import_small_molecule_protein_interactions: Interactions from the small molecule-protein dataset of...

In saezlab/OmnipathR: OmniPath web service client and more

Interactions from the small molecule-protein dataset of OmniPath

Description

Imports the dataset from: https://omnipathdb.org/interactions?datasets=small_molecule, which contains small molecule-protein interactions. Small molecules can be metabolites, intrinsic ligands or drug compounds.

Usage

import_small_molecule_protein_interactions(
  resources = NULL,
  organism = 9606,
  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.
fields	Optional fields to be added.
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 small molecule-protein interactions

See Also

• get_interaction_resources

• import_all_interactions

• interaction_graph

• print_interactions

Examples

# What are the targets of aspirin?
interactions <-
    import_small_molecule_protein_interactions(
        sources = 'ASPIRIN'
    )
# The prostaglandin synthases:
interactions

saezlab/OmnipathR documentation built on July 13, 2024, 6:18 p.m.