XYomics (version 0.1.2)

get_string_network: Download and Process STRING Protein-Protein Interaction Network

Description

Downloads and processes the STRING protein-protein interaction network, converting it to a simplified igraph object. The function downloads the network from STRING database, filters interactions by confidence score, converts STRING IDs to ENTREZ IDs, and returns the largest connected component as an undirected graph.

Usage

get_string_network(
  organism = "9606",
  score_threshold = 700,
  use_default = TRUE
)

Value

An igraph object representing the largest connected component of the filtered STRING network, with the following properties:

• Undirected edges

• No self-loops

• No multiple edges

• Edge weights (1000 - combined_score)

• Vertex names as ENTREZ IDs

Arguments

organism

Character string specifying the NCBI taxonomy identifier. Default is "9606" (Homo sapiens).

score_threshold

Numeric value between 0 and 1000 specifying the minimum combined score threshold for including interactions. Default is 700.

use_default

it will return the default network (9606 and score of 700)

Details

The function performs the following steps:

1. Downloads protein interactions from STRING database

2. Filters interactions based on combined score

3. Downloads and processes STRING ID to ENTREZ ID mappings

4. Creates an igraph object with filtered interactions

5. Removes self-loops and multiple edges

6. Extracts the largest connected component