import_tf_target_interactions: Imports interactions from the TF-target dataset of OmniPath

In OmnipathR: OmniPath web service client

Description

Imports the dataset from: https://omnipathdb.org/interactions?datasets=tf_target, which contains transcription factor-target protein coding gene interactions. Note: this is not the only TF-target dataset in OmniPath, 'dorothea' is the other one and the 'tf_mirna' dataset provides TF-miRNA gene interactions.

Usage

import_tf_target_interactions(
  cache_file = NULL,
  resources = NULL,
  organism = 9606,
  fields = NULL,
  default_fields = TRUE,
  references_by_resource = TRUE,
  ...
)

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
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.
...	optional additional arguments

Value

A dataframe containing TF-target interactions

See Also

get_interaction_resources, import_all_interactions

Examples

interactions <-
    import_tf_target_interactions(
        resources = c('DoRothEA_A', 'SIGNOR')
    )

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