import_kinaseextra_interactions: Imports interactions from the 'kinase extra' dataset of...

In saezlab/OmnipathR: OmniPath web service client and more

Imports interactions from the 'kinase extra' dataset of OmniPath

Description

Imports the dataset from: https://omnipathdb.org/interactions?datasets=kinaseextra, which contains enzyme-substrate interactions without literature reference. The enzyme-substrate interactions supported by literature references are part of the 'omnipath' dataset.

Usage

import_kinaseextra_interactions(
  resources = NULL,
  organism = 9606,
  fields = NULL,
  default_fields = TRUE,
  references_by_resource = TRUE,
  exclude = NULL,
  strict_evidences = FALSE,
  ...
)

Arguments

resources	interactions not reported in these databases are removed. See get_interaction_resources for more information.
organism	Interactions 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.
exclude	Character: datasets or resources to exclude.
strict_evidences	Logical: restrict the evidences to the queried datasets and resources. If set to FALSE, the directions and effect signs and references might be based on other datasets and resources.
...	Optional additional arguments.

Value

A dataframe containing enzyme-substrate interactions without literature reference

See Also

• get_interaction_resources

• import_all_interactions

• interaction_graph

• print_interactions

Examples

interactions <-
   import_kinaseextra_interactions(
       resources = c('PhosphoPoint', 'PhosphoSite'),
       organism = 9606
   )

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