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.

...

## Value

A dataframe containing TF-target interactions from DoRothEA

• get_interaction_resources

• import_all_interactions

• interaction_graph

• print_interactions

## Examples

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