Package 'DiffLogo'

Title: DiffLogo: A comparative visualisation of biooligomer motifs
Description: DiffLogo is an easy-to-use tool to visualize motif differences.
Authors: c( person("Martin", "Nettling", role = c("aut", "cre"), email = "[email protected]"), person("Hendrik", "Treutler", role = c("aut", "cre"), email = "[email protected]"), person("Jan", "Grau", role = c("aut", "ctb"), email = "[email protected]"), person("Andrey", "Lando", role = c("aut", "ctb"), email = "[email protected]"), person("Jens", "Keilwagen", role = c("aut", "ctb"), email = "[email protected]"), person("Stefan", "Posch", role = "aut", email = "[email protected]"), person("Ivo", "Grosse", role = "aut", email = "[email protected]"))
Maintainer: Hendrik Treutler<[email protected]>
License: GPL (>= 2)
Version: 2.31.0
Built: 2024-11-29 05:25:37 UTC
Source: https://github.com/bioc/DiffLogo

Help Index

Multiple PWMs alignment

Description

Align two sets of pwms

Usage

alignPwmSets(left_pwms_set, left_alignment, right_pwms_set,
  right_alignment, try_reverse_complement)

Arguments

left_pwms_set

list of pwms(matrixes)
left_alignment

alignment of left_pwms_set.
right_pwms_set

list of pwms;
right_alignment

alignment of right_pwms_set.
try_reverse_complement

if true(default), also try reverse complement.

Value

list - alignment of concatination of left_pwms_set and right_pwms_set

Author(s)

Lando Andrey

built alphabet

Description

builts an object of class Alphabet from the given set of symbols and colors

Usage

Alphabet(chars, cols, supportReverseComplement)

Arguments

chars

set of symbols
cols

set of colors; one for each symbol
supportReverseComplement

boolean whether the alphabet supports reverse complementation (like DNA/RNA) or not (like ASN)

Value

the Alphabet object

Author(s)

Martin Nettling

Examples

DNA = Alphabet(c("A","C","G","T"),c("green4","blue","orange","red"),TRUE)

ASN alphabet

Description

the amino acid alphabet (20 symbols), i.e. A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y

Usage

ASN

Format

An object of class Alphabet of length 4.

Author(s)

Martin Nettling

Examples

ASN

Generates a PWM

Description

Generates a PWM consisting of only the uniform distribution or the given base_distribution (if defined).

Usage

baseDistributionPwm(pwm_length, alphabet_length,
  base_distribution = NULL)

Arguments

pwm_length

the number of positions
alphabet_length

the alphabet size
base_distribution

optional base distribution for each PWM position

Value

a PWM

p-value that two PWM-positions are from the same distribution

Description

Calculates the p-value for the null-hypothesis that two given probability vectors p1, p2 calculated from n1/n2 observations arise from the same distribution

Usage

calculatePvalue(p1, p2, n1, n2, stackHeight = shannonDivergence,
  numberOfPermutations = 100, plotGammaDistributionFit = FALSE)

Arguments

p1

first probability vector with one probability for each symbol of the alphabet
p2

second probability vector with one probability for each symbol of the alphabet
n1

number of observations for the calculation of p1
n2

number of observations for the calculation of p2
stackHeight

function for the calculation of a divergence measure for two probability vectors
numberOfPermutations

the number of permutations to perform for the calculation of stackHeights
plotGammaDistributionFit

if TRUE the fit of a gamma distribution to the sampled stackHeights is plotted

Value

a numeric p-value

Author(s)

Hendrik Treutler

Examples

p1 <- c(0.2, 0.3, 0.1, 0.4)
p2 <- c(0.2, 0.1, 0.3, 0.4)
n1 <- 100
n2 <- 200
numberOfPermutations = 100
plotGammaDistributionFit = TRUE

pValue <- calculatePvalue(p1 = p1, p2 = p2, n1 = n1, n2 = n2, stackHeight = shannonDivergence, numberOfPermutations = numberOfPermutations, plotGammaDistributionFit = plotGammaDistributionFit)

DiffLogo object

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)

normalized information content differences

Description

information content differences normalized by the sum of absolute information content differences for the given pair of probability vectors

Usage

differenceOfICs(p1, p2)

Arguments

p1

probability vector representing the first symbol distribution
p2

probability vector representing the second symbol distribution

Value

a vector with one result for each symbol

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]]]]

diffLogoFromPwm(pwm1 = pwm1, pwm2 = pwm2, baseDistribution = differenceOfICs)

Draw DiffLogo from PWM

Description

Draws the difference of two sequence logos.

