nichenet_gr_network {OmnipathR} | 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.

### 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)

[Package OmnipathR version 3.2.0 Index]