empiricalPvalueSequenceSet: Empirical P-value for a set of sequences
In PWMEnrich: PWM enrichment analysis

Calculate empirical P-value for a set of sequences, using either affinity or cutoff. When cutoff is used, the score is a number of motif hits above a certain log-odds cutoff.

empiricalPvalueSequenceSet(
  scores,
  seq.len,
  pwm.len,
  bg.fwd,
  bg.rev,
  cutoff = NULL,
  B = 10000,
  verbose = FALSE
)

`scores`	a matrix of scores, rows for sequences, columns for PWMs
`seq.len`	the lengths of sequences
`pwm.len`	the lengths of PWMs
`bg.fwd`	raw odds scores for the forward strand of background
`bg.rev`	raw odds scores for the reverse strand of background
`cutoff`	if not NULL, will use hit count above this cutoff. The cutoff should be specified in log2.
`B`	the number of random replicates
`verbose`	if to give verbose progress reports