multipleLocalPwmsAlignment {DiffLogo} | R Documentation

## Multiple PWMs alignment

### Description

Creates a multiple alignment of pwms

### Usage

    multipleLocalPwmsAlignment(pwms, divergence = shannonDivergence,
      unaligned_penalty = divergencePenaltyForUnaligned,
      try_reverse_complement = TRUE, base_distribution = NULL,
      length_normalization = FALSE)

### Arguments

`pwms` | list of pwms
`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` | 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

### Author(s)

Lando Andrey

### Examples

    file1 = system.file("extdata/homer/Max.motif",   package = "DiffLogo")
    file2 = system.file("extdata/homer/c-Myc.motif", package = "DiffLogo")
    pwm1 = getPwmFromFile(file1)
    pwm2 = getPwmFromFile(file2)

    multiple_pwms_alignment = multipleLocalPwmsAlignment(list(pwm1, pwm2))

[Package DiffLogo version 2.4.0 Index]