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(
      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,
      consensus_percentile = NULL,
      loc_consensus_percentile = NULL,
      ...
    )

### Arguments

`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 codeget_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).
`consensus_percentile` | Numeric: a percentile cut off for the consensus score of generic categories. The consensus score is the number of resources supporting the classification of an entity into a category based on combined information of many resources. Here you can apply a cut-off, keeping only the annotations supported by a higher number of resources than a certain percentile of each category. If `NULL` no filtering will be performed. The value is either in the 0-1 range, or will be divided by 100 if greater than 1. The percentiles will be calculated against the generic composite categories and then will be applied to their resource specific annotations and specific child categories.
`loc_consensus_percentile` | Numeric: similar to codeconsensus_percentile for major localizations. For example, with a value of 50, the secreted, plasma membrane transmembrane or peripheral attributes will be true only where at least 50 percent of the resources support these.
`...` | Additional optional arguments, ignored.

### Value

A dataframe cotaining information about roles in intercellular signaling.

### See Also

- `get_intercell_categories`

- `get_intercell_generic_categories`

- `import_intercell_network`

- `intercell_consensus_filter`

### Examples

    intercell <- import_omnipath_intercell(categories = 'ecm')

[Package OmnipathR version 3.0.0 Index]