import_omnipath_interactions: Imports interactions from the 'omnipath' dataset of Omnipath

In OmnipathR: OmniPath web service client

Description

Imports the database from https://omnipathdb.org/interactions, which contains only interactions supported by literature references. This part of the interaction database compiled a similar way as it has been presented in the first paper describing OmniPath (Turei et al. 2016).

Usage

import_omnipath_interactions(
  cache_file = NULL,
  resources = NULL,
  organism = 9606,
  datasets = "omnipath",
  fields = NULL,
  default_fields = TRUE,
  references_by_resource = TRUE,
  ...
)

import_Omnipath_Interactions(...)

import_OmniPath_Interactions(...)

Arguments

cache_file	path to an earlier data file
resources	interactions not reported in these databases are removed. See get_interaction_resources for more information.
organism	Interactions are available for human, mouse and rat. Choose among: 9606 human (default), 10116 rat and 10090 Mouse
datasets	Names of the interaction datasts to download: omnipath (by default). Other possiblites are: pathwayextra, kinaseextra, ligrecextra, dorothea,tf_target, mirnatarget, tf_mirna, lncrna_mrna. The user can select multiple datasets as for example: c('omnipath', 'pathwayextra', 'kinaseextra')
fields	The user can define here the fields to be added. If used, set the next argument, 'default_fields', to FALSE.
default_fields	whether to include the default fields (columns) for the query type. If FALSE, only the fields defined by the user in the 'fields' argument will be added.
references_by_resource	if FALSE, removes the resource name prefixes from the references (PubMed IDs); this way the information which reference comes from which resource will be lost and the PubMed IDs will be unique.
...	Passed to import_omnipath_interactions.

Value

A dataframe of protein-protein interactions

See Also

get_interaction_resources, import_all_interactions

Examples

interactions = import_omnipath_interactions(
    resources = c('SignaLink3'),
    organism = 9606
)

OmnipathR documentation built on Nov. 8, 2020, 8:10 p.m.