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( 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, ... )
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 |
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). |
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
|
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. |
A dataframe cotaining information about roles in intercellular signaling.
intercell <- import_omnipath_intercell(categories = 'ecm')