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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 import_omnipath_interactions.

Value

Data frame with the columns source, target and sign.

Examples

op_cosmos <- omnipath_for_cosmos()
#> NULL
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>