Compute energies / response for a PBM on given sequences

Compute energies / response for a PBM on given sequences

Usage

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

Arguments

pbm

A PBM object

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 data frame containing the computed energies.