nichenet_lr_network {OmnipathR} | R Documentation

## Builds a NicheNet ligand-receptor network

### Description

Builds ligand-receptor network prior knowledge for NicheNet using multiple resources.

### Usage

    nichenet_lr_network(
      omnipath = list(),
      guide2pharma = list(),
      ramilowski = list(),
      only_omnipath = FALSE,
      quality_filter_param = list()
    )

### Arguments

`omnipath` | List with paramaters to be passed to `nichenet_lr_network_omnipath`.
`guide2pharma` | List with paramaters to be passed to `nichenet_lr_network_guide2pharma`.
`ramilowski` | List with paramaters to be passed to `nichenet_lr_network_ramilowski`.
`only_omnipath` | Logical: a shortcut to use only OmniPath as network resource.
`quality_filter_param` | Arguments for `filter_intercell_network` (quality filtering of the OmniPath ligand-receptor network). It is recommended to check these parameters and apply some quality filtering. The defaults already ensure certain filtering, but you might want more relaxed or stringent options.

### Value

A network data frame (tibble) with ligand-receptor interactions suitable for use with NicheNet.

### See Also

- `nichenet_lr_network_omnipath`

- `nichenet_lr_network_guide2pharma`

- `nichenet_lr_network_ramilowski`

- `filter_intercell_network`

### Examples

    # load everything with the default parameters:
    lr_network <- nichenet_lr_network()

    # don't use Ramilowski:
    lr_network <- nichenet_lr_network(ramilowski = NULL)

    # use only OmniPath:
    lr_network_omnipath <- nichenet_lr_network(only_omnipath = TRUE)

[Package OmnipathR version 3.2.0 Index]