pfm-methods {motifStack} | R Documentation

## "pfm" methods

### Description

methods for pfm objects.

### Usage

    	## S4 method for signature 'pfm,numeric,logical'
    addBlank(x,n,b)
    	## S4 method for signature 'pfm,ANY'
    getIC(x,p="missing")
    	## S4 method for signature 'matrix,numeric'
    getIC(x,p)
    	## S4 method for signature 'pfm'
    matrixReverseComplement(x)
    	## S4 method for signature 'pfm,ANY'
    plot(x,y="missing",...)
    	## S4 method for signature 'pfm,numeric'
    trimMotif(x,t)
    	## 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.
`y` | Not use.
`p` | p is the background frequency.
`n` | how many spaces should be added.
`b` | logical value to indicate where the space should be added.
`t` | numeric value of information content threshold for trimming.
`...` | Further potential arguments passed to `plotMotifLogo`.
`row.names,optional` | see as.data.frame

### 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")
    getIC(motif)
    matrixReverseComplement(motif)
    addBlank(motif, 1, FALSE)
    addBlank(motif, 3, TRUE)
    as(motif,"matrix")
    as.data.frame(motif)
    format(motif)

[Package motifStack version 1.31.2 Index]