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\name{scoringMatrix}
\alias{scoringMatrix}
\title{
scoringMatrix
}
\description{
Generates the scoring matrix for \emph{lastz} aligner.
}
\usage{
scoringMatrix(distance = c("far", "medium", "near"))
}
\arguments{
\item{distance}{
It can be "far", "medium" or "close". It defines the scoring matrix used in
\emph{lastz} aligner.
Generally, if two species are close to each other, for example human and chimp,
"close" should be used.
If two species have a divergence time of 100 MYA, "far" should be used.
In other cases, "medium" should be used.
}
}
\value{
A \code{matrix} of the scoring matrix is returned.
}
\references{
\url{http://genomewiki.ucsc.edu/index.php/Hg38_17-way_conservation_lastz_parameters}
}
\author{
Ge Tan
}
\note{
HOXD70 is medium. HoxD55 is far. human-chimp.v2 is close.
}
\seealso{
\code{\link{lastz}}
}
\examples{
scoringMatrix(distance="far")
}
|
