stitch_network: Chemical-protein interactions from STITCH

In saezlab/OmnipathR: OmniPath web service client and more

Chemical-protein interactions from STITCH

Description

Chemical-protein interactions from STITCH

Usage

stitch_network(
  organism = "human",
  min_score = 700L,
  protein_ids = c("uniprot", "genesymbol"),
  metabolite_ids = c("hmdb", "kegg"),
  cosmos = FALSE
)

Arguments

organism	Character or integer: name or NCBI Taxonomy ID of an organism. STITCH supports many organisms, please refer to their web site at https://stitch.embl.de/.
min_score	Confidence cutoff used for STITCH connections (700 by default).
protein_ids	Character: translate the protein identifiers to these ID types. Each ID type results two extra columns in the output, for the "a" and "b" sides of the interaction, respectively. The default ID type for proteins is Esembl Protein ID, and by default UniProt IDs and Gene Symbols are included.
metabolite_ids	Character: translate the protein identifiers to these ID types. Each ID type results two extra columns in the output, for the "a" and "b" sides of the interaction, respectively. The default ID type for metabolites is PubChem CID, and HMDB IDs and KEGG IDs are included.
cosmos	Logical: use COSMOS format?

Value

A data frame of STITCH chemical-protein and protein-chemical interactions with their effect signs, and optionally with identifiers translated.

See Also

• stitch_actions

• stitch_links

• stitch_remove_prefixes

Examples

stn <- stitch_network(protein_ids = 'genesymbol', metabolite_ids = 'hmdb')

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