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Interactions from the small molecule-protein dataset of OmniPath

Source: R/interactions.R
import_small_molecule_protein_interactions.Rd

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,
  ...
)

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

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.

...

optional additional arguments

Value

A dataframe of small molecule-protein interactions

See also

Examples

# What are the targets of aspirin?
interactions <-
    import_small_molecule_protein_interactions(
        sources = 'ASPIRIN'
    )
# The prostaglandin synthases:
interactions
#> # A tibble: 0 × 14
#> # ℹ 14 variables: source <chr>, target <chr>, source_genesymbol <chr>,
#> #   target_genesymbol <chr>, is_directed <chr>, is_stimulation <chr>,
#> #   is_inhibition <chr>, consensus_direction <chr>,
#> #   consensus_stimulation <chr>, consensus_inhibition <chr>, sources <chr>,
#> #   references <chr>, curation_effort <chr>, n_references <lgl>