TFFM-class: The TFFM class

In ge11232002/TFBSTools: Software Package for Transcription Factor Binding Site (TFBS) Analysis

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)

ge11232002/TFBSTools documentation built on June 12, 2025, 8:31 p.m.