The interaction network within a set of genes

High-confidence edges among the genes you asked about, with the endpoints reconciled back to your symbols.

Usage

string_network(
  symbols,
  species = STRING_HUMAN,
  required_score = STRING_MIN_SCORE,
  reconcile = TRUE,
  ...
)

Arguments

symbols

Gene symbols. At least two, since one gene has no network.

species

An NCBI taxon id. Defaults to human.

required_score

STRING's 0-1000 combined-score threshold.

reconcile

Whether to fetch the identifier map and translate edge endpoints back into your symbols. Costs one extra request and is skipped automatically when there are no edges to translate.

...

Passed to biohttp::get_json(), for example throttle.

Value

A biohttp envelope whose data is a list of edges (see string_parse_network()), queried, n_query, truncated, and n_dropped.

Knowing what was asked

The result carries queried, the exact symbol set STRING was asked about after the 500-identifier cap, plus truncated and n_dropped. That is what lets a caller tell a gene measured to have no partners from a gene that was never sent. Reporting the second as the first would invent a negative result.

References

Szklarczyk et al. (2023). The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Research 51(D1), D638-D646. doi:10.1093/nar/gkac1000

Service documentation: https://string-db.org/

Examples

# \donttest{
res <- string_network(c("TP53", "NF1", "EGFR"))
biohttp::body_or_null(res)$edges
#> # A tibble: 3 × 3
#>   gene_a gene_b score
#>   <chr>  <chr>  <dbl>
#> 1 TP53   NF1    0.947
#> 2 TP53   EGFR   0.977
#> 3 EGFR   NF1    0.949
# }