Usage

diffLogoFromPwm(pwm1, pwm2, ymin = 0, ymax = 0,
  stackHeight = shannonDivergence,
  baseDistribution = normalizedDifferenceOfProbabilities,
  sparse = FALSE, alphabet = DNA, align_pwms = FALSE,
  unaligned_penalty = divergencePenaltyForUnaligned,
  try_reverse_complement = TRUE, base_distribution = NULL,
  length_normalization = FALSE)

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
ymin

minimum value on the y-axis
ymax

maximum value on the y-axis
stackHeight

function for the height of a stack at position i
baseDistribution

function for the heights of the individual bases
sparse

if TRUE margins are reduced and tickmarks are removed from the logo
alphabet

of type Alphabet
align_pwms

if true, DiffLogo will align pwms before plotting
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

none (draws difference logo)

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]]]]

diffLogoFromPwm(pwm1 = pwm1, pwm2 = pwm2)

Draw DiffLogo-table

Description

Draws a table of DiffLogos.

Usage

diffLogoTable(PWMs, sampleSizes = NULL, alphabet = DNA,
  configuration = list(), ...)

Arguments

PWMs

a list/vector of position weight matrices (PWMs) each of type pwm, data.frame, or matrix
sampleSizes

the number of sequences behind each PWM
alphabet

the alphabet of the given PWMs
configuration

list of (probably part of) of configuration options. See diffLogoTableConfiguration.
...

set of parameters passed to the function 'axis' for plotting

Value

none (draws table of difference logos)

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)
}

diffLogoTable(motifs)

Configuration object for diffLogoTable

Description

Default configuration list for diffLogoTable

Usage

diffLogoTableConfiguration(alphabet, stackHeight = shannonDivergence,
  baseDistribution = normalizedDifferenceOfProbabilities,
  uniformYaxis = TRUE, sparse = TRUE, showSequenceLogosTop = TRUE,
  enableClustering = TRUE, treeHeight = 0.5, margin = 0.02,
  ratio = 1, align_pwms = FALSE, multiple_align_pwms = TRUE,
  unaligned_penalty = divergencePenaltyForUnaligned,
  try_reverse_complement = TRUE, length_normalization = FALSE,
  numberOfPermutations = 100)

Arguments

alphabet

used alphabet of type Alphabet
stackHeight

function for the height of a stack at position i
baseDistribution

function for the heights of the individual bases
uniformYaxis

if TRUE each DiffLogo is plotted with the same scaling of the y-axis
sparse

if TRUE margins are reduced and tickmarks are removed from the logo
showSequenceLogosTop

if TRUE the classical sequence logos are drawn above each column of the table
enableClustering

if TRUE the motifs are reordered, so that similar motifs have a small vertical and horizontal distance in the table
treeHeight

the height of the plotted cluster tree above the columns of the table; set equal to zero to omit the cluster tree
margin

the space reseverved for labels
ratio

the ratio of the plot; this is needed to determine the margin sizes correctly
align_pwms

if True, will align and extend pwms in each cell of diffLogoTable independently.
multiple_align_pwms

if True, will align and extend pwms in the diffLogoTable jointly.
unaligned_penalty

is a function for localPwmAlignment.
try_reverse_complement

if True, alignment will try reverse complement pwms
length_normalization

if True, divergence between pwms is divided by length of pwms.
numberOfPermutations

number of permutations for the permutation test for the calculation of p-values

Value

list of parameters

Author(s)

Lando Andrey

Examples

diffLogoTableConfiguration(DNA)

DNA alphabet

Description

the DNA alphabet, i.e. A, C, G, T

Usage

DNA

Format

An object of class Alphabet of length 4.

