pwmsDistanceMatrix: Multiple PWMs alignment
In mgledi/DiffLogo: DiffLogo: A comparative visualisation of biooligomer motifs

Description Usage Arguments Value Author(s)

Creates a distance matrix for pwms

pwmsDistanceMatrix(pwms, diagonal_value = 0,
  bottom_default_value = NULL, divergence = shannonDivergence,
  unaligned_penalty = divergencePenaltyForUnaligned,
  try_reverse_complement = TRUE, base_distribution = NULL,
  length_normalization = FALSE)

`pwms`	list of pwms
`diagonal_value`	value to put on diagonal.
`bottom_default_value`	value to put on bottom triangle. Set to NULL to get symmetric distance matrix.
`divergence`	divergence measure.
`unaligned_penalty`	is a function for localPwmAlignment.
`try_reverse_complement`	if True, alignment will try reverse complement pwms
`base_distribution`	is a vector of length nrow(pwm) that is added to unaligned columns of pwms for comparing. If NULL, uniform distribution is used
`length_normalization`	is a vector of length nrow(pwm) that is added to unaligned columns of pwms for comparing. If NULL, uniform distribution is used