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,
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.

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.

...

## Value

A dataframe cotaining information about roles in intercellular signaling.

• get_intercell_categories

• get_intercell_generic_categories

• import_intercell_network

• intercell_consensus_filter

## Examples

intercell <- import_omnipath_intercell(categories = 'ecm')