pcm-class {motifStack} | R Documentation |
"pcm"
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.
## 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
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)