1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
|
\name{readAxt}
\alias{readAxt}
\title{
Read \sQuote{Axt} file
}
\description{
This function reads the \sQuote{Axt} files into an \code{\link{Axt}} object.
}
\usage{
readAxt(axtFiles, tAssemblyFn=NULL, qAssemblyFn=NULL)
}
\arguments{
\item{axtFiles}{
\code{character}(n): filenames of the \sQuote{Axt} files to read.
}
\item{tAssemblyFn,qAssemblyFn}{
\code{character}(1): filename of the \sQuote{twoBit} or \sQuote{fasta}
file for the target and query genome.
}
}
\details{
This function reads the \sQuote{Axt} files of two assemblies.
It can be a single big \sQuote{Axt} file or several small \sQuote{Axt} files.
Contrary to the start coordinate in \sQuote{Axt} file,
the start coordinate in \code{Axt} object is 1-based.
When \sQuote{tAssemblyFn} and \sQuote{qAssemblyFn} are
not \code{NULL}, the corresponding \code{Seqinfo}
will be added into the returned \code{Axt} object.
}
\value{
A object \code{\link{Axt}} is returned.
}
\author{
Ge Tan
}
\seealso{
\code{\link{Axt}}
}
\examples{
axtFile <- file.path(system.file("extdata", package="CNEr"),
"hg38.danRer10.net.axt")
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")
axt <- readAxt(axtFile, tAssemblyFn, qAssemblyFn)
}
|
