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
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 ¹source_genesymbol, ²target_genesymbol,
#> # ³is_directed, ⁴is_stimulation, ⁵is_inhibition, ⁶consensus_direction,
#> # ⁷consensus_stimulation, ⁸consensus_inhibition