Compute energies / response for a list of PBMs on given sequences

This function computes the energies for a list of PBMs on given sequences.

Usage

pbm_list.compute(
  pbm_list,
  sequences,
  response = FALSE,
  func = "logSumExp",
  normalize_energies = TRUE
)

Arguments

pbm_list

A list of PBM objects

sequences

A set of sequences on which to compute the energies.

response

A logical flag indicating whether to compute the response. Default is FALSE.

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