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\name{runMEME}
\docType{methods}
\alias{runMEME}
\alias{runMEME,character-method}
\alias{runMEME,DNAStringSet-method}
\title{Wrapper function for MEME}
\description{
This function builds position frequency matrices using
an external program \strong{MEME} written by \emph{Bailey} and \emph{Elkan}.
}
\usage{
\S4method{runMEME}{character}(x, binary="meme", seqtype="DNA",
arguments=list(), tmpdir=tempdir())
\S4method{runMEME}{DNAStringSet}(x, binary="meme", seqtype="DNA",
arguments=list(), tmpdir=tempdir())
}
\arguments{
\item{x}{
A \code{character}(1) vector of the path of fasta file
or a \code{XStringSet}.
}
\item{binary}{
\code{character}(1): the path of MEME binary.
By default, we assume the meme is in the \emph{PATH}.
}
\item{seqtype}{
The sequence type. "AA" and "DNA" are allowed.
}
\item{arguments}{
A \code{list}: the addtional arguments for meme.
This list takes the parameter of MEME as names of the elements,
and the values of the parameters as the elements.
For examples, arguments=list("-nmotifs"=3).
}
\item{tmpdir}{
A \code{character}(1) vector to change the defult R's temp directory.
}
}
\value{
A \code{MotifSet} object is returned.
}
\references{
Bailey, T. L., Boden, M., Buske, F. A., Frith, M., Grant, C. E., Clementi, L., et al. (2009). MEME SUITE: tools for motif discovery and searching. Nucleic acids research, 37(Web Server issue), W202-8. doi:10.1093/nar/gkp335
\url{http://meme-suite.org/}
}
\author{
Ge Tan
}
\note{
This wrapper is tested on \dQuote{MEME} 4.10.1 and 4.12.0.
}
\seealso{
\code{\linkS4class{MotifSet}}
}
\examples{
\dontrun{
motifSet <- runMEME(file.path(system.file("extdata", package="TFBSTools"),
"crp0.s"),
binary="/usr/local/Cellar/meme/4.10.1/bin/meme",
arguments=list("-nmotifs"=3))
## Get the site sequences
sitesSeq(motifSet, type="all")
sitesSeq(motifSet, type="none")
## Get the consensu matrix, then it can be used as a PFMatrix
consensusMatrix(motifSet)
}
}
\keyword{methods}
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