import_all_interactions {OmnipathR} | R Documentation

## Imports all interaction datasets available in OmniPath

### Description

The interaction datasets currently available in OmniPath:

### Usage

    import_all_interactions(
      cache_file = NULL,
      resources = NULL,
      organism = 9606,
      dorothea_levels = c("A", "B"),
      exclude = NULL,
      fields = NULL,
      default_fields = TRUE,
      references_by_resource = TRUE,
      ...
    )

    import_AllInteractions(...)

### 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
`dorothea_levels` | The confidence levels of the dorothea interactions (TF-target) which range from A to D. Set to A and B by default.
`exclude` | datasets to exclude
`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_all_interactions`.

### Details

omnipath: the OmniPath data as defined in the paper, an arbitrary optimum between coverage and quality pathwayextra: activity flow interactions without literature reference kinaseextra: enzyme-substrate interactions without literature reference ligrecextra: ligand-receptor interactions without literature reference dorothea: transcription factor (TF)-target interactions from DoRothEA tf_target: transcription factor (TF)-target interactions from other resources mirnatarget: miRNA-mRNA interactions tf_mirna: TF-miRNA interactions lncrna_mrna: lncRNA-mRNA interactions

### Value

A dataframe containing all the datasets in the interactions query

### See Also

`get_interaction_resources`

### Examples

    interactions <- import_all_interactions(
        resources = c('HPRD', 'BioGRID'),
        organism = 9606
    )

[Package OmnipathR version 2.0.0 Index]