import_tf_target_interactions {OmnipathR}R Documentation

Imports interactions from the TF-target dataset of OmniPath

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(
  resources = NULL,
  organism = 9606,
  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

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.

...

Optional additional arguments

Value

A dataframe containing TF-target interactions

See Also

Examples

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


[Package OmnipathR version 3.1.13 Index]