fixCoordinates {CNEr} | R Documentation

## Fix the coordinates in `Axt` object

### Description

In ‘axt’ file and `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

`x` | `Axt` object.

### Details

In `Axt`, the ‘strand’ is for the aligning organism. If the strand value is “-”, the values of the aligning organism's start and end fields are relative to the reverse-complemented coordinates of its chromosome.

### Value

A `Axt` object.

### Author(s)

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))

[Package CNEr version 1.30.0 Index]