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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.

Value

A dataframe containing TF-target interactions.

See also

Examples

interactions <-
    import_transcriptional_interactions(
        resources = c('PAZAR', 'ORegAnno', 'DoRothEA')
    )