import_omnipath_intercell {OmnipathR} | R Documentation

## Imports OmniPath intercell annotations

### Description

Imports the OmniPath intercellular communication role annotation database from https://omnipathdb.org/intercell. It provides information on the roles in inter-cellular signaling. E.g. if a protein is a ligand, a receptor, an extracellular matrix (ECM) component, etc.

### Usage

    import_omnipath_intercell(
      cache_file = NULL,
      categories = NULL,
      resources = NULL,
      parent = NULL,
      scope = NULL,
      aspect = NULL,
      source = NULL,
      transmitter = NULL,
      receiver = NULL,
      secreted = NULL,
      plasma_membrane_peripheral = NULL,
      plasma_membrane_transmembrane = NULL,
      proteins = NULL,
      topology = NULL,
      causality = NULL,
      ...
    )

    import_Omnipath_intercell(...)

    import_OmniPath_intercell(...)

### Arguments

`cache_file` | path to an earlier data file
`categories` | vector containing the categories to be retrieved. All the genes belonging to those categories will be returned. For further information about the categories see `get_intercell_categories`
`resources` | limit the query to certain resources; see the available resources by `get_intercell_resources`
`parent` | vector containing the parent classes to be retrieved. All the genes belonging to those classes will be returned. For furter information about the main classes see `get_intercell_categories`
`scope` | either 'specific' or 'generic'
`aspect` | either 'locational' or 'functional'
`source` | either 'resource_specific' or 'composite'
`transmitter` | logical, include only transmitters i.e. proteins delivering signal from a cell to its environment
`receiver` | logical, include only receivers i.e. proteins delivering signal to the cell from its environment
`secreted` | logical, include only secreted proteins
`plasma_membrane_peripheral` | logical, include only plasma membrane peripheral membrane proteins
`plasma_membrane_transmembrane` | logical, include only plasma membrane transmembrane proteins
`proteins` | limit the query to certain proteins
`topology` | topology categories: one or more of 'secreted' (sec), 'plasma_membrane_peripheral' (pmp), 'plasma_membrane_transmembrane' (pmtm) (both short or long notation can be used)
`causality` | 'transmitter' (trans), 'receiver' (rec) or 'both' (both short or long notation can be used)
`...` | Passed to `import_omnipath_intercell`.

### Value

A dataframe cotaining information about roles in intercellular signaling.

### See Also

`get_intercell_categories, get_intercell_generic_categories, import_intercell_network`

### Examples

    intercell = import_omnipath_intercell(categories = c('ecm'))

[Package OmnipathR version 2.0.0 Index]