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\name{subAxt-methods}
\docType{methods}
\alias{subAxt}
\alias{subAxt-methods}
\alias{subAxt,Axt,character,missing,missing-method}
\alias{subAxt,Axt,character,numeric,numeric-method}
\alias{subAxt,Axt,character,integer,integer-method}
\alias{subAxt,Axt,GRanges,missing,missing-method}
\title{Subset an \code{Axt} object}
\description{
A \sQuote{subAxt} method for extracting a set of alignments from
an \code{Axt} object.
}
\usage{
subAxt(x, chr, start, end, select=c("target", "query"), qSize=NULL)
}
\arguments{
\item{x}{
An object of \code{Axt}.
}
\item{chr}{
An object of \code{character} containing the names of the sequences
in 'x' where to get the alignments from, or a \code{GRanges} object
where 'start' and 'end' are missing.
In the case of \code{GRanges}, the strand information is ignored.
}
\item{start, end}{
An object of \code{integer}() or missing.
These ranges should be based on the positive strand.
When select is "query",
the reverse complement alignments which lay inside this range will also be
selected.
}
\item{select}{
When select is \sQuote{target},
the subset criteria are applied on target alignments in \code{Axt}.
When select is \sQuote{query},
the subset criteria are applied on query alignments in \code{Axt}.
}
\item{qSize}{
\code{integer}(n): When select is \sQuote{query},
\sQuote{qSize} must exist in
\sQuote{x} or can be provided as a vector of chromosome lengths.
}
}
\details{
Usually when we want to subset some axts from a \code{Axt} object,
we care about all the axts within a certain range.
The axts can come from the axt file with chr as reference
(\emph{i.e.}, target sequence),
or the axt file with chr as query sequence.
When the chr is query sequence, it can be on the negative strand.
Hence, the size of chromosome is necessary to
convert the search range to a range on negative strand coordinate.
When one Axt alignment partially overlaps the range,
the whole Axt alignment will be extracted.
}
\value{
An extracted \code{Axt} object is returned.
}
\author{
Ge Tan
}
\seealso{
\code{\link{psubAxt}}
}
\examples{
library(GenomicRanges)
library(rtracklayer)
## Prepare the axt object
tAssemblyFn <- file.path(system.file("extdata",
package="BSgenome.Hsapiens.UCSC.hg38"),
"single_sequences.2bit")
qAssemblyFn <- file.path(system.file("extdata",
package="BSgenome.Drerio.UCSC.danRer10"),
"single_sequences.2bit")
axtFilesHg38DanRer10 <- file.path(system.file("extdata", package="CNEr"),
"hg38.danRer10.net.axt")
axtHg38DanRer10 <- readAxt(axtFilesHg38DanRer10, tAssemblyFn, qAssemblyFn)
## "character", "integer", "integer" on "target" sequence
subAxt(axtHg38DanRer10, chr="chr1", start=148165963L, end=222131835L,
select="target")
## "GRanges"" on "target" sequence
searchGRanges <- GRanges(seqnames="chr1",
ranges=IRanges(start=148165963L,
end=222131835L),
strand="+")
subAxt(axtHg38DanRer10, searchGRanges, select="target")
## multiple "character", "integer", "integer" on "target" sequence
subAxt(axtHg38DanRer10, chr=c("chr1", "chr13"),
start=c(148165963L, 94750629L),
end=c(222131835L, 94966991L), select="target")
## "character" only on "target" sequence
subAxt(axtHg38DanRer10, chr="chr1", select="target")
## GRanges on "query" sequence
searchGRanges <- GRanges(seqnames="chr6",
ranges=IRanges(start=25825774,
end=26745499),
strand="+")
subAxt(axtHg38DanRer10, searchGRanges, select="query")
}
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