readAncora {CNEr} | R Documentation

## 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)

[Package CNEr version 1.20.0 Index]