Imports interactions from the `pathway extra` dataset of Omnipath
Source:R/interactions.R
import_pathwayextra_interactions.Rd
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,
strict_evidences = FALSE,
...
)
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.
- strict_evidences
Logical: restrict the evidences to the queried datasets and resources. If set to FALSE, the directions and effect signs and references might be based on other datasets and resources.
- ...
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
)