partner {StructuralVariantAnnotation}

R Documentation

GRanges representing the breakend coordinates of structural variants #@export Partner breakend for each breakend.

Description

GRanges representing the breakend coordinates of structural variants #@export Partner breakend for each breakend.

Usage

partner(gr, selfPartnerSingleBreakends = FALSE)

Arguments

gr	GRanges object of SV breakends
selfPartnerSingleBreakends	treat single breakends as their own partner.

Details

All breakends must have their partner breakend included in the GRanges.

Value

A GRanges object in which each entry is the partner breakend of those in the input object.

Examples

#reading in a VCF file as \code{vcf}
vcf.file <- system.file("extdata", "gridss.vcf", package = "StructuralVariantAnnotation")
vcf <- VariantAnnotation::readVcf(vcf.file, "hg19")
#parsing \code{vcf} to GRanges object \code{gr}
gr <- breakpointRanges(vcf)
#output partner breakend of each breakend in \code{gr}
partner(gr)

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