import_omnipath_intercell: Imports OmniPath intercell annotations

In saezlab/OmnipathR: OmniPath web service client and more

Imports OmniPath intercell annotations

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(
  organism = "human",
  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,
  genesymbol_resource = NULL,
  ...
)

Arguments

organism	Character or integer: Name or NCBI Taxonomy ID of one or organisms. The web service currently provides intercell annotations only for human. For other organisms, the data will be translated by orthologous gene pairs from human.
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 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 consensus_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.
genesymbol_resource	Character: either "uniprot" or "ensembl". The former leaves intact the gene symbols returned by the web service, originally set from UniProt. The latter updates the gene symbols from Ensembl, which uses a slightly different gene symbol standard. In this case a few records will be duplicated, where Ensembl provides ambiguous translation.
...	Additional optional arguments, ignored.

Value

A dataframe cotaining information about roles in intercellular signaling.

See Also

• get_intercell_categories

• get_intercell_generic_categories

• import_intercell_network

• intercell_consensus_filter

Examples

intercell <- import_omnipath_intercell(categories = 'ecm')

saezlab/OmnipathR documentation built on July 13, 2024, 6:18 p.m.