import_omnipath_enzsub {OmnipathR} | R Documentation

## Imports enzyme-substrate relationships from OmniPath

### Description

Imports the enzyme-substrate (more exactly, enzyme-PTM) relationship database from https://omnipathdb.org/enzsub

### Usage

    import_omnipath_enzsub(
      resources = NULL,
      organism = 9606,
      fields = NULL,
      default_fields = TRUE,
      references_by_resource = TRUE,
      exclude = NULL,
      ...
    )

### Arguments

`resources` | PTMs not reported in these databases are removed. See `get_ptms_databases` for more information.
`organism` | PTMs are available for human, mouse and rat. Choose among: 9606 human (default), 10116 rat and 10090 Mouse
`fields` | You can define here additional fields to be added to the result. 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 data frame containing the information about ptms

### See Also

- `get_enzsub_resources`

- `import_omnipath_interactions`

- `enzsub_graph`

- `print_interactions`

### Examples

    enzsub <- import_omnipath_enzsub(
        resources = c('PhosphoSite', 'SIGNOR'),
        organism = 9606
    )

[Package OmnipathR version 3.0.0 Index]