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\name{TFFM}
\alias{TFFM}
\alias{TFFMFirst}
\alias{TFFMDetail}
\alias{ncol,TFFMFirst-method}
\alias{ncol,TFFMDetail-method}
\alias{totalIC,TFFM-method}
\title{
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())
}
\section{Methods}{
\describe{
\item{ncol}{\code{signature(x = "TFFMFirst")}:
Get the length of First-order TFFM.}
\item{ncol}{\code{signature(x = "TFFMDetail")}:
Get the length of detail TFFM.}
\item{totalIC}{\code{signature(x = "TFFM")}:
Get the information content at each position.}
}
}
\arguments{
\item{ID,name,matrixClass,strand,bg,tags,profileMatrix}{
See \code{\link{XMatrix}}
}
\item{type}{
The type of TFFM.
}
\item{emission}{
The emission distribution parameters.
}
\item{transition}{
The transition probability matrix.
}
}
\value{
A \code{TFFM} object.
}
\references{
Mathelier, A., and Wasserman, W.W. (2013). The next generation of transcription factor binding site prediction. PLoS Comput. Biol. 9, e1003214.
\url{http://cisreg.cmmt.ubc.ca/TFFM/doc/#}
}
\author{
Ge Tan
}
\examples{
xmlFirst <- file.path(system.file("extdata", package="TFBSTools"),
"tffm_first_order.xml")
tffmFirst <- readXMLTFFM(xmlFirst, type="First")
tffm <- getPosProb(tffmFirst)
}
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