pwm-class: An S4 class to represent a PWM matrix.

In seqLogo: Sequence logos for DNA sequence alignments

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)

Example output

Loading required package: grid
    1   2   3   4   5   6   7   8
A 0.0 0.0 0.0 0.3 0.2 0.0 0.0 0.0
C 0.8 0.2 0.8 0.3 0.4 0.2 0.8 0.2
G 0.2 0.8 0.2 0.4 0.3 0.8 0.2 0.8
T 0.0 0.0 0.0 0.0 0.1 0.0 0.0 0.0
[1] 1.2780719 1.2780719 1.2780719 0.4290494 0.1535607 1.2780719 1.2780719
[8] 1.2780719
[1] "CGCGCGCG"

seqLogo documentation built on Nov. 8, 2020, 8:20 p.m.