Imports interactions from the `omnipath` dataset of Omnipath
Source:R/interactions.R
import_omnipath_interactions.Rd
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).
Usage
import_omnipath_interactions(
resources = NULL,
organism = 9606,
datasets = "omnipath",
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 among: 9606 human (default), 10116 rat and 10090 Mouse
- datasets
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')
- 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
Examples
interactions = import_omnipath_interactions(
resources = c('SignaLink3'),
organism = 9606
)