import_ligrecextra_interactions {OmnipathR} | R Documentation

## Imports interactions from the 'ligrec extra' dataset of OmniPath

### Description

Imports the dataset from: https://omnipathdb.org/interactions?datasets=ligrecextra, which contains ligand-receptor interactions without literature reference. The ligand-receptor interactions supported by literature references are part of the 'omnipath' dataset.

### Usage

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

    import_LigrecExtra_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
`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_ligrecextra_interactions`.

### Value

A dataframe containing ligand-receptor interactions including the ones without literature references

### See Also

`get_interaction_resources, import_all_interactions`

### Examples

    interactions <- import_ligrecextra_interactions(
        resources = c('HPRD', 'Guide2Pharma'),
        organism = 9606
    )

[Package OmnipathR version 2.0.0 Index]