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, ... )
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 datasts 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.
optional additional arguments
interactions = import_omnipath_interactions( resources = c('SignaLink3'), organism = 9606 )