import_omnipath_interactions: Imports interactions from the 'omnipath' dataset of Omnipath

In saezlab/OmnipathR: OmniPath web service client and more

Imports interactions from the 'omnipath' dataset of Omnipath

Description

Imports the database from https://omnipathdb.org/interactions, which contains only interactions supported by literature references. This part of the interaction database compiled a similar way as it has been presented in the first paper describing OmniPath (Turei et al. 2016).

Usage

import_omnipath_interactions(
  resources = NULL,
  organism = 9606,
  datasets = "omnipath",
  fields = NULL,
  default_fields = TRUE,
  references_by_resource = TRUE,
  exclude = NULL,
  strict_evidences = FALSE,
  genesymbol_resource = NULL,
  ...
)

Arguments

resources	interactions not reported in these databases are removed. See get_interaction_resources 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. For other organisms, the data will be translated by orthologous gene pairs from human. In this case, only one organism can be provided.
datasets	Names of the interaction datasets to download: omnipath (by default). Other possiblites are: pathwayextra, kinaseextra, ligrecextra, dorothea,tf_target, mirnatarget, tf_mirna, lncrna_mrna. The user can select multiple datasets as for example: c('omnipath', 'pathwayextra', 'kinaseextra')
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.
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 dataframe of protein-protein interactions

See Also

• get_interaction_resources

• import_all_interactions

• interaction_graph

• print_interactions

Examples

interactions = import_omnipath_interactions(
    resources = c('SignaLink3'),
    organism = 9606
)

saezlab/OmnipathR documentation built on June 17, 2024, 2:24 a.m.