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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,
  ...
)

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.

...

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: 2 × 15
#>   source target source…¹ targe…² is_di…³ is_st…⁴ is_in…⁵ conse…⁶ conse…⁷ conse…⁸
#>    <dbl> <chr>  <chr>    <chr>     <dbl>   <dbl>   <dbl>   <dbl>   <dbl>   <dbl>
#> 1   2244 P23219 ASPIRIN  PTGS1         1       0       1       1       0       1
#> 2   2244 P35354 ASPIRIN  PTGS2         1       0       1       1       0       1
#> # … with 5 more variables: sources <chr>, references <chr>,
#> #   curation_effort <dbl>, n_references <int>, n_resources <int>, and
#> #   abbreviated variable names ¹​source_genesymbol, ²​target_genesymbol,
#> #   ³​is_directed, ⁴​is_stimulation, ⁵​is_inhibition, ⁶​consensus_direction,
#> #   ⁷​consensus_stimulation, ⁸​consensus_inhibition