import_TFregulons_Interactions {OmnipathR} | R Documentation |
Imports the dataset from: http://omnipathdb.org/interactions?datasets=tfregulons which contains transcription factor (TF)-target interactions from DoRothEA https://github.com/saezlab/DoRothEA
import_TFregulons_Interactions( from_cache_file = NULL, filter_databases = get_interaction_databases(), select_organism = 9606, confidence_level = c("A", "B") )
from_cache_file |
path to an earlier data file |
filter_databases |
interactions not reported in these databases are
removed. See |
select_organism |
Interactions are available for human, mouse and rat. Choose among: 9606 human (default), 10116 rat and 10090 Mouse |
confidence_level |
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 ( |
A dataframe containing TF-target interactions from DoRothEA
get_interaction_databases,
import_AllInteractions
interactions <- import_TFregulons_Interactions(filter_databases=c("DoRothEA_A", "ARACNe-GTEx_DoRothEA"), select_organism=9606)