import_dorothea_interactions {OmnipathR} | R Documentation

## From the OmniPath webservice imports interactions from the DoRothEA dataset

### 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(
      resources = NULL,
      organism = 9606,
      dorothea_levels = c("A", "B"),
      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
`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.
`exclude` | Character: datasets or resources to exclude.
`...` | optional additional arguments

### Value

A dataframe containing TF-target interactions from DoRothEA

### See Also

- `get_interaction_resources`

- `import_all_interactions`

- `interaction_graph`

- `print_interactions`

### Examples

    interactions <- import_dorothea_interactions(
        resources = c('DoRothEA', 'ARACNe-GTEx_DoRothEA'),
        organism = 9606,
        dorothea_levels = c('A', 'B', 'C')
    )

[Package OmnipathR version 3.0.0 Index]