motifStack (version 1.16.0)

pfm-methods: "pfm" methods

Description

methods for pfm objects.

Usage

"addBlank"(x,n,b)
	"getIC"(x,p="missing")
	"getIC"(x,p)
	"matrixReverseComplement"(x)
	"plot"(x,y="missing",...)
	"trimMotif"(x,t)

Arguments

x

An object of class pfm. For getIC, if parameter p is followed, x should 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.

t

numeric value of information content threshold for trimming.

...

Further potential arguments passed to plotMotifLogo.

Methods

addBlank

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.

getIC

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

getIC

signature(x = "matrix", p = "numeric") Calculate information content profile for matrix. p is the background frequency

matrixReverseComplement

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

plot

signature(x = "pfm") Plots the sequence logo of the position frequency matrix.

trimMotif

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

$, $<-

Get or set the slot of pfm

Examples

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")