% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/utils-core-genes.R
\name{build_edge_list_safely}
\alias{build_edge_list_safely}
\title{Build Pathway Similarity Network Edges (Safe Version)}
\usage{
build_edge_list_safely(core_genes_list, min_shared_genes = 2)
}
\arguments{
\item{core_genes_list}{Named list: pathway_id -> core_gene_vector}

\item{min_shared_genes}{Minimum number of shared genes between pathways to form an edge}
}
\value{
Data frame with columns: from, to, shared, weight (Jaccard index),
  overlap_coef, dice_coef, shared_genes
}
\description{
Safely construct edge list for pathway network based on Jaccard
  similarity of core genes. Includes defensive checks for edge cases.
  Now includes Overlap Coefficient and Dice Coefficient for comprehensive
  similarity assessment.
}
\examples{
# Build edges from two pathways sharing 2 core genes
core_genes <- list(
  PATHWAY_A = c("GENE_A", "GENE_B", "GENE_C"),
  PATHWAY_B = c("GENE_B", "GENE_C", "GENE_D")
)
edges <- build_edge_list_safely(core_genes, min_shared_genes = 2)
print(edges)
}
