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\name{MotifSet}
\Rdversion{1.1}
\docType{class}
\alias{MotifSet}
\alias{MotifSet-class}
\alias{[,MotifSet-method}
\alias{consensusMatrix,MotifSet-method}
\alias{[,MotifSet,ANY,ANY-method}
\alias{[,MotifSet,ANY,ANY,ANY-method}
\alias{length,MotifSet-method}
\alias{sitesSeq}
\alias{sitesSeq,MotifSet-method}
\title{Class \code{"MotifSet"}}
\description{
This MotifSet object is a container for storing the generated
motifs from Motif identification softwares, such as MEME.
}
\usage{
## Constructor
MotifSet(motifList=GRangesList(), motifEvalues=numeric(),
subjectSeqs=DNAStringSet())
}
\arguments{
\item{motifList}{
A GRangesList. Each GRanges store the starts, ends, strand, seqnames
and scores information of one motif sites sequences.
}
\item{motifEvalues}{
A numeric vector of the E values generated from MEME for each motif.
}
\item{subjectSeqs}{
A DNAStringSet object. It stores the original sequences
which are scanned by the software.
}
}
\section{Methods}{
\describe{
\item{[}{\code{signature(x = "MotifSet")}: Getter}
\item{consensusMatrix}{\code{signature(x = "MotifSet")}(x, as.prob = FALSE,
shift = 0L, width = NULL, ...):
Calculate the consensus matrix. Other arguments,
please check the \code{consensusMatrix} in \code{Biostrings} package.}
\item{length}{\code{signature(x = "MotifSet")}:
Returns the number of motifs.}
\item{sitesSeq}{\code{signature(x = "MotifSet")}(x, n=10L, type="none"):
Gets the sites sequences.
\code{n} is the number of bases to include from flanking region.
\code{type} controls "all", "left", "right" or "none"
flanking sequences are included.
}
}
}
\value{
A \code{MotifSet} object is returned.
}
\author{
Ge Tan
}
\seealso{
\code{\link{runMEME}}
}
\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))
sitesSeq(motifSet, type="all")
sitesSeq(motifSet, type="none")
consensusMatrix(motifSet)
}
}
\keyword{classes}
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