import_transcriptional_interactions: Imports all TF-target interactions from OmniPath

In saezlab/OmnipathR: OmniPath web service client and more

Imports all TF-target interactions from OmniPath

Description

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,
  strict_evidences = FALSE,
  ...
)

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.
strict_evidences	Logical: restrict the evidences to the queried datasets and resources. If set to FALSE, the directions and effect signs and references might be based on other datasets and resources.
...	Optional additional arguments.

Value

A dataframe containing TF-target interactions.

See Also

• get_interaction_resources

• import_all_interactions

• interaction_graph

• print_interactions

Examples

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

saezlab/OmnipathR documentation built on May 3, 2024, 5:32 a.m.