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

    import_Omnipath_PTMS(...)

    import_OmniPath_PTMS(...)

### Arguments

`cache_file` | path to an earlier data file
`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` | 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_enzsub`.

### Value

A data frame containing the information about ptms

### See Also

`get_ptms_databases, import_omnipath_interactions`

### Examples

    ptms = import_omnipath_enzsub(
        resources = c('PhosphoSite', 'SIGNOR'),
        organism = 9606
    )

[Package OmnipathR version 2.0.0 Index]