import_omnipath_enzsub: Imports enzyme-substrate relationships from OmniPath

In OmnipathR: OmniPath web service client

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
)

OmnipathR documentation built on Nov. 8, 2020, 8:10 p.m.