Package 'seqLogo'

Constructing a pwm object

Description

This function constructs an object of class pwm from a matrix. It checks that the matrix has correct dimensions and that columns add up to 1.0.

Usage

makePWM(pwm, alphabet = "DNA")

Arguments

pwm	matrix. Numerical matrix representing the position weight matrix.
alphabet	character. The alphabet making up the sequence. Currently, only 'DNA' and 'RNA' is supported.

Value

An object of class pwm.

Author(s)

Oliver Bembom

Examples

mFile <- system.file("extdata/pwm1", package = "seqLogo")
m <- read.table(mFile)
pwm <- makePWM(m)

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An S4 class to represent a PWM matrix.

Description

An object of class 'pwm' represents the alphabet*width position weight matrix of a sequence motif. In case of DNA sequence motif, the entry in row i, column j gives the probability of observing nucleotide c('A','C','G','T')[i] in position j of the motif.

Usage

## S4 method for signature 'pwm'
show(object)

## S4 method for signature 'pwm'
summary(object, ...)

## S4 method for signature 'pwm,ANY'
plot(x, y = "missing", ...)

## S4 method for signature 'pwm'
pwm(pwm)

## S4 method for signature 'pwm'
ic(pwm)

## S4 method for signature 'pwm'
consensus(pwm)

Arguments

object	object of pwm-class
...	additional parameters for plot function
x	object of pwm-class
y	default (missing) for plot function
pwm	object of pwm-class

Value

pwm-class object with slots: pwm, width, ic and alphabet.

Functions

• show,pwm-method: Shows the position weight matrix.

• summary,pwm-method: Prints the summary information about position weight matrix.

• plot,pwm,ANY-method: Plots the sequence logo of the position weight matrix.

• pwm,pwm-method: Access to 'pwm' slot

• ic,pwm-method: Access to 'ic' slot

• consensus,pwm-method: Access to 'consensus' slot

Slots

pwm

matrix. The position weight matrix.

width

numeric. The width of the motif.

ic

numeric. The information content (IC).

alphabet

character. The sequence alphabet. Currently, only 'DNA' and 'RNA' is supported.

consensus

character. The consensus sequence.

Author(s)

Oliver Bembom

Examples

mFile <- system.file("extdata/pwm1", package = "seqLogo")
m <- read.table(mFile)
p <- makePWM(m)
#
# slot access
pwm(p)
ic(p)
consensus(p)

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Plot a sequence logo for a given position weight matrix

Description

This function takes the alphabet*width position weight matrix of a sequence motif and plots the corresponding sequence logo.

Usage

seqLogo(pwm, ic.scale=TRUE, xaxis=TRUE, yaxis=TRUE, xfontsize=15, yfontsize=15,
        fill=c(A='#61D04F', C='#2297E6', G='#F5C710', T='#DF536B'))

Arguments

pwm	numeric. The alphabet*width position weight matrix.
ic.scale	logical. If TRUE, the height of each column is proportional to its information content. Otherwise, all columns have the same height.
xaxis	logical. If TRUE, an X-axis will be plotted.
yaxis	logical. If TRUE, a Y-axis will be plotted.
xfontsize	numeric. Font size to be used for the X-axis.
yfontsize	numeric. Font size to be used for the Y-axis.
fill	character. Fill color to be used for the letters. Must be a named character vector of length equal to number of rows in pwm slot and names identical to its rownames.

Value

NULL.

Author(s)

Oliver Bembom

Examples

mFile <- system.file("extdata/pwm1", package = "seqLogo")
m <- read.table(mFile)
p <- makePWM(m)
seqLogo(p)

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