localPwmAlignment: Align pwms
In DiffLogo: DiffLogo: A comparative visualisation of biooligomer motifs

Description Usage Arguments Value Author(s)

Finds best local alignment for two PWMs.

localPwmAlignment(pwm_left, pwm_right, divergence = shannonDivergence,
  unaligned_penalty = divergencePenaltyForUnaligned,
  try_reverse_complement = TRUE, base_distribution = NULL,
  length_normalization = FALSE)

`pwm_left`	first PWM, a matrix of type matrix
`pwm_right`	first PWM, a matrix of type matrix
`divergence`	is a measure of difference between two pwm columns. Smaller is more similar. If you want to use non-uniform background distribution, provide your own function.
`unaligned_penalty`	distance for unaligned columns at edges of matrixes. See divergencePenaltyForUnaligned as an example for providing your own function
`try_reverse_complement`	If false the alignment will not be performed on reverse complements. If true, the input pwms should have column order of ACTG/ACGU.
`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`	If true, will minimize the average divergence between PWMs. Otherwise will minimize the sum of divergences between positions. In both cases unalignes positions are compared to base_distribution and are counted when computing the alignment length.