Author(s)

Martin Nettling

Examples

DNA

Draws a table of DiffLogos

Description

Draws a table of DiffLogos.

Usage

drawDiffLogoTable(diffLogoTableObj, ...)

Arguments

diffLogoTableObj

the diffLogoTable-Object created by function prepareDiffLogoTable(...)
...

optional parameters for functon axis

Value

none (draws difference logo)

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)
}

diffLogoTableObj = prepareDiffLogoTable(motifs)
drawDiffLogoTable(diffLogoTableObj)

Enriches a difflogo object with p-values

Description

Enriches a difflogo object with p-values which quantifies the probability that two PWM-positions are from the same distribution

Usage

enrichDiffLogoObjectWithPvalues(diffLogoObj, n1, n2,
  stackHeight = shannonDivergence, numberOfPermutations = 100)

Arguments

diffLogoObj

matrix of difflogo objects
n1

the number of sequences behind the first pwm behind the given difflogo object
n2

the number of sequences behind the second pwm behind the given difflogo object
stackHeight

function for the calculation of a divergence measure for two probability vectors
numberOfPermutations

the number of permutations to perform for the calculation of stackHeights

Value

enriched difflogo object

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]]]]
n1 <- 100
n2 <- 100
diffLogoObj = createDiffLogoObject(pwm1 = pwm1, pwm2 = pwm2)
diffLogoObj = enrichDiffLogoObjectWithPvalues(diffLogoObj, n1, n2)

Enriches a matrix of difflogo objects with p-values

Description

Enriches a matrix of difflogo objects with p-values which quantifies the probability that two PWM-positions are from the same distribution

Usage

enrichDiffLogoTableWithPvalues(diffLogoObjMatrix, sampleSizes,
  stackHeight = shannonDivergence, numberOfPermutations = 100)

Arguments

diffLogoObjMatrix

matrix of difflogo objects
sampleSizes

number of sequences behind the pwms behind the given difflogo objects
stackHeight

function for the calculation of a divergence measure for two probability vectors
numberOfPermutations

the number of permutations to perform for the calculation of stackHeights

Value

matrix of difflogo objects enriched with p-values

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)
}
sampleSizes <- c(100, 150, 200, 250)
names(sampleSizes) <- motif_names

diffLogoTableObj = prepareDiffLogoTable(motifs);
diffLogoTableObj$diffLogoObjMatrix = enrichDiffLogoTableWithPvalues(diffLogoTableObj$diffLogoObjMatrix, sampleSizes)

Extend pwms with respect to alignment

Description

Extends pwms by adding base_distribution to both sides, so that they keep aligned, but have equal length.

Usage

extendPwmsFromAlignmentVector(pwms, alignment_vector,
  base_distribution = NULL)

Arguments

pwms

is a list of matrixes
alignment_vector

is a list of shifts ($shift) and orientations ($direction)
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

Value

extended pwms

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)

pwms <- list(pwm1, pwm2)
multiple_pwms_alignment = multipleLocalPwmsAlignment(pwms)
aligned_pwms = extendPwmsFromAlignmentVector(pwms, multiple_pwms_alignment$alignment$vector)

Complete character alphabet

Description

the alphabet of all 26 characters

Usage

FULL_ALPHABET

Format

An object of class Alphabet of length 4.

Author(s)

Hendrik Treutler

Examples

FULL_ALPHABET

returns the alphabet which fits to the given characters

Description

returns the alphabet which fits to the given characters

Usage

getAlphabetFromCharacters(characters)

Arguments

characters

a character vector of characters

Value

an alphabet of type Alphabet

Examples

alphabet = getAlphabetFromSequences(c("A","A","C","C","G","G","T","T"))

returns the alphabet which fits to the given sequences

Description

returns the alphabet which fits to the given sequences

Usage

getAlphabetFromSequences(sequences)

Arguments

sequences

a character vector of sequences

Value

an alphabet of type Alphabet

Examples

alphabet = getAlphabetFromSequences("AACCGGTT")

