localPwmAlignment {DiffLogo} | R Documentation

## Align pwms

### Description

Finds best local alignment for two PWMs.

### Usage

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

### Arguments

`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.

### Value

list of length two containing the alignment and the divergence

### Author(s)

Lando Andrey

[Package DiffLogo version 2.4.0 Index]