readAxt {CNEr} | R Documentation

## Read ‘Axt’ file

### Description

This function reads the ‘Axt’ files into an `Axt` object.

### Usage

      readAxt(axtFiles, tAssemblyFn=NULL, qAssemblyFn=NULL)

### Arguments

`axtFiles` | `character`(n): filenames of the ‘Axt’ files to read.
`tAssemblyFn,qAssemblyFn` | `character`(1): filename of the ‘twoBit’ or ‘fasta’ file for the target and query genome.

### Details

This function reads the ‘Axt’ files of two assemblies. It can be a single big ‘Axt’ file or several small ‘Axt’ files. Contrary to the start coordinate in ‘Axt’ file, the start coordinate in `Axt` object is 1-based.

When ‘tAssemblyFn’ and ‘qAssemblyFn’ are not `NULL`, the corresponding `Seqinfo` will be added into the returned `Axt` object.

### Value

A object `Axt` is returned.

### Author(s)

Ge Tan

### See Also

`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)

[Package CNEr version 1.20.0 Index]