"pcm" methods

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Description

methods for pcm objects.

Usage

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	## 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)

Arguments

x

An object of class pcm. For getIC, if parameter p is followed, x should be an object of matrix. For pcm2pfm, x also could be an object of matrix.

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 "numeric" vector. The background frequency.

t

numeric value of information content threshold for trimming.

...

Further potential arguments passed to plotMotifLogo.

Methods

addBlank

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.

coerce

signature(from = "pcm", to = "matrix"): convert object pcm to matrix

getIC

signature(x = "pcm",) Calculate information content profile for position frequency matrix.

matrixReverseComplement

signature(x = "pcm") get the reverse complement of position frequency matrix.

plot

signature(x = "pcm") Plots the sequence logo of the position count matrix.

trimMotif

signature(x = "pcm", t= "numeric") trim motif by information content.

$, $<-

Get or set the slot of pcm

Examples

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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)

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