TFBSTools (version 1.10.3)

TFFM: 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.

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)