Turn a STRING network response into an edge table — string_parse

Pure. Edge endpoints come back in STRING's preferredName space; see string_reconcile_edges() for why that matters.

Usage

string_parse_network(body)

Arguments

body: A parsed STRING network response, a JSON array of edges.

Value

A tibble of gene_a, gene_b, and score, upper-cased. A zero-row tibble when there are no edges, because "no high-confidence edges" is a real answer about a set rather than an absence of one.

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

body <- list(list(
  preferredName_A = "TP53", preferredName_B = "NF1", score = 0.88
))
string_parse_network(body)
#> # A tibble: 1 × 3
#>   gene_a gene_b score
#>   <chr>  <chr>  <dbl>
#> 1 TP53   NF1     0.88