search_string_db: Search STRING Database

In DeSciDe: Tool for Unbiased Literature Searching and Gene List Curation

Search STRING Database

Description

Search the STRING database for protein interactions.

Usage

search_string_db(
  genes_list,
  species = 9606,
  network_type = "full",
  score_threshold = 400
)

Arguments

genes_list	A list of gene IDs.
species	The NCBI taxon ID of the species. Defaults to 9606 (Homo sapiens).
network_type	The type of network to use, either "full" or "physical". Defaults to "full".
score_threshold	The minimum score threshold for string interactions. Defaults to 400.

Value

A list containing the following elements:

string_results

A data frame with STRING interaction metrics.

string_db

The STRINGdb object used.

string_ids

The STRING IDs for the input genes.

Examples

## Not run: 
library(STRINGdb)
genes <- c("TP53", "BRCA1")
results <- search_string_db(genes)
print(results)

## End(Not run)

DeSciDe documentation built on Sept. 1, 2025, 1:08 a.m.