Create PWM from alignment

Description

Creates a matrix-representation of a PWM from a set of sequences

Usage

getPwmFromAlignment(alignment, alphabet = NULL, pseudoCount = 0)

Arguments

alignment

a vector or list of sequences each with equal length
alphabet

of type Alphabet
pseudoCount

the number of pseudo-observations for each character in the alphabet

Value

PWM as matrix

Author(s)

Hendrik Treutler

Examples

motif_folder= "extdata/alignments"
motif_name = "calamodulin_1"
fileName = paste(motif_folder,"/",motif_name,".txt",sep="")
file = system.file(fileName, package = "DiffLogo")
motif = getPwmFromAlignment(readLines(file), ASN, 1)
seqLogo(pwm = motif, alphabet=ASN)

generates a pwm from an alignment file

Description

generates a pwm from an alignment file

Usage

getPwmFromAlignmentFile(filename, alphabet = NULL)

Arguments

filename

the alignment file
alphabet

the desired alphabet of type Alphabet

Value

a pwm

Examples

fileName = "extdata/alignments/calamodulin_1.txt"
file = system.file(fileName, package = "DiffLogo")
pwm = getPwmFromAlignmentFile(file)

generates a pwm from a FASTA file

Description

generates a pwm from a FASTA file

Usage

getPwmFromFastaFile(filename, alphabet = NULL)

Arguments

filename

the FASTA file
alphabet

the desired alphabet of type Alphabet

Value

a pwm

Examples

fileName = "extdata/alignments/F-box_bacteria.seq.fa"
file = system.file(fileName, package = "DiffLogo")
pwm = getPwmFromFastaFile(file)

generates a pwm from a file of different formats

Description

Generates a pwm from a file of different formats. Supported formats are FASTA files (.fa, .fasta), alignment files (.txt, .text, .al, .alignment), PWM files (.pwm), JASPAR / Position Frequency Matrix files (.pfm), and homer files (.motif).

Usage

getPwmFromFile(filename)

Arguments

filename

the file

Value

a pwm

Examples

fileName = "extdata/pwm/H1-hESC.pwm"
file = system.file(fileName, package = "DiffLogo")
pwm = getPwmFromFile(file)

generates a pwm from a homer file

Description

generates a pwm from a homer file

Usage

getPwmFromHomerFile(filename)

Arguments

filename

the homer file

Value

a pwm

Examples

fileName = "extdata/homer/CTCF_Zf_CD4.motif"
file = system.file(fileName, package = "DiffLogo")
pwm = getPwmFromHomerFile(file)

generates a pwm from a jaspar file

Description

generates a pwm from a jaspar file

Usage

getPwmFromPfmOrJasparFile(filename)

Arguments

filename

the jaspar file

Value

a pwm

Examples

fileName = "extdata/pfm/ctcf_jaspar.pfm"
file = system.file(fileName, package = "DiffLogo")
pwm = getPwmFromPfmOrJasparFile(file)

generates a pwm from a pwm file

Description

generates a pwm from a pwm file

Usage

getPwmFromPwmFile(filename)

Arguments

filename

the pwm file

Value

a pwm

Examples

fileName = "extdata/pwm/H1-hESC.pwm"
file = system.file(fileName, package = "DiffLogo")
pwm = getPwmFromPwmFile(file)

extracts the sequences from an alignment file

Description

extracts the sequences from an alignment file

Usage

getSequencesFromAlignmentFile(filename)

Arguments

filename

the alignment file

Value

a vector of sequences

Examples

fileName = "extdata/alignments/calamodulin_1.txt"
file = system.file(fileName, package = "DiffLogo")
sequences = getSequencesFromAlignmentFile(file)

extracts the sequences from a FASTA file

Description

extracts the sequences from a FASTA file

Usage

getSequencesFromFastaFile(filename)

Arguments

filename

the FASTA file

Value

a vector of sequences

Examples

fileName = "extdata/alignments/F-box_bacteria.seq.fa"
file = system.file(fileName, package = "DiffLogo")
sequences = getSequencesFromFastaFile(file)

information content

Description

the information content for the given probability vector

Usage

informationContent(p)

Arguments

p

probability vector representing the symbol distribution

Value

an object consisting of height a ylab

Author(s)

Martin Nettling

Examples

motif_folder= "extdata/pwm"
motif_name = "HepG2"
fileName = paste(motif_folder,"/",motif_name,".pwm",sep="")
file = system.file(fileName, package = "DiffLogo")
motif = getPwmFromPwmFile(file)
seqLogo(pwm = motif, stackHeight = informationContent)

Align pwms

Description

Finds best local alignment for two PWMs.

