pcm-class: Class '"pcm"'

In jianhong/motifStack: Plot stacked logos for single or multiple DNA, RNA and amino acid sequence

Class "pcm"

Description

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.

Usage

## 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, ...)

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.
name	slot name of pcm object.
y	Not use.
...	Further potential arguments passed to plotMotifLogo.
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 "numeric" vector. The background frequency.
row.names, optional	see as.data.frame

Objects from the Class

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

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-class

as.data.frame

convert pcm-class to a data.frame

format

return the name_pcm of pcm-class

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 <- 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)

jianhong/motifStack documentation built on Nov. 5, 2024, 7:47 a.m.