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
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).
- 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
NULLno 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
consensus_percentilefor 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.