TFFM-class: The TFFM class

Description Usage Arguments Value Methods Author(s) References Examples

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

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## 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

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  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 Sept. 12, 2021, 12:07 p.m.