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\name{psubAxt}
\alias{psubAxt}
\title{
Parallel subset of Axt alignment
}
\description{
Given two \code{GRanges} objects, select the \code{Axt} alignments
whose the target and query alignments are both within each pair of ranges.
}
\usage{
psubAxt(x, targetSearch, querySearch)
}
\arguments{
\item{x}{
\code{Axt} object.
}
\item{targetSearch,querySearch}{
\code{GRanges} objects: the ranges to keep for target and query alignments.
They must be of the same length. Strand information is ignored.
}
}
\details{
The \sQuote{targetSearch} and \sQuote{querySearch} have the coordinates
relative to the positive strand.
For each pair of the ranges, the alignments that lie within both the target
and query range are kept.
}
\value{
A \code{Axt} object.
}
\author{
Ge Tan
}
\seealso{
\code{\link{psubAxt}}
}
\examples{
library(GenomicRanges)
tAssemblyFn <- file.path(system.file("extdata",
package="BSgenome.Drerio.UCSC.danRer10"),
"single_sequences.2bit")
qAssemblyFn <- file.path(system.file("extdata",
package="BSgenome.Hsapiens.UCSC.hg38"),
"single_sequences.2bit")
axtFn <- file.path(system.file("extdata", package="CNEr"),
"danRer10.hg38.net.axt")
axt <- readAxt(axtFn, tAssemblyFn, qAssemblyFn)
targetSearch <- GRanges(seqnames=c("chr6"),
ranges=IRanges(start=c(24000000, 26900000),
end=c(24060000, 26905000)),
strand="+"
)
querySearch <- GRanges(seqnames=c("chr7", "chr2"),
ranges=IRanges(start=c(12577000, 241262700),
end=c(12579000, 241268600)),
strand="+"
)
psubAxt(axt, targetSearch, querySearch)
}
|
