Imports OmniPath intercell annotations

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,
  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.

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.

...

Arguments passed on to omnipath_query

organism: Character or integer: name or NCBI Taxonomy ID of the organism. OmniPath is built of human data, and the web service provides orthology translated interactions and enzyme-substrate relationships for mouse and rat. For other organisms and query types, orthology translation will be called automatically on the downloaded human data before returning the result.
resources: Character vector: name of one or more resources. Restrict the data to these resources. For a complete list of available resources, call the `get_<query_type>_resources` functions for the query type of interst.
datasets: Character vector: name of one or more datasets. In the interactions query type a number of datasets are available. The default is caled "omnipath", and corresponds to the curated causal signaling network published in the 2016 OmniPath paper.
genesymbols: Character or logical: TRUE or FALS or "yes" or "no". Include the `genesymbols` column in the results. OmniPath uses UniProt IDs as the primary identifiers, gene symbols are optional.
fields: Character vector: additional fields to include in the result. For a list of available fields, call `query_info("interactions")`.
default_fields: Logical: if TRUE, the default fields will be included.
silent: Logical: if TRUE, no messages will be printed. By default a summary message is printed upon successful download.
logicals: Character vector: fields to be cast to logical.
format: Character: if "json", JSON will be retrieved and processed into a nested list; any other value will return data frame.
download_args: List: parameters to pass to the download function, which is `readr::read_tsv` by default, and `jsonlite::safe_load`.
references_by_resource: Logical: if TRUE,, in the `references` column the PubMed IDs will be prefixed with the names of the resources they are coming from. If FALSE, the `references` column will be a list of unique PubMed IDs.
add_counts: Logical: if TRUE, the number of references and number of resources for each record will be added to the result.
license: Character: license restrictions. By default, data from resources allowing "academic" use is returned by OmniPath. If you use the data for work in a company, you can provide "commercial" or "for-profit", which will restrict the data to those records which are supported by resources that allow for-profit use.
password: Character: password for the OmniPath web service. You can provide a special password here which enables the use of `license = "ignore"` option, completely bypassing the license filter.
exclude: Character vector: resource or dataset names to be excluded. The data will be filtered after download to remove records of the excluded datasets and resources.
json_param: List: parameters to pass to the `jsonlite::fromJSON` when processing JSON columns embedded in the downloaded data. Such columns are "extra_attrs" and "evidences". These are optional columns which provide a lot of extra details about interactions.
strict_evidences: Logical: reconstruct the "sources" and "references" columns of interaction data frames based on the "evidences" column, strictly filtering them to the queried datasets and resources. Without this, the "sources" and "references" fields for each record might contain information for datasets and resources other than the queried ones, because the downloaded records are a result of a simple filtering of an already integrated data frame.
genesymbol_resource: Character: "uniprot" (default) or "ensembl". The OmniPath web service uses the primary gene symbols as provided by UniProt. By passing "ensembl" here, the UniProt gene symbols will be replaced by the ones used in Ensembl. This translation results in a loss of a few records, and multiplication of another few records due to ambiguous translation.
cache: Logical: use caching, load data from and save to the. The cache directory by default belongs to the user, located in the user's default cache directory, and named "OmnipathR". Find out about it by omnipath_get_cachedir. Can be changed by omnipath_set_cachedir.

Value

A dataframe cotaining information about roles in intercellular signaling.

Examples

intercell <- import_omnipath_intercell(categories = 'ecm')
#> Error in import_omnipath_intercell(categories = "ecm"): object 'genesymbol_resource' not found

Usage

Arguments

Value

See also

Examples