pwm-class {seqLogo}R Documentation

Class "pwm"

Description

An object of class "pwm" represents the 4xW position weight matrix of a 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.

Objects from the Class

Objects can be created by calls of the form new("pwm", ...).

Slots

pwm:
Object of class "matrix" The position weight matrix.
width:
"numeric" The width of the motif.
alphabet:
"character" The sequence alphabet. Currently, only "DNA" is supported.

Methods

summary
signature(object = "pwm",...) Prints the position weight matrix.
print
signature(x = "pwm",...) Prints the position weight matrix.
show
signature(object = "pwm") Prints the position weight matrix.
plot
signature(x = "pwm") Plots the sequence logo of the position weight matrix.

Note

Author(s)

Oliver Bembom, bembom@berkeley.edu

References

See Also

Examples






[Package seqLogo version 1.4.0 Index]