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Retrieve Neighboring Nodes in a Knowledge Graph

get_neighboring_nodes.Rd

This function returns all neighboring nodes for a given gene node ID in the tKOI knowledge graph. The neighborhood is defined by the number of hops (degree_expansion) from the input node.

Usage

get_neighboring_nodes(gene_node_id, degree_expansion, subnetwork)

Arguments

gene_node_id

A character string representing the unique node ID of a gene in the tkoi::tkoi_net igraph object.

degree_expansion

An integer indicating the radius (in number of hops) to expand the search for neighbors. For example, degree_expansion = 1 returns first-degree (direct) neighbors, while degree_expansion = 2 includes both direct and second-degree (indirect) neighbors.

subnetwork

An igraph object (typically a subgraph of tkoi_net) in which the neighborhood search will be performed.

Value

A character vector of node IDs representing the neighbors of the specified gene node.

Details

The function leverages the igraph::ego() function to extract the subgraph containing all nodes within a specified path length from the target node. It then returns the node IDs (as character vector) of these neighbors. This is useful in the tKOI pipeline for assessing local network topology around significantly altered genes.

See also

ego, run_tkoi

Examples

if (FALSE) { # \dontrun{
# Get direct neighbors of a gene node with ID "ENSG00000123456"
get_neighboring_nodes("ENSG00000123456", degree_expansion = 1)

# Get both direct and indirect (2-hop) neighbors
get_neighboring_nodes("ENSG00000123456", degree_expansion = 2)
} # }