pcm-class {motifStack} | R Documentation

## 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)

[Package motifStack version 1.38.0 Index]