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,
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. For other organisms, the data will be translated by orthologous gene pairs from human. In this case, only one organism can be provided.
- 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.
- 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, passed to
import_omnipath_interactions
.
Examples
pathways <- omnipath()
#> NULL
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>