Get STRINGdb PPI data from full local or live source — GetSTRINGdb.edges • PTMsToPathways

Retrieve STRINGdb protein-protein interaction edges for a supplied gene set, either from a precomputed local file derived from protein.links.full.v12.0.txt.gz or live via the STRINGdb R package.

In local mode, this function performs no web/API queries. To avoid symbol mismatches, users are encouraged to standardize their node list in advance with StandardizeGeneSymbols().

Usage

GetSTRINGdb.edges(
  gene.cccn.edges,
  gene.cccn.nodes,
  local = FALSE,
  string.local.path = "string_hs_hugo_full.tsv",
  combined.score.threshold = 400,
  include.transferred = TRUE,
  symbol.map = NULL
)

Arguments

gene.cccn.edges: Data frame of CCCN edges (currently unused; retained for compatibility with older package API).
gene.cccn.nodes: Character vector of gene symbols to retain.
local: Logical. If TRUE, read only from a local precomputed file and do not query STRINGdb online. Default is FALSE.
string.local.path: Path to local TSV produced from protein.links.full with transferred columns included. Default is "string_hs_hugo_full.tsv".
combined.score.threshold: Integer (0-1000). Minimum combined_score to retain an edge. Default is 400.
include.transferred: Logical. If TRUE, include *_transferred evidence channels. If FALSE, omit them. Default is TRUE.
symbol.map: Optional data frame produced by StandardizeGeneSymbols(). If supplied, gene.cccn.nodes will be converted to standard_symbol before filtering. Useful for keeping local mode fully offline.

Value

Data frame with columns: source, target, interaction, Weight

Examples

# sym.map <- StandardizeGeneSymbols(ex.gene.cccn.nodes)
# x <- GetSTRINGdbEdgesFull(
#   ex.gene.cccn.edges,
#   ex.gene.cccn.nodes,
#   local = TRUE,
#   string.local.path = "string_hs_hugo_full.tsv",
#   combined.score.threshold = 400,
#   include.transferred = TRUE,
#   symbol.map = sym.map
# )