omnipath_for_cosmos: OmniPath PPI for the COSMOS PKN

In saezlab/OmnipathR: OmniPath web service client and more

OmniPath PPI for the COSMOS PKN

Description

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.

Value

Data frame with the columns source, target and sign.

See Also

• cosmos_pkn

• omnipath-interactions

Examples

op_cosmos <- omnipath_for_cosmos()
op_cosmos

saezlab/OmnipathR documentation built on Oct. 16, 2024, 11:49 a.m.