pwm-class: Class "pwm"
In thephilross/seqLogo: Sequence logos for DNA sequence alignments

Description Objects from the Class Slots Methods Author(s)

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

consensus: Object of class"character"
ic: Object of class "numeric"
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.

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.