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\name{blatCNE}
\alias{blatCNE}
\title{
Wrapper function of blat for \code{CNE} object
}
\description{
This wrapper function blat the CNEs against the reference genome. Note that blat must be installed on your system.
}
\usage{
blatCNE(cne, blatOptions=NULL, cutIdentity=90)
}
\arguments{
\item{cne}{
\code{cne} object after \code{cneMerge} step.
}
\item{blatOptions}{
\code{character}(1): the \command{blat} options.
When it is NULL, the options will be chosen based on the window size for
scanning CNEs.
}
\item{cutIdentity}{
\code{integer}(1): the minimum sequence identity (in percent) for a match
in \command{blat}. By default, it is 90.
}
}
\details{
When winSize > 45, the blat option is
"-tileSize=11 -minScore=30 -repMatch=1024".
When 35 < winSize <= 45, the blat option is
"-tileSize=10 -minScore=28 -repMatch=4096".
When the winSize <= 35, the blat option is
"-tileSize=9 -minScore=24 -repMatch=16384".
}
\value{
A \code{CNE} object with a final set of CNEs.
}
\author{
Ge Tan
}
\examples{
\dontrun{
data(CNEDanRer10Hg38)
data(CNEHg38DanRer10)
cne <- CNE(assembly1Fn=file.path(system.file("extdata",
package="BSgenome.Drerio.UCSC.danRer10"),
"single_sequences.2bit"),
assembly2Fn=file.path(system.file("extdata",
package="BSgenome.Hsapiens.UCSC.hg38"),
"single_sequences.2bit"),
window=50L, identity=45L, CNE12=CNEDanRer10Hg38[["45_50"]],
CNE21=CNEHg38DanRer10[["45_50"]], aligner="blat")
cne <- cneMerge(cne)
cne <- blatCNE(cne)
}
}
|
