import_pathwayextra_interactions: Imports interactions from the 'pathway extra' dataset of...

In OmnipathR: OmniPath web service client

Description

Imports the dataset from: https://omnipathdb.org/interactions?datasets=pathwayextra, which contains activity flow interactions without literature reference. The activity flow interactions supported by literature references are part of the 'omnipath' dataset.

Usage

import_pathwayextra_interactions(
  cache_file = NULL,
  resources = NULL,
  organism = 9606,
  fields = NULL,
  default_fields = TRUE,
  references_by_resource = TRUE,
  ...
)

import_PathwayExtra_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 one of those: 9606 human (default), 10116 rat or 10090 Mouse.
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_pathwayextra_interactions.

Value

A dataframe containing activity flow interactions between proteins without literature reference

See Also

get_interaction_resources, import_all_interactions

Examples

interactions <-
    import_pathwayextra_interactions(
        resources = c('BioGRID', 'IntAct'),
        organism = 9606
    )

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