makeAxtTracks: makeAxtTracks

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

View source: R/Axt-methods.R

Description

Make the bed tracks for the ‘Axt’ alignment.

Usage

1

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

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  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)

CNEr documentation built on Nov. 8, 2020, 5:36 p.m.