createDiffLogoObject: DiffLogo object

Description Usage Arguments Value Author(s) Examples

View source: R/diffSeqLogo.R

Description

Creates a DiffLogo object

Usage

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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)

Arguments

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

Value

DiffLogo object

Author(s)

Martin Nettling

Examples

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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)
(diffLogoObj)

DiffLogo documentation built on Nov. 1, 2018, 2:24 a.m.