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Query the STRING database for protein-protein interactions

query_string_ppi.Rd

Queries the STRING database REST API to retrieve a protein-protein interaction (PPI) network for a list of gene symbols. Large gene lists are automatically split into batches to respect API limits.

Usage

query_string_ppi(
  gene_list,
  species = 9606L,
  score_threshold = 400L,
  batch_size = 500L
)

Arguments

gene_list

Character vector of gene symbols (e.g. c("TP53", "BRCA1")).

species

NCBI taxonomy ID. Default 9606 (Homo sapiens). Use 10090 for mouse, 10116 for rat.

score_threshold

Minimum combined STRING score, in the 0–1000 range. Default 400 (medium confidence).

batch_size

Maximum number of genes per API request. Default 500.

Value

A tibble::tibble() with columns:

gene1, gene2

Preferred gene symbols of the interaction partners.

score

Combined STRING score (0–1000).

Examples

if (FALSE) { # \dontrun{
ppi <- query_string_ppi(c("TP53", "BRCA1", "EGFR", "VEGFA", "TNF"))
head(ppi)
} # }