import_transcriptional_interactions {OmnipathR} | R Documentation |
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, ... )
resources |
interactions not reported in these databases are
removed. See |
organism |
Interactions are available for human, mouse and rat. Choose among: 9606 human (default), 10116 rat and 10090 Mouse |
dorothea_levels |
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 ( |
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. |
... |
optional additional arguments |
A dataframe containing TF-target interactions
get_interaction_resources,
import_all_interactions
interactions <- import_transcriptional_interactions( resources = c('PAZAR', 'ORegAnno', 'DoRothEA_A') )