Imports all TF-target interactions from OmniPathSource:
Imports the dataset from: https://omnipathdb.org/interactions?datasets=tf_target,dorothea, which contains transcription factor-target protein coding gene interactions.
import_transcriptional_interactions( resources = NULL, organism = 9606, dorothea_levels = c("A", "B"), 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
Vector detailing the confidence levels of the interactions to be downloaded. In dorothea, every TF-target interaction has a confidence score ranging from A to E, being A the most reliable interactions. By default we take A and B level interactions (
c(A, B)). It is to note that E interactions are not available in OmnipathR.
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_transcriptional_interactions( resources = c('PAZAR', 'ORegAnno', 'DoRothEA') )