import_dorothea_interactions: From the OmniPath webservice imports interactions from the...

In OmnipathR: OmniPath web service client

Description

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

import_TFregulons_Interactions(...)

import_tfregulons_interactions(...)

Arguments

cache_file	path to an earlier data file
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.
...	Passed to import_dorothea_interactions.

Value

A dataframe containing TF-target interactions from DoRothEA

See Also

get_interaction_resources, import_all_interactions

Examples

interactions <- import_dorothea_interactions(
    resources = c('DoRothEA_A', 'ARACNe-GTEx_DoRothEA'),
    organism = 9606
)

OmnipathR documentation built on Nov. 8, 2020, 8:10 p.m.