Builds a NicheNet gene regulatory network

Builds gene regulatory network prior knowledge for NicheNet using multiple resources.

Usage

nichenet_gr_network(
  omnipath = list(),
  harmonizome = list(),
  regnetwork = list(),
  htridb = list(),
  remap = list(),
  evex = list(),
  pathwaycommons = list(),
  trrust = list(),
  only_omnipath = FALSE
)

Arguments

omnipath

List with paramaters to be passed to nichenet_gr_network_omnipath.

harmonizome

List with paramaters to be passed to nichenet_gr_network_harmonizome.

regnetwork

List with paramaters to be passed to nichenet_gr_network_regnetwork.

htridb

List with paramaters to be passed to nichenet_gr_network_htridb.

remap

List with paramaters to be passed to nichenet_gr_network_remap.

evex

List with paramaters to be passed to nichenet_gr_network_evex.

pathwaycommons

List with paramaters to be passed to nichenet_gr_network_pathwaycommons.

trrust

List with paramaters to be passed to nichenet_gr_network_trrust.

only_omnipath

Logical: a shortcut to use only OmniPath as network resource.

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

# load everything with the default parameters:
gr_network <- nichenet_gr_network()

# less targets from ReMap, not using RegNetwork:
gr_network <- nichenet_gr_network(
    # I needed to disable ReMap here due to some issues
    # of one of the Bioconductor build servers
    # remap = list(top_targets = 200),
    remap = NULL,
    regnetwork = NULL,
)

# use only OmniPath:
gr_network_omnipath <- nichenet_gr_network(only_omnipath = TRUE)