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,
...
)Arguments
- resources
interactions not reported in these databases are removed. See
get_interaction_resourcesfor more information.- organism
Interactions are available for human, mouse and rat. Choose among: 9606 human (default), 10116 rat and 10090 Mouse
- 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.
- ...
optional additional arguments, passed to
import_omnipath_interactions.
Examples
pathways <- omnipath()
pathways
#> # A tibble: 81,529 × 15
#> source target source_genesymbol target_genesymbol is_directed is_stimulation
#> <chr> <chr> <chr> <chr> <dbl> <dbl>
#> 1 P0DP23 P48995 CALM1 TRPC1 1 0
#> 2 P0DP25 P48995 CALM3 TRPC1 1 0
#> 3 P0DP24 P48995 CALM2 TRPC1 1 0
#> 4 Q03135 P48995 CAV1 TRPC1 1 1
#> 5 P14416 P48995 DRD2 TRPC1 1 1
#> 6 Q99750 P48995 MDFI TRPC1 1 0
#> 7 Q14571 P48995 ITPR2 TRPC1 1 1
#> 8 P29966 P48995 MARCKS TRPC1 1 0
#> 9 Q13255 P48995 GRM1 TRPC1 1 1
#> 10 Q13586 P48995 STIM1 TRPC1 1 1
#> # ℹ 81,519 more rows
#> # ℹ 9 more variables: is_inhibition <dbl>, consensus_direction <dbl>,
#> # consensus_stimulation <dbl>, consensus_inhibition <dbl>, sources <chr>,
#> # references <chr>, curation_effort <dbl>, n_references <int>,
#> # n_resources <int>