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\name{chainPreNet}
\alias{chainPreNet}
\title{
chainPreNet
}
\description{
Wrapper function of \command{chainPreNet}:
Removes chains that don't have a chance of being netted.
This function doesn't work on Windows platform since Kent utilities only
support Linux and Unix platforms.
}
\usage{
chainPreNet(allChain, assemblyTarget, assemblyQuery,
allPreChain=paste0(sub("\\\.2bit$", "", basename(assemblyTarget),
ignore.case = TRUE), ".",
sub("\\\.2bit$", "", basename(assemblyQuery),
ignore.case = TRUE), ".all.pre.chain"),
removeAllChain=TRUE, binary="chainPreNet")
}
\arguments{
\item{allChain}{
\code{character}(1): file names of input \emph{allChain} file.
}
\item{assemblyTarget}{
\code{character}(1): the file name of target assembly \emph{twoBit} file.
}
\item{assemblyQuery}{
\code{character}(1): the file name of query assembly \emph{twoBit} file.
}
\item{allPreChain}{
\code{character}(1): file names of merged \emph{allPreChain} file.
}
\item{removeAllChain}{
\code{boolean}: When \code{TRUE}, the input \emph{allChain} file will be
removed after the conversion.
}
\item{binary}{
\code{character}(1): the name/filename of the binary \command{chainPreNet}
to call.
}
}
\value{
\code{character}(1): the file names of merged \emph{allPreChain} file.
}
\references{
\url{http://hgdownload.cse.ucsc.edu/admin/exe/}
}
\author{
Ge Tan
}
\seealso{
\code{\link{chainMergeSort}}
}
\examples{
\dontrun{
## This example doesn't run because it requires two bit files and external
## Kent utilities.
allChain <- file.path("/Users/gtan/OneDrive/Project/CSC/CNEr/axt",
"danRer10.hg38.all.chain")
assemblyTarget <- "/Users/gtan/OneDrive/Project/CSC/CNEr/2bit/danRer10.2bit"
assemblyQuery <- "/Users/gtan/OneDrive/Project/CSC/CNEr/2bit/hg38.2bit"
chainPreNet(allChain, assemblyTarget, assemblyQuery,
allPreChain=file.path(
"/Users/gtan/OneDrive/Project/CSC/CNEr/axt",
paste0(sub("\\\.2bit$", "",
basename(assemblyTarget),
ignore.case = TRUE), ".",
sub("\\\.2bit$", "",
basename(assemblyQuery),
ignore.case = TRUE),
".all.pre.chain")),
removeAllChain=FALSE, binary="chainPreNet")
}
}
|
