nichenet_lr_network_omnipath {OmnipathR} | R Documentation

## Builds ligand-receptor 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_lr_network_omnipath(quality_filter_param = list(), ...)

### Arguments

`quality_filter_param` | List with arguments for `filter_intercell_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.
`...` | Passed to `import_intercell_network`

### Value

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

### See Also

- `nichenet_lr_network`

- `import_intercell_network`

### Examples

    # use only ligand-receptor interactions (not for example ECM-adhesion):
    op_lr_network <- nichenet_lr_network_omnipath(ligand_receptor = TRUE)

    # use only CellPhoneDB and Guide to Pharmacology:
    op_lr_network <- nichenet_lr_network_omnipath(
        resources = c('CellPhoneDB', 'Guide2Pharma')
    )

    # only interactions where the receiver is a transporter:
    op_lr_network <- nichenet_lr_network_omnipath(
        receiver_param = list(parent = 'transporter')
    )

[Package OmnipathR version 3.0.0 Index]