pwm-class {seqLogo} | R Documentation |
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.
## 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)
object |
object of |
... |
additional parameters for |
x |
object of |
y |
default (missing) for |
pwm |
object of |
pwm-class
object with slots: pwm
, width
, ic
and alphabet
.
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
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.
Oliver Bembom
mFile <- system.file("extdata/pwm1", package = "seqLogo") m <- read.table(mFile) p <- makePWM(m) # # slot access pwm(p) ic(p) consensus(p)