readAncora: Read the cne file from Ancora format.
In CNEr: CNE Detection and Visualization

Description Usage Arguments Details Value Note Author(s) Examples

Read the Ancora CNE file into a GRanges or GRangePairs object.

1	readAncora(fn, assembly=NULL, tAssemblyFn=NULL, qAssemblyFn=NULL)

`fn`	`character`(1): the path of the Ancora CNE file in the format of "cne2wBf_hg38_mm10_50_50".
`assembly`	`character`(1): the assembly to fetch. When it is NULL, CNEs on both assemblies are returned.
`tAssemblyFn,qAssemblyFn`	`character`(1): filename of the ‘twoBit’ or ‘fasta’ file for the target and query genomes.

The Ancora CNE filename has its own naming style. For example, "cne2wBf_hg38_mm10_50_50" denotes human coordinates for the first three columns of the file and mouse coordinates from the forth to the sixth column.

The start coordinate system is 0-based.

A GRanges object of the CNE ranges when assembly is specified, or a GRangePairs object when assembly is NULL.

This function is mainly for internal use in Lenhard group.

Ge Tan

  fn <- file.path(system.file("extdata", package="CNEr"),
                  "cne2wBf_danRer10_hg38_45_50")
  zebrafishCNEs <- readAncora(fn, "danRer10")
  humanCNEs <- readAncora(fn, "hg38")
  zebrafishHumanCNEs <- readAncora(fn)