Usage

localPwmAlignment(pwm_left, pwm_right, divergence = shannonDivergence,
  unaligned_penalty = divergencePenaltyForUnaligned,
  try_reverse_complement = TRUE, base_distribution = NULL,
  length_normalization = FALSE)

Arguments

pwm_left

first PWM, a matrix of type matrix
pwm_right

first PWM, a matrix of type matrix
divergence

is a measure of difference between two pwm columns. Smaller is more similar. If you want to use non-uniform background distribution, provide your own function.
unaligned_penalty

distance for unaligned columns at edges of matrixes. See divergencePenaltyForUnaligned as an example for providing your own function
try_reverse_complement

If false the alignment will not be performed on reverse complements. If true, the input pwms should have column order of ACTG/ACGU.
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 of length two containing the alignment and the divergence

Author(s)

Lando Andrey

the change of information content

Description

the change of information content for the given probability vectors

Usage

lossOfAbsICDifferences(p1, p2)

Arguments

p1

probability vector representing the first symbol distribution
p2

probability vector representing the second symbol distribution

Value

an object consisting of height and ylab

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]]]]

diffLogoFromPwm(pwm1 = pwm1, pwm2 = pwm2, stackHeight = lossOfAbsICDifferences)

Multiple PWMs alignment

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))

normalized probability differences

Description

probability differences normalized by the sum of absolute probability differences for the given pair of probability vectors

Usage

normalizedDifferenceOfProbabilities(p1, p2)

Arguments

p1

probability vector representing the first symbol distribution
p2

probability vector representing the second symbol distribution

Value

a vector with one result for each symbol

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]]]]

diffLogoFromPwm(pwm1 = pwm1, pwm2 = pwm2, baseDistribution = normalizedDifferenceOfProbabilities)

normalizes the given pwm

Description

normalizes the given pwm to column-sums of 1.0

Usage

normalizePWM(pwm)

Arguments

pwm

a pwm

Value

a normalized pwm

Examples

pwm = matrix(1:40, nrow = 4, dimnames = list(c("A","C","G","T"), 1:10))
pwm = normalizePWM(pwm)

Prepare a table of difflogo objects

Description

Prepares a DiffLogoTable and generates an object that contains the hirarchical clustering and a matrix of prepared difference logos.

Usage

prepareDiffLogoTable(PWMs, alphabet = DNA, configuration = list())

Arguments

PWMs

a list/vector of position weight matrices (PWMs) each of type pwm, data.frame, or matrix
alphabet

the alphabet of the given PWMs
configuration

list of (probably part of) of configuration options. See diffLogoTableConfiguration.

Value

matrix of difference logos

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)
}
sampleSizes <- c(100, 150, 200, 250)

diffLogoTableObj = prepareDiffLogoTable(motifs);

probabilities

Description

the given probabilities

Usage

probabilities(p)

Arguments

p

probability vector representing the symbol distribution

Value

the given vector

Author(s)

Martin Nettling

Examples

motif_folder= "extdata/pwm"
motif_name = "HepG2"
fileName = paste(motif_folder,"/",motif_name,".pwm",sep="")
file = system.file(fileName, package = "DiffLogo")
motif = getPwmFromPwmFile(file)
seqLogo(pwm = motif, baseDistribution = probabilities)

PWM divergence

Description

Counts PWM divergence as sum of divergencies of their columns.

Usage

pwmDivergence(pwm_left, pwm_right, divergence = shannonDivergence)

Arguments

pwm_left

is a PWM representation in type of matrix
pwm_right

is a PWM representation in type of matrix. The result is symmetric on pwm_left and pwm_right
divergence

is a Divergence function on columns.

