TFFM {TFBSTools} | R Documentation

## The TFFM class

### Description

The TFFM is a virtual class. Two classes are derived from this class: TFFMFirst and TFFMDetail.

TFFMFirst class stands for the first-order TFFMs and TFFMDetail stands for the more detailed and descriptive TFFMs.

### Usage

    ## constructors:
      TFFMFirst(ID="Unknown", name="Unknown", matrixClass="Unknown",
                strand="+", bg=c(A=0.25, C=0.25, G=0.25, T=0.25),
                tags=list(), profileMatrix=matrix(),
                type=character(), emission=list(),
                transition=matrix())
      TFFMDetail(ID="Unknown", name="Unknown", matrixClass="Unknown",
                 strand="+", bg=c(A=0.25, C=0.25, G=0.25, T=0.25),
                 tags=list(), profileMatrix=matrix(),
                 type=character(), emission=list(),
                 transition=matrix())

### Arguments

`ID,name,matrixClass,strand,bg,tags,profileMatrix` | See `XMatrix`
`type` | The type of TFFM.
`emission` | The emission distribution parameters.
`transition` | The transition probability matrix.

### Value

A `TFFM` object.

### Methods

ncol

  `signature(x = "TFFMFirst")`: Get the length of First-order TFFM.

ncol

  `signature(x = "TFFMDetail")`: Get the length of detail TFFM.

totalIC

  `signature(x = "TFFM")`: Get the information content at each position.

### Author(s)

Ge Tan

### References

Mathelier, A., and Wasserman, W.W. (2013). The next generation of transcription factor binding site prediction. PLoS Comput. Biol. 9, e1003214.

http://cisreg.cmmt.ubc.ca/TFFM/doc/#

### Examples

      xmlFirst <- file.path(system.file("extdata", package="TFBSTools"),
                            "tffm_first_order.xml")
      tffmFirst <- readXMLTFFM(xmlFirst, type="First")
      tffm <- getPosProb(tffmFirst)

[Package TFBSTools version 1.18.0 Index]