createDiffLogoObject: DiffLogo object
In mgledi/DiffLogo: DiffLogo: A comparative visualisation of biooligomer motifs

Description Usage Arguments Value Author(s) Examples

Creates a DiffLogo object

createDiffLogoObject(pwm1, pwm2, stackHeight = shannonDivergence,
  baseDistribution = normalizedDifferenceOfProbabilities,
  alphabet = DNA, align_pwms = FALSE,
  unaligned_penalty = divergencePenaltyForUnaligned,
  try_reverse_complement = TRUE, base_distribution = NULL,
  length_normalization = FALSE, unaligned_from_left = 0,
  unaligned_from_right = 0)

`pwm1`	representation of the first position weight matrix (PWM) of type pwm, data.frame, or matrix
`pwm2`	representation of the second position weight matrix (PWM) of type pwm, data.frame, or matrix
`stackHeight`	function for the height of a stack at position i
`baseDistribution`	function for the heights of the individual bases
`alphabet`	of type Alphabet
`align_pwms`	if True, will aling and extend pwms.
`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.
`unaligned_from_left`	the number of unaligned positions on the left
`unaligned_from_right`	the number of unaligned positions on the right

DiffLogo object

Martin Nettling

motif_folder= "extdata/pwm"
motif_names = c("HepG2","MCF7","HUVEC","ProgFib")
motifs = list()
for (name in motif_names) {
  fileName = paste(motif_folder,"/",name,".pwm",sep="")
  file = system.file(fileName, package = "DiffLogo")
  motifs[[name]] = getPwmFromPwmFile(file)
}

pwm1 = motifs[[motif_names[[1]]]]
pwm2 = motifs[[motif_names[[2]]]]

diffLogoObj = createDiffLogoObject(pwm1 = pwm1, pwm2 = pwm2)
diffLogo(diffLogoObj)