nichenet_gr_network: Builds a NicheNet gene regulatory network
In saezlab/OmnipathR: OmniPath web service client and more

nichenet_gr_network

R Documentation

Builds a NicheNet gene regulatory network

Description

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.

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)

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