omnipath: Literature curated signaling pathways

In saezlab/OmnipathR: OmniPath web service client and more

Literature curated signaling pathways

Description

Imports interactions from the 'omnipath' dataset of Omnipath, a dataset that inherits most of its design and contents from the original OmniPath core from the 2016 publication. This dataset consists of about 40k interactions.

Usage

omnipath(
  resources = NULL,
  organism = 9606L,
  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.
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, passed to import_omnipath_interactions.

Value

A dataframe of literature curated, post-translational signaling interactions.

See Also

• import_omnipath_interactions

• import_post_translational_interactions

• get_interaction_resources

• import_all_interactions

• interaction_graph

• print_interactions

Examples

pathways <- omnipath()
pathways

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