import_tf_target_interactions {OmnipathR} | R Documentation |
Imports the dataset from: https://omnipathdb.org/interactions?datasets=tf_target, which contains transcription factor-target protein coding gene interactions. Note: this is not the only TF-target dataset in OmniPath, 'dorothea' is the other one and the 'tf_mirna' dataset provides TF-miRNA gene interactions.
import_tf_target_interactions( cache_file = NULL, resources = NULL, organism = 9606, fields = NULL, default_fields = TRUE, references_by_resource = TRUE, ... )
cache_file |
path to an earlier data file |
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 |
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. |
... |
optional additional arguments |
A dataframe containing TF-target interactions
get_interaction_resources,
import_all_interactions
interactions <- import_tf_target_interactions( resources = c('DoRothEA_A', 'SIGNOR') )