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\name{fixCoordinates}
\alias{fixCoordinates}
\alias{fixCoordinates,Axt-method}
\title{
Fix the coordinates in \code{Axt} object
}
\description{
In \sQuote{axt} file and \code{Axt} object, the coordinates of negative
query alignments are relative to the reverse-complemented coordinates of
its chromosome.
This is different from the convention in Bioconductor.
This function fixes the coordinates which are always relative to the
positive strand.
}
\usage{
fixCoordinates(x)
}
\arguments{
\item{x}{
\code{Axt} object.
}
}
\details{
In \code{Axt}, the \sQuote{strand} is for the aligning organism.
If the strand value is \dQuote{-}, the values of the aligning organism's
start and end fields are relative to the reverse-complemented coordinates of
its chromosome.
}
\value{
A \code{Axt} object.
}
\author{
Ge Tan
}
\examples{
axtFnDanRer10Hg38 <- file.path(system.file("extdata", package="CNEr"),
"danRer10.hg38.net.axt")
qAssemblyFn <- file.path(system.file("extdata",
package="BSgenome.Hsapiens.UCSC.hg38"),
"single_sequences.2bit")
tAssemblyFn <- file.path(system.file("extdata",
package="BSgenome.Drerio.UCSC.danRer10"),
"single_sequences.2bit")
axtDanRer10Hg38 <- readAxt(axtFnDanRer10Hg38, tAssemblyFn=tAssemblyFn,
qAssemblyFn=qAssemblyFn)
## Fix the coordinates
fixCoordinates(axtDanRer10Hg38)
## Restore it
fixCoordinates(fixCoordinates(axtDanRer10Hg38))
}
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