export.chiasig: Export interactions in a BEDPE-like format for use with...

In ComputationalRegulatoryGenomicsICL/GenomicInteractions: Utilities for handling genomic interaction data

Export interactions in a BEDPE-like format for use with ChiaSig

Description

Exports a GInteractions object to BEDPE like format, (anchor specifications and a column for reads connecting them) and writes to a specified file. If filename is not specified, then a data.frame containing the information is returned. The value of the score parameter defines which field is used to populate the score field.

Usage

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

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

Arguments

GIObject	A GInteractions object.
fn	A filename to write the interactions data to
score	Which metadata column to use as the score: counts or normalised

Value

invisible(1) if outputting to file or a data.frame containing all of the corresponding information

Examples

data(hic_example_data)
export.chiasig(hic_example_data, fn = tempfile(), score = 'counts')

ComputationalRegulatoryGenomicsICL/GenomicInteractions documentation built on April 16, 2022, 4:09 a.m.