import_TFregulons_Interactions {OmnipathR}R Documentation

Imports from Omnipath webservice the interactions from Dorothea dataset

Description

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

Usage

import_TFregulons_Interactions(
  from_cache_file = NULL,
  filter_databases = get_interaction_databases(),
  select_organism = 9606,
  confidence_level = c("A", "B")
)

Arguments

from_cache_file

path to an earlier data file

filter_databases

interactions not reported in these databases are removed. See get_interaction_databases for more information.

select_organism

Interactions are available for human, mouse and rat. Choose among: 9606 human (default), 10116 rat and 10090 Mouse

confidence_level

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.

Value

A dataframe containing TF-target interactions from DoRothEA

See Also

get_interaction_databases, import_AllInteractions

Examples

interactions <- import_TFregulons_Interactions(filter_databases=c("DoRothEA_A",
    "ARACNe-GTEx_DoRothEA"), select_organism=9606)

[Package OmnipathR version 1.2.1 Index]