breakpointgr2bedpe: Converting breakpoint GRanges to BEDPE-like dataframe

In PapenfussLab/StructuralVariantAnnotation: Variant annotations for structural variants

Description

Converting breakpoint GRanges to BEDPE-like dataframe

Usage

breakpointgr2bedpe(gr)

Arguments

gr	A GRanges object.

Details

breakpointgr2bedpe converts a breakpoint GRanges to a BEDPE-formatted dataframe. The BEDPE format consists of two sets of genomic loci, optional columns of name, score, strand1, strand2 and any user-defined fields. See https://bedtools.readthedocs.io/en/latest/content/general-usage.html for more details on the BEDPE format.

Value

A BEDPE-formatted data frame.

Examples

#coverting a GRanges object to BEDPE-like dataframe
vcf.file <- system.file("extdata", "gridss.vcf", package = "StructuralVariantAnnotation")
vcf <- VariantAnnotation::readVcf(vcf.file, "hg19")
gr <- breakpointRanges(vcf)
breakpointgr2bedpe(gr)

PapenfussLab/StructuralVariantAnnotation documentation built on Dec. 25, 2021, 1:20 a.m.