Class "pfm"

Description

An object of class "pfm" represents the position frequency matrix of a DNA/RNA/amino-acid sequence motif. The entry stores a matrix, which in row i, column j gives the frequency of observing nucleotide/or amino acid i in position j of the motif.

Objects from the Class

Objects can be created by calls of the form new("pfm", mat, name, alphabet, color, background).

Slots

mat

Object of class "matrix" The position frequency matrix

name

code"character" The motif name

alphabet

"character" The sequence alphabet. "DNA", "RNA", "AA" or "others".

color

a "character" vector. The color setting for each symbol

background

a "numeric" vector. The background frequency.

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.

coerce

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

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.

trimMotif

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

plot

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

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")
plot(motif)