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
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.
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.