Generate diffusion profiles — generate

Runs one constrained personalised PageRank per seed (Ruiz et al.). The graph is built once in Rust and the seeds run in parallel. Each call replaces the stored profiles, so pass drugs and diseases together if you want to compare them afterwards.

Usage

generate_profiles(
  object,
  seeds,
  diffusion_profile_params = params_diffusion_profiles(),
  .verbose = TRUE
)

Arguments

object: A DiffusionProfiles object, see DiffusionProfiles().
seeds: Character vector. Node ids to start the walks from; one profile per seed.
diffusion_profile_params: Named list. The PageRank parameters, see params_diffusion_profiles().
.verbose: Boolean. Controls verbosity. Defaults to TRUE.

Value

The DiffusionProfiles object with profiles populated as a numeric matrix of nodes x seeds. Each column sums to 1.