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,
  genesymbol_resource = NULL,
  ...
)

Arguments

resources	PTMs not reported in these databases are removed. See get_ptms_databases for more information.
organism	Character or integer: Name or NCBI Taxonomy ID of one or organisms. The web service currently provides interactions for human, mouse and rat.
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.
genesymbol_resource	Character: either "uniprot" or "ensembl". The former leaves intact the gene symbols returned by the web service, originally set from UniProt. The latter updates the gene symbols from Ensembl, which uses a slightly different gene symbol standard. In this case a few records will be duplicated, where Ensembl provides ambiguous translation.
...	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 July 13, 2024, 6:18 p.m.