dot-ga_make_individual: Build a GA individual from a logical genome

In pathfindR: Enrichment Analysis Utilizing Active Subnetworks

Build a GA individual from a logical genome

Description

Computes the connected subnetworks induced by the on-nodes and stores their scores (sorted descending) for fast fitness comparison. The scores are obtained with the C++ component scorer over the precomputed CSR adjacency, which is the only thing the fitness comparison (.ga_compare / .ga_sort_desc) ever reads. The node membership of a genome is not materialized here — it is reconstructed once, for the best individual, at the end of .genetic_algorithm().

Usage

.ga_make_individual(rep_logical, csr_offsets, csr_nbrs, z_vec, means, stds)

Arguments

rep_logical	A logical vector aligned to network$nodes (TRUE = node on). May be empty.
csr_offsets, csr_nbrs	CSR adjacency from build_network().
z_vec	Per-node z-scores aligned to the node order.
means, stds	Score-context calibration vectors.

Value

A list with elements rep (the genome) and scores (the descending component scores).

pathfindR documentation built on July 2, 2026, 1:06 a.m.