partner: GRanges representing the breakend coordinates of structural...
In StructuralVariantAnnotation: Variant annotations for structural variants

Description Usage Arguments Details Value Examples

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

1	partner(gr, selfPartnerSingleBreakends = FALSE)

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

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

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

#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)