import_transcriptional_interactions {OmnipathR} | R Documentation

## Imports all TF-target interactions from OmniPath

### Description

Imports the dataset from: https://omnipathdb.org/interactions?datasets=tf_target,dorothea, which contains transcription factor-target protein coding gene interactions.

### Usage

    import_transcriptional_interactions(
      resources = NULL,
      organism = 9606,
      dorothea_levels = c("A", "B"),
      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
`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.
`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

- `get_interaction_resources`

- `import_all_interactions`

- `interaction_graph`

- `print_interactions`

### Examples

    interactions <-
        import_transcriptional_interactions(
            resources = c('PAZAR', 'ORegAnno', 'DoRothEA')
        )

[Package OmnipathR version 3.0.0 Index]