import_intercell_network {OmnipathR} | R Documentation

## Imports an intercellular network combining annotations and interactions

### Description

Imports an intercellular network by mapping intercellular annotations and protein interactions. First imports a network of protein-protein interactions. Then, it retrieves annotations about the proteins intercellular communication roles, once for the transmitter (delivering information from the expressing cell) and second, the receiver (receiving signal and relaying it towards the expressing cell) side. These 3 queries can be customized by providing parameters in lists which will be passed to the respective methods (`import_omnipath_interactions` for the network and `import_omnipath_intercell` for the annotations). Finally the 3 data frames combined in a way that the source proteins in each interaction annotated by the transmitter, and the target proteins by the receiver categories. If undirected interactions present (these are disabled by default) they will be duplicated, i.e. both partners can be both receiver and transmitter. If a cache file provided, its content will be returned without any further filtering.

### Usage

    import_intercell_network(
      cache_file = NULL,
      interactions_param = list(),
      transmitter_param = list(),
      receiver_param = list()
    )

### Arguments

`cache_file` | path to an earlier data file; if exists, will be loaded as it is, the further arguments have no effect; if does not exists, the result will be dumped into this file.
`interactions_param` | a list with arguments for an interactions query: `import_omnipath_interactions, import_pathwayextra_interactions, import_kinaseextra_interactions, import_ligrecextra_interactions`
`transmitter_param` | a list with arguments for `import_omnipath_intercell`, to define the transmitter side of intercellular connections
`receiver_param` | a list with arguments for `import_omnipath_intercell`, to define the receiver side of intercellular connections

### Value

A dataframe containing information about protein-protein interactions and the inter-cellular roles of the protiens involved in those interactions.

### See Also

`get_intercell_categories, get_intercell_generic_categories, import_omnipath_intercell, import_omnipath_interactions, import_pathwayextra_interactions, import_kinaseextra_interactions, import_ligrecextra_interactions`

### Examples

    intercellNetwork <- import_intercell_network(
       interactions_param = list(datasets = 'ligrecextra'),
       receiver_param = list(categories = c('receptor', 'transporter')),
       transmitter_param = list(categories = c('ligand', 'secreted_enzyme')))

[Package OmnipathR version 2.0.0 Index]