Extract PBM scores / response for a list of PBMs — pbm

This function extracts PBM scores for genomic intervals and optionally computes the response for a list of PBMs.

Usage

pbm_list.gextract(
  pbm_list,
  intervals,
  response = FALSE,
  func = "logSumExp",
  normalize_energies = TRUE
)

pbm_list: A list of PBM objects
intervals: Genomic intervals to extract
response: Logical, 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.

The intervals, with an additional column containing the PBM scores / response for each PBM