only the "controls-transport-of" interactions:
pc_signaling_network <- nichenet_signaling_network_pathwaycommons(
    interaction_types = 'controls-transport-of'
)

saezlab/OmnipathR documentation built on May 3, 2024, 5:32 a.m.