Description Usage Arguments Objects from the Class Methods Examples
An object of class "pfm"
represents the position frequency matrix of
a DNA/RNA/amino-acid sequence motif. The entry stores a matrix, which in row
i, column j gives the frequency of observing nucleotide/or amino acid i in
position j of the motif.
methods for pfm objects.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | ## S4 method for signature 'pfm'
x$name
## S4 method for signature 'pfm,ANY'
plot(x, y = "missing", ...)
## S4 method for signature 'pfm,ANY'
getIC(x, p = "missing")
## S4 method for signature 'pfm,numeric'
trimMotif(x, t)
## S4 method for signature 'pfm'
matrixReverseComplement(x)
## S4 method for signature 'pfm,numeric,logical'
addBlank(x, n, b)
## S4 method for signature 'pfm'
as.data.frame(x, row.names = NULL, optional = FALSE, ...)
## S4 method for signature 'pfm'
format(x, ...)
|
x |
An object of class |
name |
Slot name. |
y |
Not use. |
... |
Further potential arguments passed to |
p |
p is the background frequency. |
t |
numeric value of information content threshold for trimming. |
n |
how many spaces should be added. |
b |
logical value to indicate where the space should be added. |
row.names, optional |
see as.data.frame |
Objects can be created by calls of the form
new("pfm", mat, name, alphabet, color, background)
.
signature(x="pfm",
n="numeric", b="logical")
add space into the position frequency matrix for
alignment. b is a bool value, if TRUE, add space to the 3' end, else add
space to the 5' end. n indicates how many spaces should be added.
signature(x = "pfm",)
Calculate information content
profile for position frequency matrix.
signature(x = "matrix", p = "numeric")
Calculate
information content profile for matrix. p is the background frequency
signature(x = "pfm")
get the reverse
complement of position frequency matrix.
signature(x = "pfm")
Plots the sequence logo of the
position frequency matrix.
signature(x = "pfm", t= "numeric")
trim motif by
information content.
Get or set the slot of pfm-class
convert pfm-class
to a data.frame
return the name_pfm of pfm-class
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | pcm <- read.table(file.path(find.package("motifStack"), "extdata", "bin_SOLEXA.pcm"))
pcm <- pcm[,3:ncol(pcm)]
rownames(pcm) <- c("A","C","G","T")
motif <- pcm2pfm(pcm)
motif <- new("pfm", mat=motif, name="bin_SOLEXA")
plot(motif)
pcm <- read.table(file.path(find.package("motifStack"), "extdata", "bin_SOLEXA.pcm"))
pcm <- pcm[,3:ncol(pcm)]
rownames(pcm) <- c("A","C","G","T")
motif <- pcm2pfm(pcm)
motif <- new("pfm", mat=motif, name="bin_SOLEXA")
getIC(motif)
matrixReverseComplement(motif)
addBlank(motif, 1, FALSE)
addBlank(motif, 3, TRUE)
as(motif,"matrix")
as.data.frame(motif)
format(motif)
|
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