Extract energy for a list of pbm lists (multiple trajectories) — pbm_list.multi_traj.gextract_energy • iceqream

Extract energy for a list of pbm lists (multiple trajectories)

Usage

pbm_list.multi_traj.gextract_energy(
  multi_traj,
  intervals,
  func = "logSumExp",
  normalize_energies = TRUE
)

Arguments

multi_traj: A list of PBM lists
intervals: Genomic intervals to extract
func: the function to use to combine the PWMs for each sequence. Either 'logSumExp' or 'max'. The default is 'logSumExp'.
normalize_energies: A logical flag indicating whether to normalize the energies to a range of 0-10. Default is TRUE. Note that response computation requires normalized energies.

Value

A matrix containing the computed energies for each PBM