Imports interactions from the `omnipath` dataset of OmnipathSource:
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).
import_omnipath_interactions( resources = NULL, organism = 9606, datasets = "omnipath", fields = NULL, default_fields = TRUE, references_by_resource = TRUE, exclude = NULL, strict_evidences = FALSE, ... )
interactions not reported in these databases are removed. See
get_interaction_resourcesfor more information.
Interactions are available for human, mouse and rat. Choose among: 9606 human (default), 10116 rat and 10090 Mouse
Names of the interaction datasets 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')
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.
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
interactions = import_omnipath_interactions( resources = c('SignaLink3'), organism = 9606 )