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From the OmniPath webservice imports interactions from the DoRothEA dataset

Source: R/interactions.R
import_dorothea_interactions.Rd

Imports the dataset from: https://omnipathdb.org/interactions?datasets=dorothea which contains transcription factor (TF)-target interactions from DoRothEA https://github.com/saezlab/DoRothEA

Usage

import_dorothea_interactions(
  resources = NULL,
  organism = 9606,
  dorothea_levels = c("A", "B"),
  fields = NULL,
  default_fields = TRUE,
  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.

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.

exclude

Character: datasets or resources to exclude.

...

optional additional arguments

Value

A dataframe containing TF-target interactions from DoRothEA

See also

Examples

interactions <- import_dorothea_interactions(
    resources = c('DoRothEA', 'ARACNe-GTEx_DoRothEA'),
    organism = 9606,
    dorothea_levels = c('A', 'B', 'C')
)