import_omnipath_intercell {OmnipathR} | R Documentation |
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.
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(...)
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 |
resources |
limit the query to certain resources; see the available
resources by |
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
|
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 |
A dataframe cotaining information about roles in intercellular signaling.
get_intercell_categories,
get_intercell_generic_categories, import_intercell_network
intercell = import_omnipath_intercell(categories = c('ecm'))