import_omnipath_intercell: Imports OmniPath intercell annotations

In OmnipathR: OmniPath web service client

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'))

OmnipathR documentation built on Nov. 8, 2020, 8:10 p.m.