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.

### 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.

`tags`

  a list to save metadata of motif.

`markers`

  a list of marker object.

### 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)

[Package motifStack version 1.31.2 Index]