multipleLocalPwmsAlignment: Multiple PWMs alignment

In DiffLogo: DiffLogo: A comparative visualisation of biooligomer motifs

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))

DiffLogo documentation built on Nov. 8, 2020, 6:09 p.m.