export.bed12: Export interactions in BED12 format

In LTLA/fugi: Further Utilities for Genomic Interactions

Description

Exports a GenomicInteractions object to file in BED12 format.

Usage

export.bed12(GIObject, fn = NULL, score = "counts")

## S4 method for signature 'GenomicInteractions'
export.bed12(GIObject, fn = NULL,
  score = "counts")

Arguments

GIObject	A GenomicInteractions object.
fn	String containing a filename to write the object to.
score	String or integer scalar specifying the metadata column to export as the score field.

Details

BED12 files provide a method for visualising interactions. However, it is not a good format for storing all of the data associated with an interaction dataset. This is particularly true for trans-chromosomal interactions, which can only be stored in the BED12 names field.

Value

If fn is supplied, NULL is invisibly returned and a file is created at fn.

Otherwise, a data.frame is returned containing all of the corresponding information from GIObject.

Author(s)

Malcolm Perry, Elizabeth Ing-Simmons

Examples

data(hic_example_data)
hic_example_data <- updateObject(hic_example_data)
export.bed12(hic_example_data, fn = tempfile(), score = "counts")

LTLA/fugi documentation built on June 22, 2019, 8:50 p.m.