Imports all interaction datasets available in OmniPathSource:
The interaction datasets currently available in OmniPath:
import_all_interactions( resources = NULL, organism = 9606, dorothea_levels = c("A", "B"), exclude = NULL, fields = NULL, default_fields = TRUE, references_by_resource = TRUE, strict_evidences = FALSE, ... ) import_AllInteractions(...)
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
The confidence levels of the dorothea interactions (TF-target) which range from A to D. Set to A and B by default.
Character: datasets or resources to exclude.
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.
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.
omnipath: the OmniPath data as defined in the paper, an arbitrary optimum between coverage and quality pathwayextra: activity flow interactions without literature reference kinaseextra: enzyme-substrate interactions without literature reference ligrecextra: ligand-receptor interactions without literature reference dorothea: transcription factor (TF)-target interactions from DoRothEA tf_target: transcription factor (TF)-target interactions from other resources mirnatarget: miRNA-mRNA interactions tf_mirna: TF-miRNA interactions lncrna_mrna: lncRNA-mRNA interactions
interactions <- import_all_interactions( resources = c('HPRD', 'BioGRID'), organism = 9606 )