pwmsDistanceMatrix {DiffLogo} | R Documentation

## Multiple PWMs alignment

### Description

Creates a distance matrix for pwms

### Usage

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

### Arguments

`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

### Value

list

### Author(s)

Lando Andrey

[Package DiffLogo version 2.4.0 Index]