R: Imports from Omnipath webservice the interactions from...

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

Examples

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