makeAxtTracks: makeAxtTracks
In CNEr: CNE Detection and Visualization

Description Usage Arguments Details Value Author(s) See Also Examples

Make the bed tracks for the ‘Axt’ alignment.

1	makeAxtTracks(x)

`x`	A `Axt` object.

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

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

Ge Tan

fixCoordinates

  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)