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\name{readJASPARMatrix}
\alias{readJASPARMatrix}
\title{
Read JASPAR format matrix
}
\description{
Read a JASPAR format matrix file with \sQuote{individual} matrix or
\sQuote{all} matrices in one file.
}
\usage{
readJASPARMatrix(fn, matrixClass=c("PFM", "PWM", "PWMProb"))
}
\arguments{
\item{fn}{
\code{character}(1): The filename of JASPAR format matrix file.
}
\item{matrixClass}{
\code{character}(1): the matrices in the files are \sQuote{PFM}, \sQuote{PWM} or
\sQuote{PFM} in probability.
}
}
\details{
An example of \sQuote{individual} format matrix file is available at
\url{http://jaspar.genereg.net/html/DOWNLOAD/JASPAR_CORE/pfm/individual/MA0001.1.pfm}
An exmaple of \sQuote{all} format matrix file is available at
\url{http://jaspar.genereg.net/html/DOWNLOAD/JASPAR_CORE/pfm/nonredundant/pfm_all.txt}
}
\value{
A \code{PFMatrixList} or \code{PWMatrixList} object is returned, depending on the
matrix class.
}
\author{
Ge Tan
}
\seealso{
\code{\link{makeFlatFileDir}}
}
\examples{
fn <- file.path(system.file("extdata", package="TFBSTools"),
"MA0001.1.pfm")
readJASPARMatrix(fn, matrixClass="PFM")
fn <- file.path(system.file("extdata", package="TFBSTools"),
"pfm_all_example.txt")
readJASPARMatrix(fn, matrixClass="PFM")
}
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