Value

float - sum of divergences

Multiple PWMs alignment

Description

Creates a distance matrix for pwms

Usage

pwmsDistanceMatrix(pwms, diagonal_value = 0,
  bottom_default_value = NULL, divergence = shannonDivergence,
  unaligned_penalty = divergencePenaltyForUnaligned,
  try_reverse_complement = TRUE, base_distribution = NULL,
  length_normalization = FALSE)

Arguments

pwms

list of pwms
diagonal_value

value to put on diagonal.
bottom_default_value

value to put on bottom triangle. Set to NULL to get symmetric distance matrix.
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

is a vector of length nrow(pwm) that is added to unaligned columns of pwms for comparing. If NULL, uniform distribution is used

Value

list

Author(s)

Lando Andrey

Reverse for alignment vector

Description

Returns alignment vector as if all pwm were reverted.

Usage

reverseAlignmentVector(alignment_vector, pwms)

Arguments

alignment_vector

list of list which $shift and $orientation
pwms

list of matrixes.

Value

list - reversed alignment vector

Author(s)

Lando Andrey

RNA alphabet

Description

the RNA alphabet, i.e. A, C, G, U

Usage

RNA

Format

An object of class Alphabet of length 4.

Author(s)

Martin Nettling

Examples

RNA

shannon divergence

Description

the shannon divergence for the given pair of probability vectors

Usage

shannonDivergence(p1, p2)

Arguments

p1

probability vector representing the first symbol distribution
p2

probability vector representing the second symbol distribution

Value

an object consisting of height and ylab

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]]]]

diffLogoFromPwm(pwm1 = pwm1, pwm2 = pwm2, stackHeight = shannonDivergence)

sum of absolute information content differences

Description

the sum of absolute information content differences for the given pair of probability vectors

Usage

sumOfAbsICDifferences(p1, p2)

Arguments

p1

probability vector representing the first symbol distribution
p2

probability vector representing the second symbol distribution

Value

an object consisting of height and ylab

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]]]]

diffLogoFromPwm(pwm1 = pwm1, pwm2 = pwm2, stackHeight = sumOfAbsICDifferences)

sum of absolute probability differences

Description

the sum of absolute probability differences for the given pair of probability vectors

Usage

sumOfAbsProbabilityDifferences(p1, p2)

Arguments

p1

probability vector representing the first symbol distribution
p2

probability vector representing the second symbol distribution

Value

an object consisting of height and ylab

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]]]]

diffLogoFromPwm(pwm1 = pwm1, pwm2 = pwm2, stackHeight = sumOfAbsProbabilityDifferences)

sum of probabilities, i.e. 1.0

Description

the sum of probabilities for the given probability vector, i.e. 1.0

Usage

sumProbabilities(p)

Arguments

p

probability vector representing the symbol distribution

Value

an object consisting of height and ylab

Author(s)

Martin Nettling

Examples

motif_folder= "extdata/pwm"
motif_name = "HepG2"
fileName = paste(motif_folder,"/",motif_name,".pwm",sep="")
file = system.file(fileName, package = "DiffLogo")
motif = getPwmFromPwmFile(file)
seqLogo(pwm = motif, stackHeight = sumProbabilities)

Switches between 'forward' and 'reverse'

Description

Switches between 'forward' and 'reverse'

Usage

switchDirection(direction)

Arguments

direction

either 'forward' or 'reverse'

Value

either 'reverse' or 'forward'

Average divergence between two sets.

Description

Computes average pwm divergence from alignment vector for two datasets. This equals to average divergence between all pairs where one pwm comes from left set, and other comes from right

Usage

twoSetsAveragePwmDivergenceFromAlignmentVector(left_pwms_list,
  left_pwms_alignment, right_pwms_list, right_pwms_alignment,
  divergence = shannonDivergence)

Arguments

left_pwms_list

is a list of matrixes
left_pwms_alignment

is a list of shifts ($shift) and orientations ($direction)
right_pwms_list

is a list of matrixes
right_pwms_alignment

is a list of shifts ($shift) and orientations ($direction)
divergence

divergence measure.

Value

float

Author(s)

Lando Andrey