import_omnipath_enzsub: Imports enzyme-substrate relationships from OmniPath

In saezlab/OmnipathR: OmniPath web service client and more

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
)

saezlab/OmnipathR documentation built on April 17, 2024, 9:39 p.m.