readAncora: Read the cne file from Ancora format.

In ge11232002/CNEr: CNE Detection and Visualization

Read the cne file from Ancora format.

Description

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

Usage

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

Arguments

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.

Details

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.

Value

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

Note

This function is mainly for internal use in Lenhard group.

Author(s)

Ge Tan

Examples

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

ge11232002/CNEr documentation built on Oct. 26, 2022, 7:08 p.m.