pfm-class {motifStack} | R Documentation

## 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.

methods for pfm objects.

### Usage

    ## S4 method for signature 'pfm'
    x$name

    ## S4 method for signature 'pfm,ANY'
    plot(x, y = "missing", ...)

    ## S4 method for signature 'pfm,ANY'
    getIC(x, p = "missing")

    ## S4 method for signature 'pfm,numeric'
    trimMotif(x, t)

    ## S4 method for signature 'pfm'
    matrixReverseComplement(x)

    ## S4 method for signature 'pfm,numeric,logical'
    addBlank(x, n, b)

    ## S4 method for signature 'pfm'
    as.data.frame(x, row.names = NULL, optional = FALSE, ...)

    ## S4 method for signature 'pfm'
    format(x, ...)

### Arguments

`x` | An object of class `pfm`. For `getIC`, if parameter p is followed, x should be an object of matrix.
`name` | Slot name.
`y` | Not use.
`...` | Further potential arguments passed to `plotMotifLogo`.
`p` | p is the background frequency.
`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.
`row.names, optional` | see as.data.frame

### Objects from the Class

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

### 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-class`

as.data.frame

  convert `pfm-class` to a data.frame

format

  return the name_pfm of `pfm-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 <- pcm2pfm(pcm)
    motif <- new("pfm", mat=motif, name="bin_SOLEXA")
    plot(motif)

    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")
    as.data.frame(motif)
    format(motif)

[Package motifStack version 1.36.1 Index]