createDiffLogoObject: DiffLogo object

In DiffLogo: DiffLogo: A comparative visualisation of biooligomer motifs

Description

Creates a DiffLogo object

Usage

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

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)

Example output

Loading required package: cba
Loading required package: grid
Loading required package: proxy

Attaching package: ‘proxy’

The following objects are masked from ‘package:stats’:

    as.dist, dist

The following object is masked from ‘package:base’:

    as.matrix

[1] "pwm must be of class matrix or data.frame. Trying to convert"
[1] "pwm must be of class matrix or data.frame. Trying to convert"

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