nichenet_gr_network_omnipath {OmnipathR} | R Documentation

## 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')
    )

[Package OmnipathR version 3.0.0 Index]