makeAxtTracks {CNEr} | R Documentation

## makeAxtTracks

### Description

Make the bed tracks for the ‘Axt’ alignment.

### Usage

      makeAxtTracks(x)

### Arguments

`x` | A `Axt` object.

### Details

The coordinates of query ‘Axt’ alignment are fixed to be relative to positive strand before output into ‘bed’ file.

### Value

A list of GRanges for target and query alignments. The two output ‘bed’ files are “targetAxt.bed” and “queryAxt.bed”.

### Author(s)

Ge Tan

### See Also

`fixCoordinates`

### Examples

      tAssemblyFn <- file.path(system.file("extdata",
                                           package="BSgenome.Drerio.UCSC.danRer10"),
                               "single_sequences.2bit")
      qAssemblyFn <- file.path(system.file("extdata",
                                           package="BSgenome.Hsapiens.UCSC.hg38"),
                               "single_sequences.2bit")
      axtFn <- file.path(system.file("extdata", package="CNEr"),
                         "danRer10.hg38.net.axt")
      axt <- readAxt(axtFn, tAssemblyFn, qAssemblyFn)
      makeAxtTracks(axt)

[Package CNEr version 1.18.1 Index]