import_omnipath_interactions {OmnipathR} | R Documentation

## Imports interactions from the 'omnipath' dataset of Omnipath

### Description

Imports the database from https://omnipathdb.org/interactions, which contains only interactions supported by literature references. This part of the interaction database compiled a similar way as it has been presented in the first paper describing OmniPath (Turei et al. 2016).

### Usage

    import_omnipath_interactions(
      cache_file = NULL,
      resources = NULL,
      organism = 9606,
      datasets = "omnipath",
      fields = NULL,
      default_fields = TRUE,
      references_by_resource = TRUE,
      ...
    )

    import_Omnipath_Interactions(...)

    import_OmniPath_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
`datasets` | Names of the interaction datasts to download: omnipath (by default). Other possiblites are: pathwayextra, kinaseextra, ligrecextra, dorothea,tf_target, mirnatarget, tf_mirna, lncrna_mrna. The user can select multiple datasets as for example: c('omnipath', 'pathwayextra', 'kinaseextra')
`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_omnipath_interactions`.

### Value

A dataframe of protein-protein interactions

### See Also

`get_interaction_resources, import_all_interactions`

### Examples

    interactions = import_omnipath_interactions(
        resources = c('SignaLink3'),
        organism = 9606
    )

[Package OmnipathR version 2.0.0 Index]