OmniPath PPI for the COSMOS PKN
Usage
omnipath_for_cosmos(
organism = 9606L,
resources = NULL,
datasets = NULL,
interaction_types = NULL,
id_types = c("uniprot", "genesymbol"),
...
)Arguments
- organism
Character or integer: name or NCBI Taxonomy ID of the organism.
- resources
Character: names of one or more resources. Correct spelling is important.
- datasets
Character: one or more network datasets in OmniPath.
- interaction_types
Character: one or more interaction type
- id_types
Character: translate the protein identifiers to these ID types. Each ID type results two extra columns in the output, for the "source" and "target" sides of the interaction, respectively. The default ID type for proteins is Esembl Gene ID, and by default UniProt IDs and Gene Symbols are included. The UniProt IDs returned by the web service are left intact, while the Gene Symbols are queried from Ensembl. These Gene Symbols are different from the ones returned from the web service, and match the Ensembl Gene Symbols used by other components of the COSMOS PKN.
- ...
Further parameters to
omnipath_interactions.
Examples
op_cosmos <- omnipath_for_cosmos()
op_cosmos
#> # A tibble: 138,492 × 8
#> source target sign record_id uniprot_source uniprot_target genesymbol_source
#> <chr> <chr> <dbl> <int> <chr> <chr> <chr>
#> 1 P0DP23 P48995 -1 1 P0DP23 P48995 CALM1
#> 2 P0DP25 P48995 -1 2 P0DP25 P48995 CALM3
#> 3 P0DP24 P48995 -1 3 P0DP24 P48995 CALM2
#> 4 Q03135 P48995 1 4 Q03135 P48995 CAV1
#> 5 P14416 P48995 1 5 P14416 P48995 DRD2
#> 6 Q99750 P48995 -1 6 Q99750 P48995 MDFI
#> 7 Q14571 P48995 1 7 Q14571 P48995 ITPR2
#> 8 P29966 P48995 -1 8 P29966 P48995 MARCKS
#> 9 Q13255 P48995 1 9 Q13255 P48995 GRM1
#> 10 Q13586 P48995 1 10 Q13586 P48995 STIM1
#> # ℹ 138,482 more rows
#> # ℹ 1 more variable: genesymbol_target <chr>