nichenet_signaling_network {OmnipathR} | R Documentation

## Builds a NicheNet signaling network

### Description

Builds signaling network prior knowledge for NicheNet using multiple resources.

### Usage

    nichenet_signaling_network(
      omnipath = list(),
      pathwaycommons = list(),
      harmonizome = list(),
      vinayagam = list(),
      cpdb = list(),
      evex = list(),
      inbiomap = list(),
      only_omnipath = FALSE
    )

### Arguments

`omnipath` | List with paramaters to be passed to `nichenet_signaling_network_omnipath`.
`pathwaycommons` | List with paramaters to be passed to `nichenet_signaling_network_pathwaycommons`.
`harmonizome` | List with paramaters to be passed to `nichenet_signaling_network_harmonizome`.
`vinayagam` | List with paramaters to be passed to `nichenet_signaling_network_vinayagam`.
`cpdb` | List with paramaters to be passed to `nichenet_signaling_network_cpdb`.
`evex` | List with paramaters to be passed to `nichenet_signaling_network_evex`.
`inbiomap` | List with paramaters to be passed to `nichenet_signaling_network_inbiomap`.
`only_omnipath` | Logical: a shortcut to use only OmniPath as network resource.

### Value

A network data frame (tibble) with signaling interactions suitable for use with NicheNet.

### See Also

- `nichenet_signaling_network_omnipath`

- `nichenet_signaling_network_pathwaycommons`

- `nichenet_signaling_network_harmonizome`

- `nichenet_signaling_network_vinayagam`

- `nichenet_signaling_network_cpdb`

- `nichenet_signaling_network_evex`

- `nichenet_signaling_network_inbiomap`

### Examples

    # load everything with the default parameters:
    # we don't load inBio Map due to the - hopefully
    # temporary - issues of their server
    sig_network <- nichenet_signaling_network(inbiomap = NULL)

    # override parameters for some resources:
    sig_network <- nichenet_signaling_network(
        omnipath = list(resources = c('SIGNOR', 'SignaLink3', 'SPIKE')),
        pathwaycommons = NULL,
        harmonizome = list(datasets = c('phosphositeplus', 'depod')),
        cpdb = list(complex_max_size = 1, min_score = .98),
        evex = list(min_confidence = 1.5),
        inbiomap = NULL
    )

    # use only OmniPath:
    sig_network_omnipath <- nichenet_signaling_network(only_omnipath = TRUE)

[Package OmnipathR version 3.0.0 Index]