Imports all TF-target interactions from OmniPath
Source:R/interactions.R
import_transcriptional_interactions.Rd
Imports the dataset from: https://omnipathdb.org/interactions?datasets=tf_target,dorothea, which contains transcription factor-target protein coding gene interactions.
Usage
import_transcriptional_interactions(
resources = NULL,
organism = 9606,
dorothea_levels = c("A", "B"),
references_by_resource = TRUE,
exclude = NULL,
...
)
Arguments
- resources
interactions not reported in these databases are removed. See
get_interaction_resources
for more information.- 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 (
c(A, B)
). It is to note that E interactions are not available in OmnipathR.- 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.
- exclude
Character: datasets or resources to exclude.
- ...
Optional additional arguments.
Examples
interactions <-
import_transcriptional_interactions(
resources = c('PAZAR', 'ORegAnno', 'DoRothEA')
)