Get STRINGdb PPI data — GetSTRINGdb.edges • PTMsToPathways

This function finds protein-protein interaction weights by consulting the STRINGdb database, either live via the STRINGdb R package or from a locally pre-downloaded flat file. The package STRINGdb is required for the live mode. To download, run:

if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("STRINGdb")

For the local mode, download the full detailed network file for Homo sapiens from: https://stringdb-downloads.org/download/protein.links.detailed.v12.0/9606.protein.links.detailed.v12.0.txt.gz and pre-process it to HUGO symbols using the companion script scripts/string_to_hugo.r. The resulting file (string_hs_hugo.tsv) is the expected input for local mode. 'Group' is the interaction category (included: "Pathway", "Physical Interactions", "Predicted", "Genetic Interactions")

Usage

GetSTRINGdb.edges(
  gene.cccn.edges,
  gene.cccn.nodes,
  local = FALSE,
  string.local.path = "string_hs_hugo.tsv"
)

Arguments

gene.cccn.edges: A dataframe showing interaction relationships between proteins using common PTM clusters derived from three distance metrics (Euclidean, Spearman, and Combined (SED))
gene.cccn.nodes: A list of nodes that are in the Gene CoCluster Correlation Network derived from common clusters between the three distance metrics (Euclidean, Spearman, and Combined (SED))
local: Logical. If TRUE, reads from a pre-downloaded local file instead of querying the live STRINGdb API. Default is FALSE.
string.local.path: Path to the pre-processed local STRING file (string_hs_hugo.tsv produced by scripts/string_to_hugo.r). Only used when local = TRUE. Default is "string_hs_hugo.tsv".
combined.score.threshold: Integer (0–1000). Minimum combined_score to retain an edge when reading from the local file. STRING thresholds: low = 150, medium = 400, high = 700, highest = 900. Default is 400.

Value

Data frame of consisting of the network of interactions from the genes of study pulled from the STRINGdb database and a list of gene names

Details

The full example takes ~10 minutes to load in live mode, so it has been commented out and the results are displayed.

Examples

# Live mode (original behaviour):
# GetSTRINGdb.edges(ex.gene.cccn.edges, ex.gene.cccn.nodes)

# Local mode (future-proof, no internet required):
# GetSTRINGdb.edges(ex.gene.cccn.edges, ex.gene.cccn.nodes,
#                   local = TRUE, string.local.path = "string_hs_hugo.tsv")

utils::head(ex.stringdb.edges)
#> Error: object 'ex.stringdb.edges' not found
utils::head(ex.nodenames)
#> Error: object 'ex.nodenames' not found