Description Usage Arguments Objects from the Class Methods Examples
An object of class "pcm"
represents the position count matrix of a
DNA/RNA/amino-acid sequence motif. The entry stores a matrix, which in row
i, column j gives the counts of observing nucleotide/or amino acid i in
position j of the motif.
methods for pcm 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 'pcm'
x$name
## S4 method for signature 'pcm,ANY'
plot(x, y = "missing", ...)
trimMotif(x, t)
matrixReverseComplement(x)
addBlank(x, n, b)
getIC(x, p)
pcm2pfm(x, background)
pcm2pssm(x, background)
## S4 method for signature 'pcm'
as.data.frame(x, row.names = NULL, optional = FALSE, ...)
## S4 method for signature 'pcm'
format(x, ...)
|
x |
An object of class |
name |
slot name of pcm object. |
y |
Not use. |
... |
Further potential arguments passed to |
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. |
p |
p is the background frequency. |
background |
a |
row.names, optional |
see as.data.frame |
Objects can be created by calls of the form
new("pcm", mat, name, alphabet, color, background)
.
signature(x="pcm",
n="numeric", b="logical")
add space into the position count 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(from = "pcm", to = "matrix")
: convert object
pcm to matrix
signature(x = "pcm",)
Calculate information content
profile for position frequency matrix.
signature(x = "pcm")
get the reverse
complement of position frequency matrix.
signature(x = "pcm")
Plots the sequence logo of the
position count matrix.
signature(x = "pcm", t= "numeric")
trim motif by
information content.
Get or set the slot of pcm-class
convert pcm-class
to a data.frame
return the name_pcm of pcm-class
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | 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 <- new("pcm", mat=as.matrix(pcm), name="bin_SOLEXA")
plot(motif)
pcm2pfm(pcm)
pcm2pssm(pcm)
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 <- new("pcm", mat=as.matrix(pcm), name="bin_SOLEXA")
getIC(motif)
matrixReverseComplement(motif)
as(motif,"matrix")
pcm2pfm(motif)
as.data.frame(motif)
format(motif)
|
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