readAxt: Read 'Axt' file

In CNEr: CNE Detection and Visualization

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)

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