multipleLocalPwmsAlignment: Multiple PWMs alignment

Description Usage Arguments Value Author(s) Examples

View source: R/pwmAlignment.R

Description

Creates a multiple alignment of pwms

Usage

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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

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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))

mgledi/DiffLogo documentation built on June 7, 2020, 8:23 a.m.