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

pbm_list.multi_traj.compute_energy.Rd

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

Usage

pbm_list.multi_traj.compute_energy(
  multi_traj,
  sequences,
  func = "logSumExp",
  normalize_energies = TRUE
)

Arguments

multi_traj

A list of PBM lists

sequences

A set of sequences on which to compute the energies.

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