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\name{readAncora}
\alias{readAncora}
\title{
Read the cne file from Ancora format.
}
\description{
Read the Ancora CNE file into a \code{GRanges} or \code{GRangePairs} object.
}
\usage{
readAncora(fn, assembly=NULL, tAssemblyFn=NULL, qAssemblyFn=NULL)
}
\arguments{
\item{fn}{
\code{character}(1): the path of the Ancora CNE file in the format of
"cne2wBf_hg38_mm10_50_50".
}
\item{assembly}{
\code{character}(1): the assembly to fetch. When it is NULL,
CNEs on both assemblies are returned.
}
\item{tAssemblyFn,qAssemblyFn}{
\code{character}(1): filename of the \sQuote{twoBit} or \sQuote{fasta}
file for the target and query genomes.
}
}
\details{
The Ancora CNE filename has its own naming style. For example,
"cne2wBf_hg38_mm10_50_50" denotes human coordinates for the first three
columns of the file and mouse coordinates from the forth to the sixth column.
The start coordinate system is 0-based.
}
\value{
A \code{GRanges} object of the CNE ranges when assembly is specified,
or a \code{GRangePairs} object when assembly is NULL.
}
\author{
Ge Tan
}
\note{
This function is mainly for internal use in Lenhard group.
}
\examples{
fn <- file.path(system.file("extdata", package="CNEr"),
"cne2wBf_danRer10_hg38_45_50")
zebrafishCNEs <- readAncora(fn, "danRer10")
humanCNEs <- readAncora(fn, "hg38")
zebrafishHumanCNEs <- readAncora(fn)
}
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