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

Arguments

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.

exclude

Character: datasets or resources to exclude.

...

optional additional arguments

Value

A dataframe containing activity flow interactions between proteins without literature reference

Examples

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