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.