Imports interactions from the `pathway extra` dataset of OmnipathSource:
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.
import_pathwayextra_interactions( resources = NULL, organism = 9606, fields = NULL, default_fields = TRUE, references_by_resource = TRUE, exclude = NULL, ... )
interactions not reported in these databases are removed. See
get_interaction_resourcesfor more information.
Interactions are available for human, mouse and rat. Choose one of those: 9606 human (default), 10116 rat or 10090 Mouse.
The user can define here the fields to be added. If used, set the next argument, `default_fields`, to FALSE.
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.
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.
Character: datasets or resources to exclude.
optional additional arguments
A dataframe containing activity flow interactions between proteins without literature reference
interactions <- import_pathwayextra_interactions( resources = c('BioGRID', 'IntAct'), organism = 9606 )