pcm-methods {motifStack} | R Documentation |
methods for pcm objects.
## S4 method for signature 'pcm,numeric,logical' addBlank(x,n,b) ## S4 method for signature 'pcm,ANY' getIC(x,p="missing") ## S4 method for signature 'pcm' matrixReverseComplement(x) ## S4 method for signature 'pcm,ANY' plot(x,y="missing",...) ## S4 method for signature 'pcm,ANY' pcm2pfm(x,background="missing") ## S4 method for signature 'matrix,ANY' pcm2pfm(x,background="missing") ## S4 method for signature 'matrix,numeric' pcm2pfm(x,background) ## S4 method for signature 'data.frame,ANY' pcm2pfm(x,background="missing") ## S4 method for signature 'data.frame,numeric' pcm2pfm(x,background) ## S4 method for signature 'pcm,numeric' trimMotif(x,t)
x |
An object of class |
y |
Not use. |
p |
p is the background frequency. |
n |
how many spaces should be added. |
b |
logical value to indicate where the space should be added. |
background |
a |
t |
numeric value of information content threshold for trimming. |
... |
Further potential arguments passed to |
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
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)